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Conservapedia talk:Lenski dialog

2010-04-15T23:43:41Z

EmersonWhitecp: /* Hsdebater comment */ I misunderstood!

[http://www.conservapedia.com/Conservapedia_talk:Lenski_dialog/archive1 Archive 1]

The discussion below concerns the letters and response set forth at [[Conservapedia:Lenski dialog]]. See also [[Flaws in Lenski Study]].

== Reply to comments in archive ==

: The comments above by defenders of withholding data have been unsatisfactory, to say the least.

: [[Lenski]] says in his published paper: "Z.D.B. and R.E.L. [Lenski] analyzed data"[http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf]

: So where are all the data [[Lenski]] said he analyzed?--[[User:Aschlafly|Aschlafly]] 00:27, 25 June 2008 (EDT)

::As clearly stated in Professor [[Lenski]]'s second response:

::: ''"Finally, let me now turn to our data. As I said before, the relevant methods and data about the [[evolution]] of the citrate-using bacteria are in our paper. In three places in our paper, we did say 'data not shown', which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website." ''

::If the additional data is not on his website by now, I'm sure it will be soon. --[[User:DinsdaleP|DinsdaleP]] 07:45, 25 June 2008 (EDT)

::: If "the relevant ... data ... are in our paper," as set forth in the above quote of Lenski, then he would not have much data. So don't pretend the data is too voluminous to turn over. The paper is only 8 pages long!

::: In fact, the graphs in the paper suggest to a reader that there is underlying data having greater resolution than a graph can provide, and yet those data have not been disclosed for public scrutiny.--[[User:Aschlafly|Aschlafly]] 19:24, 26 June 2008 (EDT)

:::: The resolution of the graphs are more than sufficient to communicate the results. If the figures didn't provide sufficient clarity for their purpose the authors would have also provided tables. For example, in figure 1 it's clear the culture shifted its growth pattern. In figure 2, one can see that the Cit+ cultures reach a higher density in the media, as indicated by the higher ODs. To a microbiologist, those results indicate that the Cit+ cells can utilize more of the nutrients in the media (in this case, citrate). --[[User:Argon|Argon]] 21:08, 26 June 2008 (EDT)

:::: I'd like to chime in here and give some professional perspective. I am a molecular biologist -- if I asked him to, Prof. Lenski would send me a sample from his bacterial stocks (I have a -80 freezer and know how to work with E. coli). Let's assume for a minute that, like you, I strongly suspected the results of the paper (I do not, but that doesn't matter for this exercise). If this were the case, two of the routes I could take would be to re-analyze Prof. Lenski's data or replicate his experiments. In some cases, data and their analysis are complex, and re-analysis can yield different results than those the original author reached. This is the case for a large-scale association study, for example -- there are tons of data to analyze, and their analysis is not straightforward. In Prof. Lenski's case, however, the data are extremely simple, consisting primarily of 1) OD readings to measure fitness, and 2) colony counts.

:::: OD readings, or optical density readings, are obtained by pipetting a sample of cultured bacteria into a cuvette, sticking that cuvette into a machine, and writing down the number that pops up on a screen. Somewhere in a grad student's notebook (or in his/her computer) is a list of these numbers, and their average and range were presented in the PNAS paper at each generation in Figure 1 (similar data are presented in Figure 2 and Figure 5). So, in other words, the data you see in the paper *are all of the data* save for a second grade computation...which was probably performed by Excel. If you don't believe the data in the paper, then what do you expect to gain from seeing these "raw" data? There is so little to gain that I seriously doubt that PNAS would take such a request seriously.

:::: The meat of the paper, in Table 1, is a presentation of colony counts. These are obtained by another grad student picking up a bacterial culture plate, counting the number of colonies on it, and moving on to the next plate. Again, the raw data are what you see in the paper. What exactly are you expecting here, photographic images of all of the tens of thousands of plates they examined? That is just not done. Why would we go to that level of self-surveillance to please a small, vocal minority of people claiming fraud? The public's interest is not served by spending inordinate amounts of effort and money on this level of surveillance. If the science is correct, his experiment will be replicated.

:::: In sum, as others have tried to explain, there really isn't any more complex data for you to reasonably request. A slightly expanded list of numbers from what's in the paper won't get you anything if you already don't believe the data. And the scientific culture doesn't even come close to expecting photographic evidence of bacterial plates. Your best bet, if you really don't believe the results, is to get an outsider to try and replicate and/or confirm some portion of his results. The easy route would be to ask for a cit+ strain and its ancestor and see if they are indeed cit- and cit+. You could even sequence them to check if the cit+ strain is indeed an ancestor of the cit- strain, but while this would be a perfectly normal approach in a molecular biology lab with impressive resources, the entire concept of evolution is anathema to you, so I can't think of a reasonable criterion you would use to determine ancestry. If you wanted to go the hard route, you could obtain the ancestral strain and grow and measure them for years as Prof. Lenski's lab did.

:::: I hope this has been somewhat instructive for you in explaining why a request for "further data" will not bear fruit beyond the small amount of data that Prof. Lenski says he will make available. And why it is not reasonable to expect further data. I am more than happy to respond to questions or requests for clarification if you would like. -- [[User:Princetonian|Princetonian]] 23:50, 26 June 2008 (EDT)

::::: For starters, most of the opposition to releasing the data has been the false claim that the data are too voluminous to release. You are making the opposite claim, one which is more consistent with Lenski's paper: there is very little important data beyond what is in the 8-page paper. But that doesn't withstand scrutiny either.

::::: The "meat" of the paper is this, and at a minimum the data should be released for it (pp. 2-3 from paper):

:::::: Evolution of Cit Function in Population Ara-3. The LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time. [DATA ON THESE OBSERVATIONS?] Owing to the low concentration of glucose in DM25 medium [DATA?], the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. [DATA?] These contaminated cultures reach much higher turbidity owing to the high concentration of citrate in the medium, which allows the contaminants to reach high density. (When contamination occurs, the affected population is restarted from the latest frozen sample.) [DATA FOR WHEN THAT OCCURRED?] After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).[HIGHER RESOLUTION DATA UNDERLYING FIGURE?] A number [DATA?] of Cit clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all [DATA?] were Ara, T5-sensitive, and T6-resistant, as expected (2) [DATA ABOUT THESE AND OTHER CHARACTERISTICS?]. DNA sequencing also showed [DATA?] that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, and each of these mutations distinguishes this population from all [DATA?] of the others (30). Therefore, the Cit variant arose within the LTEE and is not a contaminant [THIS CONCLUSION NEEDS TO BE CHECKED BY INDEPENDENT REVIEW OF THE ACTUAL DATA, WHICH I DOUBT OCCURRED IN THE BRIEF PEER REVIEW OF THIS PAPER]

::::: Note, by the way, how the opponents of data disclosure seem to have no idea about what data Lenski actually has, which raises further questions about the merits of the conclusion.--[[User:Aschlafly|Aschlafly]] 09:15, 27 June 2008 (EDT)

:::::: I know some people here have claimed that the data are too voluminous to release...I didn't know what they were talking about, which is one reason I chimed in. Anyway, here are point by point responses to each of these cases. <i>Turbidity checking</i>: these data are either in a grad student's notebook somewhere, or were not recorded. I wouldn't at all be surprised if they weren't recorded due to the nature of the data (it's just a visual check of turbidity, and wouldn't be reported in a paper). <i>Low concentration of glucose in DM25</i>: this is a factual statement about DM25 media, not an observation. <i>Contaminants</i>: Same comment as the turbidity checking. Either there's a one-liner in a notebook somewhere ("Flask 25 contaminated, re-grew from stock") or nothing at all, since it's tangential to the experiment. <i>Figure 1</i>: As I already mentioned, the data in Figure 1 are actually comprehensive -- three data points went into each plotted point. They report the range (which give you a max and a min) and they also show you the average, which allows you to impute the third data point. <i>Number of Cit clones, and the following comments except the last</i>: these data are probably recorded in a lab notebook somewhere, since they're rather not tangential to the experiment. In addition, I'm sure they have a frozen stock of each cit+ bacterial clone that they checked, so this is something that could be easily independently verified. <i>Cit+ is not a contaminant</i>: no this would not be a part of the peer review...peer reviewers are not out to find fraud in general. Especially in the inaugural paper of somebody just nominated into the national academy. And the data underlying contamination checking are also extremely simple -- you plate the bacteria on an Ara+ plate and check sensitivity by eye, for example -- so there is no need to verify methodology as long as you trust the source.

:::::: You're basically asking for the lab notebooks of all of the grad students involved in the experiment over the 20 years. The data in these notebooks is going to be, in general, very simple (e.g., the statement "colony grew on Ara-, is a contaminant") since as I mentioned, there is no photographic evidence of this. Additionally, while biotech companies generally have document retention policies as required by law, no such policies exist at the academic level (although specific institutions may have them). A very few labs are run like well-oiled machines -- lab notebooks are kept up-to-date and thorough, and every observation is recorded. This is the ideal, but almost no labs actually achieve it, since most labs are working at 125% speed in an effort to get experiments finished and published.

:::::: If you're really interested in monitoring the quotidien details of these experiments, that falls outside of the scope of what PNAS and professional standards would require Lenski to release, I believe. You're not asking to re-analyze data so much as to oversee the entire experiment for fraud. This would require giving you all of Lenski's graduate students' lab notebooks for an indefinite period of time, which would be quite disruptive, and as I said probably wouldn't even yield the level of data you seem to want. In this case your best bet is to contact MSU and ask for a comprehensive review of Lenski's lab and his notes for this experiment. But without any evidence to point to said fraud, they will certainly deny your request for oversight. Your expectations here just aren't in line with professional standards in the field in the absence of any evidence of fraud. -- [[User:Princetonian|Princetonian]] 10:49, 27 June 2008 (EDT)

::::::: You've confirmed that the strident claims by Lenski defenders here that the data are too voluminous to release were nonsense. We'll see how many of them now admit they were wrong. Let's not hold our breaths!

::::::: But your opposite approach above, which essentially suggests there are no data that can be released, doesn't withstand scrutiny either. Figure 1 is plainly a low-resolution representation of underlying data that must exist. The greater resolution should be released. Similarly, there should be data underlying the essential assertion that a particular sample was not contaminated, while others had been. For example, the paper asserts that "[a] number of Cit clones were isolated." How many were isolated? If those data exist, then it should be released along with the other data. If those data do not exist, then that is even more telling.--[[User:Aschlafly|Aschlafly]] 11:34, 27 June 2008 (EDT)

:::::Regarding the questions highlighted by [[User:Aschlafly|Aschlafly]] to which [[User:Princetonian|Princetonian]] also responded: Many of the techniques questioned are standard procedures that a trained microbiologist would understand. Let's take this apart by question:
:::::'''''...the turbidity of each is checked visually at that time. [DATA ON THESE OBSERVATIONS?]'''''
:::::This is qualitative observation. Every microbiologist does this when they pull their cultures out of the incubator. The evaluation an experimenter asks: Can you see through the test tube or not? Is the culture denser or lighter than the last time you looked? The reported observations are the data.

:::::: Show us the data. Are you suggesting that no record was kept of these observations??? I hope that's not what you mean. But say so if that is your view.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::I described how the observation was performed. How the observations are recorded is up to the lab or technician culturing the cells.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Owing to the low concentration of glucose in DM25 medium [DATA?]'''''
:::::A reference to the description of the media is provided in the paper and is included on Lenksi's web pages. I linked to that page recently in another comment. It is general knowledge among microbiologists that nutrient limited cultures will reach a peak density that depends on the concentration of the limiting nutrient.

:::::: Again, show us the data. What was the concentration of glucose and, more importantly, did it ever change?--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Consider rereading the paper and pull out references provided. It's there.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. [DATA?]'''''
:::::Observation. Either they saw contaminated cultures or not.

:::::: No kidding. The point, obviously, is to disclose the data of what they saw. How many is "occasional"? Show us the records supporting that claim, so we can assess the frequency of contamination compared to alleged evolution. At a minimum, it appears that contamination was significantly more frequent than the alleged evolution.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Contamination is a problem every microbiology lab understands and encounters. What matters and what is particularly relevant to this experiment is the means of detecting and controlling for it. They outline the steps for detecting contaminating and restarting the experiment from uncontaminated stocks in their papers and web pages.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...(When contamination occurs, the affected population is restarted from the latest frozen sample.) [DATA FOR WHEN THAT OCCURRED?]'''''
:::::Not relevant for the results. It's just the researchers describing how they restarted the experiment whenever they suspected a contamination. It does not alter the experimental outcome.

:::::: It is relevant, at a minimum for reasons stated in my above response. Also, did the restarting ever result in repeats of the observed contamination?--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::They controlled for contamination. If their previous stock was contaminated they would likely return to ones before that last stock. Clearly, they would not want to work with contaminated stocks as it would damage the experiment.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).[HIGHER RESOLUTION DATA UNDERLYING FIGURE?]'''''
:::::Higher resolution is not really necessary. The graph provides a ''qualitative'' visualization that starkly reveals that the cultures underwent a change that allowed them to grow to a significantly higher density than previously. They report in the text the actual generation were the change occurred and that seems to line up with the transition in the figure (take out a ruler, if necessary). Their subsequent experiments bracketed the strains from points before, during and after the obvious population transition.

:::::: Your answer here is absurd. Higher resolution in science is always helpful. The precise rate of change among the population would reveal much about what was really occurring. The data must exist to generate the graph. Disclose it rather than obscuring it with a low-resolution graph.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::If one reads the paper, one finds that weakly Cit+ clones arise earlier than the visible transition. Reading the paper one would see that they analyze the emergence times: ''Cit+ clones could be readily isolated from the frozen sample of population Ara-3 taken at generation 33,000. To estimate the time of origin of the Cit+ trait, we screened 1,280 clones randomly chosen from generations 30,000, 30,500, 31,000, 31,500, 32,000, 32,500, and 33,000 for the capacity to produce a positive reaction on Christensen’s citrate agar, which provides a sensitive means to detect even weakly citrate-using cells.'' As for the visible transition: ''After ~33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days''. Note also that they performed 'replay' experiments (which took up the rest of the paper) to specifically analyze the frequency and times when Cit+ strains could be generated. The last half of the paper contains the work that provides information about the possible nature of the mutations and addresses your question.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all [DATA?] were Ara, T5-sensitive, and T6-resistant, as expected (2) [DATA ABOUT THESE AND OTHER CHARACTERISTICS'''''
:::::Derived from observation. The phenotypic markers are described elsewhere and the means of testing them are well known by professional microbiologists. The origin of the strain and its markers can be determined by following the references provided. The strain is also referenced on Lenski's pages here: https://myxo.css.msu.edu/ecoli/strainsource.html Other information about how they tested markers can also be found starting from here (provided by Lenski): https://myxo.css.msu.edu/ecoli/

:::::: Disclose the data so that independent reviewers can assess how reliable the claims are here. The methodology may be "well known" but only disclosure of the data will demonstrate whether the methodology was applied in a flawless manner.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Those are all based on visual observation. Reporting the observation *is* reporting data. Lenksi's group provides information how they performed the tests so that any professional microbiologist would be able to follow the work. The way for someone to test the methodology is to repeat the tests on the strains themselves. Recall that Lenski did say that the strains would be made available to labs. So, for anyone interested in seeing for themselves that "the methodology was applied in a flawless manner", I suggest they go find a friendly microbiologist to request and perform the tests for them.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...DNA sequencing also showed [DATA?] that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations'''''
:::::Report of observation. They sequenced the specified genes and found no difference in base-by-base comparisons. There is no need in this paper to print all sequences side by side as they're the same. The words, "no difference" transmits the same information in less space as showing all the identical sequences side-by-side with the original, previously released sequence. See also the next lines.

:::::: No one suggested that the DNA be published "in this paper," but rather that the data be made publicly available for independent review and verification.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Again, the sequences are available. If someone wants to confirm that the sequencing was done correctly they can request the strains from Lenski and repeat the sequencing. The protocols are published.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...each of these mutations distinguishes this population from all [DATA?] of the others (30).'''''
:::::See reference (30) from Lenksi's paper. It describes how the genes in those populations were originally sequenced. The ancestral sequences were uploaded into GeneBank, a publically accessible sequence repository, and the identifying mutations were presented in the supplemental table published on the PNAS web site along with the original paper.

:::::: That's spelled "publicly", not "publically", and again disclosure of the data concerning the mutations is necessary to verify the claims made.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::If someone wants to confirm that the sequencing was done correctly they can request the strains from Lenski and repeat the sequencing. The protocols are published and Lenski has stated he would make the strains available.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Therefore, the Cit variant arose within the LTEE and is not a contaminant [THIS CONCLUSION NEEDS TO BE CHECKED BY INDEPENDENT REVIEW OF THE ACTUAL DATA, WHICH I DOUBT OCCURRED IN THE BRIEF PEER REVIEW OF THIS PAPER]'''''
:::::The authors reported the actual data in a manner that is readily understood and accepted by microbiologists. The data and analysis is not terribly complex or confusing for someone familiar with the field (and quite a few who aren't expert microbiologists). Andy, I've seen little requested that isn't standard practice & generally understood among microbiologists or not already available if one follows the references provided in the paper.

:::::: You're right that the "data and analysis" are "not terribly complex." Which is why the odd withholding the data merely serves to heighten skepticism towards the claims made.
:::::::YMMV. I've encountered no one on the web or elsewhere and trained in microbiology who thinks the data is being 'oddly' withheld. Most of us manage to locate the references and other sources provided.

:::::: The bottom line is that some think that Lenski's claims must be accepted on faith rather than independent verification of the data. That is not science.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)

:::::Just a word about reading the professional, scientific literature: Scientific papers are by the nature of their medium, mostly brief, to the point and highly condensed. Rather than repeat all the background information that others in the field may already know and encouraged to limit the length by journals with page limits, authors provide references to other papers that contain the previously published information. They also use terms that are well-defined within their profession to shorten the text further. One wouldn't expect a layman with no experience in biology to easily digest the paper. To point is not to obfuscate but to simmer the paper down to essentials that others in the field can readily understand. With some effort to become familiar with the underlying & established techniques & science, determined, non-experts can eventually pick up this information. I'd respectfully suggest to anyone *seriously* interested in the paper but not comfortable with the technical details, that they may want to find a knowledgeable biologist willing to explain. At least they should read the entire paper and the additional papers referenced within. Consider asking DI's research institute or Behe for help with understanding the techniques behind the work.--[[User:Argon|Argon]] 20:11, 27 June 2008 (EDT)

:::::: Your sermon is misplaced. Taxpayers paid for Lenski's study, and any real scientist should reject the inexplicable withholding the data underlying its conclusions.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::YMMV but in my view, it's like going to a librarian and demanding they provide something made from paper: Books? Magazines? Newspapers? What type of books? What subjects? My opinion is that if someone: doesn't know what one wants, doesn't appear to understand the report, demands to see 'the data' without appearing to know what they're asking for in the first place or how to process the information, I'm not sure how any experimental scientist would comply with that request. Furthermore, I'd find it odd that the requests persist despite the fact that the paper was indeed published in compliance with establish profession standards and the strains were made available (in compliance with journal and university research policy). Again, if someone thinks the work was done incorrectly they can get a lab to request the strains and try to repeat many of the observations. That is why the materials and methods sections exist in papers: To allow others to repeat and confirm the work.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

Unfortunately, there are essentially no real scientists left. Peer review is almost never done with the amount of scrutiny Aschlafly discusses. Reviewers, even for journals with long submission-to-publication times, do not request the original data. When original data are requested, it is by researchers who want to continue the work and write publications of their own on the subject. There just aren't incentives to do thorough reviews.

Aschlafly, I think you're right that review should have been more stringent. I think you're wrong, however, to conclude that an exception was made here. Its true that review time was very short in this case. The total number of man-hours devoted to '''any''' review, however, is seldom more than 40.

What does "real scientists" mean? If it means practicing academics today, it's sadly wrong. Most [[professor values|professors]] are self-centered, and would see true peer review as impinging on their personal freedom. "Who has time," they think, "to transcribe lab notebooks? I've got more papers to publish!" I bet the majority would even resist your request to Lenski. This liberal attitude towards truth is what leads to claptrap like [[Particle/wave duality theory]] and [[COBE|the theory of cosmic microwave background radiation]]. [[User:Drochld|Drochld]] 09:19, 28 June 2008 (EDT)

: With respect to your comments on peer review, note that there were merely 14 days between the time the Lenski manuscript was sent for review and the time it was confirmed for publication. I doubt even 10 good hours of real peer review were devoted to the Lenski manuscript, let alone the 40 you mention. The 14 days included administrative and communication delays, and business and weekend days. It looks like a "rubber stamp" process to me for evaluating this Lenski manuscript, in contrast to other papers published by the same journal. It seems possible to me that there was no meaningful peer review at all for the Lenski manuscript, and it may be worth making inquiries of the Journal on this point alone.--[[User:Aschlafly|Aschlafly]] 09:44, 28 June 2008 (EDT)

::The paper is straightforward and the data clear. Lenski's work is well known within the microbiology community and therefore much of the preceding information is already generally understood (i.e. reviewers don't need to dig through all the references). I can see it sailing through review.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

::: In other words, you seem to be saying the latest paper was not given a thorough, independent peer review. I agree with that analysis. In fact, it probably "sailed through" without any meaningful peer review at all, despite published journal procedures claiming to require meaningful peer review.--[[User:Aschlafly|Aschlafly]] 11:08, 28 June 2008 (EDT)

::::On the contrary. I see it sailing through review because the experiment is straightforward, clearly reported and very interesting to the field. The techniques are uncontroversial and well understood among microbiologists. Easy reviews proceed faster, plain and simple. That reveals nothing about whether the paper received more, less or the same of scrutiny as the typical paper.

::::Are you familiar with PNAS review policy? I ask because in previous notes you've wondered whether authors submit original (raw?) data in addition to their paper's actual manuscripts. Have you perhaps discussed review policies with other Nation Academy of Sciences members or at least, publishing biologists? It might be more productive than polling anonymous sources on the internet.--[[User:Argon|Argon]] 11:28, 30 June 2008 (EDT)

:::::Aschlafly, the purpose of a Peer Review is not to make sure the entire experiment wasn't a massive fraud - it is to ensure that the work adhered to scientific principles and guidelines. In this case, the work was short and did adhere to principal. Lenski has, as required, laid out how the experiment can be repeated. Are you saying that he risked his entire reputation on results that can be checked and refuted by another lab? {{unsigned|Falsehood}}

::::Aschlafly, peer reviews are not suitable to detect all experiment flaws or outright fraud. Reviewers can't always know whether a lab assistent made a mistake or even if the experiment was done at all. The primary goal is to make sure that the experiment can be repeated so completely independent researchers can verify the results. This is the only good verification. A mistake in the experiment means that the data cannot be trusted. That is true for fraudulent data as well. There are several reasons to repeat an experiment. First of all, a groundbreaking result will nearly always be repeated. Scientists want to be sure they can trust the result and not waste years on related experiments. The second reason is to test yourself. A scientist may want to repeat an important experiment before starting their own related experiments. It may also be done to test a new lab or test setup. Thirdly, indications of fraud are an obvious reason. Fourthly, highly complicated experiments that can easily go wrong may be replicated. Fifthly, new scientists are less trusted and more likely to be checked. Now, this experiment is not particularly likely to be repeated. It is not particularly groundbreaking (evolutionary changes have been observed in many other experiments), complicated and there are no indications of fraud. Of course, you/Conservapedia may want to appeal to colleages of mr. Lenski for a repeat of (parts of) the experiment, but I doubt that they will be swayed by your arguments that seem to boil down to: 'I don't understand the science, but I don't like the result, so there must be a mistake'. It would be wiser to point to an actual lack of evidence or methodology flaw in the paper (if it exists), so an experiment can be drafted to test the significance of that mistake. --[[User:Aapje|Aapje]] 07:29, 8 July 2008 (EDT)

== More replies to archived comments ==

:"''Why do you say that it does not support evolution?''" ([[Conservapedia talk:Lenski dialog/archive1#Questions for Aschlafly , not Bugler]] (Asked by JPohl of me):
See my post (now in the archive) dated 23:05, 16 June 2008 (search for that text).

:"''The current living species of coelacanth are not the same as the ones in fossils''" ([[Conservapedia talk:Lenski dialog/archive1#E. coli in our bowels]]) (in a question by Wandering to me)
:"''Modern coelacanths are anything but unchanged. For example, they're roughly three times as large as their ancient predecessors. Of the two known living species, neither are in the same genus as ancient coelacanths. Your statement is ''blatantly'' false''" (Same section) (by Rspeed in a response to Jimxchue)
How do we know that they are not the same species or genus? "Species" is defined in terms of interfertility, something that cannot be determined for fossils. And size doesn't mean much. Great Danes and Chihuahuas are in the same ''sub''-species, but the ratio of size difference is greater than 1:3.

[[User:Philip J. Rayment|Philip J. Rayment]] 23:14, 26 June 2008 (EDT)

:Hi Philip, I read your post and I don't think it addresses anything other than semantics. The bacteria was standard E Coli, and then after tens of thousands of generations, it started to metabolise citrate, which normally ''distinguishes'' E Coli from other species. That's very clearly the process of changing inherited traits over generations - ie, evolution.[[User:JPohl|JPohl]] 08:45, 27 June 2008 (EDT)
:: I can't help wondering if you skimmed it too quickly and didn't pick which bit I was referring to here. I'll explain it in a different way:
::* According to evolution, there must be millions of information-generating mutations to go from microbes to man.
::* According to creation, mutations do ''not'' produce new genetic information, although ''very rarely'', you might by chance get the odd one.
::Lenski has allegedly found ''one'' information-generating mutation. So which of those two competing predictions does this evidence match the best?
:: I also pointed out two weeks ago on Andy's talk page the following:
{{QuoteBox|It took 31,500 generations before the bacteria acquired a single new ability (even assuming they actually do have some new genetic information). 31,500 generations for humans is around 600,000 to 900,000 years (depending on the average time between generations). Yet humans have supposedly evolved ''hundreds'' if not ''thousands'' of new abilities from their supposed primate forbears in a time span only three to five times that long. So this research can be seen as evidence (not absolute proof, of course) that evolution simply does not occur fast enough for us humans to have evolved, which is therefore ''evidence'' that evolution can't explain our existence.}}
:: [[User:Philip J. Rayment|Philip J. Rayment]] 09:37, 27 June 2008 (EDT)

:::There are some flaws in that logic though:
:::*Simple cells likely first appeared 4 billion years ago. Given how many existed simultaneously (an entire planet at some times v. a few petri dishes) and that simpler living beings have shorter lifespans, going from "microbes to man" (or something as genetically complex as man) is really a matter of time.
:::*31,500 generations is not a minimum number of generations for a rare, complex trait to manifest. That just happened to be the case here. Dumb luck could have had significant mutations develop at any earlier (or later) point.
:::*What definition of "ability" are you using here? All of the bacteria also evolved larger cells - would you count that as an "ability"? According to Lenski's work, "enough bacterial cells had lived and died that all simple mutations must already have occurred several times over"
:::*Bacteria are asexual. Animals and plants reproduce through sex, which causes significantly more genetic variation.[[User:JPohl|JPohl]] 12:18, 27 June 2008 (EDT)

:::: No, going from microbe to man is ''not'' a matter of time. If you are travelling south from Sydney, how long will it take you to reach Brisbane? Answer: It's not a question of how long, because you are going in the wrong direction. The same applies here: you can't go from microbes to man when mutations destroy information rather than create it. See also [http://creationontheweb.com/content/view/431/ here].
::::: We both know the Earth is round, so the trip is still possible, if not extended. [http://www.talkorigins.org/faqs/information/infotheory.html This] and [http://www.talkorigins.org/faqs/information/apolipoprotein.html this] are good links on information theory.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: Yes, perhaps 31,500 generations just ''happened'' to be the case here. As you say, it ''might'' occur sooner, and it ''might'' take longer. But my argument was based on the ''evidence'' of this example, not on what speculation ''might'' allow for. The ''evidence'' is not ''proof'', but the ''evidence'' in this case is ''against'' evolution.
::::: I'm not following your claim here. The mutation happened, and it is proof against evolution?[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: I'm talking about the ability claimed by the research, to metabolise citrate, that apparently requires new genetic information. Being bigger presumably does not require that, else they would have trumpeted that as well.
::::: They didn't trumpet the metabolisation of citrate as "new information", but rather as a complex mutation that dramatically distinguished it from earlier generations. It would be like coming back to Earth in 100,000 years and finding that humans suddenly have two-foot-long third legs.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: Genetic variation through sexual reproduction is a variation ''within'' the existing genetic information; sexual reproduction does not create ''new'' genetic information.
::::: It varies the gene pool, which allows for different types of mutation and more dramatic diversification.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: [[User:Philip J. Rayment|Philip J. Rayment]] 23:31, 27 June 2008 (EDT)
:::::: "''We both know the Earth is round, so the trip is still possible, if not extended.''": So? Like all analogies, it's not perfect. Evolution doesn't go around in circles like travelling around the Earth, so that reply is invalid, and the objection remains: mutations go in the wrong direction.
:::::: "''[http://www.talkorigins.org/faqs/information/infotheory.html This] and [http://www.talkorigins.org/faqs/information/apolipoprotein.html this] are good links on information theory.''": No, they are not good links at all. From memory of checking the first one out before, it has little of substance. The second is a disagreement over a particular case, not a general look at information, and has some errors in it that I can identify.
:::::: "''I'm not following your claim here. The mutation happened, and it is proof against evolution?''": I said "evidence", not "proof". If you don't understand the difference, read the relevant sections in my [[Essay: Accuracy vs. neutrality on Conservapedia]]. Creationism ''also'' proposes mutations, so the fact that a mutation happened is not evidence favouring evolution.
:::::: "''They didn't trumpet the metabolisation of citrate as "new information", but rather as a complex mutation that dramatically distinguished it from earlier generations. It would be like coming back to Earth in 100,000 years and finding that humans suddenly have two-foot-long third legs.''": The New Scientist article quoted Jerry Coyne saying "it says you can get these complex traits evolving by a combination of unlikely events, ... That's just what creationists say can't happen.". What creationists say "can't happen" is an ''increase in information''. So if you are claiming that nobody is claiming this to be an increase in information, they you are claiming that Jerry Coyne doesn't know what he's talking about regarding what creationists claim (which could be the case, actually!). As for your example, a short third leg probably doesn't require new information anyway. We already have the information for legs, so failure (mutation) of a switch might result in a third one (it's happened with animals), and another fault (mutation) might cause that third leg to be stunted. So if Lenski's discovery is like this, then it really is the case that it doesn't support evolution, because microbes-to-microbiologist evolution requires ''new'' genetic information.
:::::: "''[Sexual reproduction] varies the gene pool, which allows for different types of mutation and more dramatic diversification.''": That sounds like hand-waving to me, rather than an argument of substance.
:::::: [[User:Philip J. Rayment|Philip J. Rayment]] 10:40, 1 July 2008 (EDT)

:::::Philip,
:::::With due respect, I see a fairly serious problem with the position you're taking. One of the central arguments against evolution is that mutations ''cannot'' produce new information. Now you're arguing that:

:::::''"According to creation, mutations do ''not'' produce new genetic information, although ''very rarely'', you might by chance get the odd one."''

:::::The problem is that, if it can "very rarely" happen "by chance," then the premise that mutations do not produce new genetic information is simply false. Instead, we're faced with a debate over ''how frequently'' mutations produce new genetic information. --[[User:Benp|Benp]] 10:41, 28 June 2008 (EDT)

Philip, I see your point about how the creation of new information through mutation does not necessarily contradict creationism at all. However, it hardly seems like evidence ''for'' it; and extrapolating as you did (trying to claim the timeframe for these bacteria applies equally to the supposed evolution of humans) honestly seems like mostly speculation... Which I admit is often overused by evolutionists as well, but it still isn't a good basis for deciding which theory the evidence favors. [[User:Feebasfactor|Feebasfactor]] 11:27, 28 June 2008 (EDT)

: BenP, it's possible to have both a rule and exceptions to that rule. For all practical purposes, mutations don't create new information. However, that doesn't rule out that, once in a blue moon (actually, far less often), you might actually get ''something'' simple that is new. And yes, I guess that there is then a debate about how frequently mutations produce new genetic information, which is sort of what I've been discussing here, in pointing out that ''in this case'' it took 31,500 generations, and even that assumes that this ''did'' happen, which I think is a long way from being accepted. But the question is not ''really'' how long it takes, but whether or not the extremely rare one is going to be swamped by all the deleterious ones. And especially with more complex creatures, it is easily going to get swamped, especially in creatures with sexual reproduction. That is, even if, once in 30,000 generations, there was the odd information-gaining mutation, then what's the chances that that mutation will get passed on to the next generation? Especially given that this won't be the only mutation being selected for (or against).
: Feebasfactor, why is not not evidence ''for'' creation? If that's the prediction that it best fits, then it ''is'' evidence for it! You're right about the timeframe not applying to humans. Because humans reproduce sexually, and therefore the next generation will not necessarily inherit the mutation, and because natural selection favours ''individuals'', not ''mutations'', then a less-fit ''individual'' will be selected ''against'' even with the odd "good" mutation. So really, it will occur a lot ''slower'' for humans than for bacteria.
: For more information on this, see [http://creationontheweb.com/content/view/4473 this] brief description of "Haldane's Dilemma".
: [[User:Philip J. Rayment|Philip J. Rayment]] 11:27, 29 June 2008 (EDT)

:: It's amusing to me that you cite Haldane's Dilemma, even though it was debunked at the same time it was given that name. As Leigh Van Valen pointed out on page in his paper [http://www.jstor.org/pss/2458906 Haldane's Dilemma, Evolutionary Rates, and Heterosis], significant evolutionary changes occur when the environmental changes cause unadapted organisms have less reproductive success. This holds with evolutionary theory, as there is abundant evidence of large changes occurring in organisms at times where their environment changes and their population is small. Mind you, this is the paper which originated the term "Haldane's Dilemma", so with the exception of J. B. S. Haldane's papers, this is the original source. --[[User:Rspeed|Rspeed]] 16:41, 30 June 2008 (EDT)

: Philip, the massive increase in size is just one (and the most readily visible) aspect of Coelacanthiforme's evolution since the end of the Cretaceous. If you want firm proof, there are significant differences in skeletal structure between the most closely-related ancient and modern species of coelacanth (Macropoma and Latimeria). It is an established fact that modern species of coelacanth are in a separate genus. --[[User:Rspeed|Rspeed]] 15:01, 30 June 2008 (EDT)
:: There have apparently been various ''attempts'' to debunk Haldane's Dilemma, but those attempts have themselves been debunked. In 1992 (well after Van Valen's paper), George C. Williams wrote of Haldane's Dilemma, "In my opinion the problem was never solved, by Wallace or anyone else."[http://saintpaulscience.com/Haldane.htm]
:: "''It is an established fact that modern species of coelacanth are in a separate genus''": Oh? Because you say so? Yet you didn't explain how this can be determined without interfertility tests. No, this "established fact" is by decree, not scientific tests of interfertility.
:: [[User:Philip J. Rayment|Philip J. Rayment]] 11:22, 1 July 2008 (EDT)
::: "Oh? Because you say so?" No, because the scientists who know how to determine taxonomy said so. Your argument is unbelievably weak, by that logic humans could be genetically compatible with T-Rex. Rather than simply dismissing everything that disagrees with the Bible, you should probably do some research from reliable sources. The scientific method exists for a reason.
::: That's fine about someone disagreeing with Van Valen's conclusions, but can you share his reasoning? I found Van Valen's debunking of Haldane's Dilemma to be quite logical and it fits with the data (such as Prof. Lenski's experiment).
::: --[[User:Rspeed|Rspeed]] 20:35, 3 July 2008 (EDT)

==Lead author won't answer simple, basic questions==

IMO the paper has no credibility because the lead author of the paper, Zachary Blount, has refused to give straight consistent answers to the following simple, basic questions about the experiment:

(1) -- whether evolution of citrate-eating (Cit+) E. coli bacteria was a goal of the experiment (I noted that a "goal" does not have to be a sure result), and

(2) -- whether the purpose or one of the purposes of the glucose-cycling (giving insufficient glucose supplies in order to cause alternating glucose feeding and glucose starvation) was to favor the evolution of citrate-eating E. coli bacteria.

Blount's refusal to properly answer these questions is discussed in the following article on my blog --

[http://im-from-missouri.blogspot.com/2008/06/co-author-of-e-coli-paper-dodges.html Co-author of E. coli paper dodges questions]

More details concerning Blount's refusal to properly answer these questions are in the comment thread under the following post on Carl Zimmer's "The Loom" blog (note particularly my most recent comments in that thread) --
[http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php A new step in evolution]

Also, I think Andy Schlafly is wrong to request all of the raw data, because (1) copying all of the raw data to send to him would be a huge job and (2) the raw data might not even be in a form that could be readily understood by someone who did not participate in the research. IMO the citrate-eating bacteria are the best evidence supporting the paper (such as it is).[[User:LarryFarma|LarryFarma]] 18:59, 26 June 2008 (EDT)
: a reading of the blog reveals that Zachary Blount did indeed address the questions that the above poster named and did so clearly. Please read more carefully next time and don't post falsehoods[[User:DeanWinter|DeanWinter]] 19:10, 26 June 2008 (EDT)

:: LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. (I did not find the answer in the paper.) Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population? The details of the data might shed light on how that goal was achieved, if in fact that was the goal. They should turn over the data for public scrutiny so that questions can be resolved.--[[User:Aschlafly|Aschlafly]] 19:33, 26 June 2008 (EDT)
::: Blount's comments on "LarryFarma's" blog make it clear that the evolution of citric eaters was not a goal, but not completely unexpected. The paper, though it was pretty technical for me, seems to indicate that as well. [[User:AndyMann|AndyMann]] 20:15, 26 June 2008 (EDT)

:::: If you're serious, then please provide some quotes and links to back up your statements. Also contribute to entries rather than violating the [[90/10 rule]].--[[User:Aschlafly|Aschlafly]] 20:32, 26 June 2008 (EDT)

:Reply to Aschlafly's comment of 19:33, 26 June 2008 (EDT) --
:''"LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. ('''I did not find the answer in the paper.''')"'' (emphasis added) I asked Zachary Blount to clarify his statements about whether evolution of Cit+ (citrate-eating) E. coli bacteria was a goal of the experiment. He answered by asking me to go on a wild goose chase by reading the whole paper, which has 8 pages of fine print -- this is called "bibliography bluffing." And when people balk at going on these wild goose chases, they are accused of not wanting to learn.

:''"Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population?"'' As I said, I asked Blount whether favoring Cit+ evolution was the purpose or one of the purposes of the glucose-cycling (giving the bacteria insufficient supplies of glucose so as to create alternating glucose feeding and glucose starvation), and he did not answer.

:''"They should turn over the data for public scrutiny so that questions can be resolved."'' I disagree with you here, for the reasons stated at the end of my first comment in this talk page.[[User:LarryFarma|LarryFarma]] 05:25, 28 June 2008 (EDT)

:: Thanks for your insightful comments and continued efforts to obtain the truth.

:: It has been conceded, finally, by Lenski defenders that the data are not too voluminous to turn over. The underlying data for Figure 1 in the paper for the population expansion during the alleged evolution of the Cit-plus phenotype, for example, could shed light on whether contamination played a role. There is no legitimate reason to withhold the greater resolution from the public, which funded the study.--[[User:Aschlafly|Aschlafly]] 09:15, 28 June 2008 (EDT)

::::People need to stop asking to "turn over the data for public scrutiny" before they've fully read and comprehended the papers and information released to date. E. Coli don't live off of citrate - it's a characteristic of the species - so there was no "goal to promote the percentage that could do it". The fact that a certain population were able to after after thousands of generations of reproduction in a controlled, monitored setting was the key observation, and Lenski's team is still investigating the specifics of when and how that characteristic was enabled. It reflects poorly on an online encyclopedia that the leadership is still questioning whether sufficient data to understand the experiment has been released. The most relevant data from the experiment is the actual bacteria itself, and Lenski has publicly offered to share samples of them with any scientist qualified to handle them, who follows the proper, professional protocols. The Consevapedia community has yet to see a specific, professional response to Professor Lenski's second letter other than a flippant remark about attitude and a continued insistence that data has not been revealed when it clearly has.

::::I'll probably earn another 90/10 block for this, but when you continue to question Lenski's work while admitting that you've only skimmed the related paper, you accomplish nothing but setting a poor example of intellectual honesty for the students who use CP as a trustworthy resource. With all respect, I would ask that instead, you retain the services of a qualified scientist who can engage in a proper review of Lenski's work, whose could then post an ongoing journal of the review process and its findings here on CP. ''That'' would be an appropriate lesson for the students in the proper application of scientific scrutiny to findings that some find questionable. Godspeed. --[[User:DinsdaleP|DinsdaleP]] 20:20, 26 June 2008 (EDT)

::::The development of citrate metabolizers wasn't the main intent (see Lenski's early papers) and it's actually tangential in the overall context of the long-term experiment. Zachary Blount describes the purpose of citrate in the media in his responses at Carl Zimmer's blog, The Loom. http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php (see replies #115 & #270). Citrate was not added to be a carbon nutrient in the media but as a non-metabolizable chelator (the three carboxyl groups of citrate can bind certain cations in solution). The recipe for the medium was taken from other microbiologists who developed the recipe as a general culture medium back in 1949. Lenski's description of the DM25 media is here: https://myxo.css.msu.edu/ecoli/dm25liquid.html. Glucose was the intended carbon source. If you read the Lenski article cited by Blount (Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. -- available here: https://www.msu.edu/~lenski/, you'll see the setup and reasons for performing the experiments (An earlier article at generation 2000 is here: http://myxo.css.msu.edu/lenski/pdf/1991,%20AmNat,%20Lenski%20et%20al.pdf). Basically, Lenksi wanted to see how mutations arise and move through populations over time. Even if the media and growth conditions remain pretty consistent over time, the populations continuously shift and change. That is because for a bacterium in the experiment the 'environment' is not just made up of the flask and media but also the *other cells in the flask* with which it must compete. This results in a continuously shifting competitive environment as mutations arise in lineages. Citrate utilization was just one of the many interesting variations acquired over the course of the experiment. Read his other papers for more details and a fuller understanding of the open-ended experiment's scope.--[[User:Argon|Argon]] 21:16, 26 June 2008 (EDT)

::::: I looked at the blog and found it to be remarkably uninformative. I saw nothing about Blount and Lenski's purpose, nothing that persuasively ruled out non-evolutionary reasons for the citrate-eating bacteria, and nothing to justify the withholding of the data to reveal greater resolution than provided by the figures in the paper.--[[User:Aschlafly|Aschlafly]] 23:00, 26 June 2008 (EDT)

::::::Blogging has limits, which is why I also provided references to Lenski's other papers, including some of those Blount mentioned would be worth reading.--[[User:Argon|Argon]] 20:37, 27 June 2008 (EDT)

::::With regard to 'competent scientists' consider that Behe, in his discussions on this topic has not argued about the 'mechanics' and data presented in Lenski's paper. In his review that can be found on the amazon.com website, he calls Lenksi's work 'fascinating' (and means it in a good way).--[[User:Argon|Argon]] 21:29, 26 June 2008 (EDT)

That was strange -- for several hours I was not able to post here, but now I can. Here is my response to Argon's comment of 21:16, 26 June 2008 (EDT)

Argon said, "The development of citrate metabolizers wasn't the main intent"

I didn't ask if Cit+ (citrate-eating E. coli bacteria) evolution was the "main intent" of the experiment -- I only asked if Cit+ evolution was one of the original "goals." There is a misunderstanding about what the word "goal" means -- a goal does not have to be a sure result. In searches for the Lost Dutchman Mine and the ivory-billed woodpecker, finding them are "goals." A "goal" can be one of many goals, a secondary goal, a longshot goal, or whatever. And "intent" is not part of the definition of "goal" -- "intent" generally means what one plans to do, but one cannot plan to achieve an uncertain result. BTW, the term "citrate metabolizers" is misleading because the bacteria already had the ability to metabolize citrate but did not have the ability to pass it through the cell walls.

Zachary Blount's following statement in comment #115 under the [http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php New step in evolution] post on Zimmer's blog indicates that Cit+ evolution was one of the original goals of the experiment:

''"When Dr. Lenski started, he figured the citrate would provide an opportunity that the populations might or might not figure out a way to exploit, thereby presenting a potential point of divergence between the populations (this is my understanding - I will need to check with him to make certain I understand this properly)."''

Blount then essentially contradicted his above statement by saying that "the intent of the experiment was never to evolve a Cit+ E. coli variant" (comment #115) and that Cit+ evolution was "not a goal" (comment #122).

Also, the following factors suggest that Cit+ evolution was an original goal of the experiment:

(1) Cit+ evolution had been observed once before. Blount reported in comment #115 under the [http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php New step in evolution] post on Zimmer's blog, ''"there has been only one report of a spontaneous Cit+ mutant of E. coli in the past century (Hall, B. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. Journal of Bacteriology, 151: 269 ï¿½ 273.)"). ''

(2) I and others assumed that a purpose of the glucose-cycling (giving the bacteria an insufficient glucose supply so as to create alternating glucose feeding and glucose starvation) was to favor Cit+ evolution. I asked Blount if this was in fact a purpose of the glucose-cycling and he did not answer. I asked what the purpose of the glucose-cycling was if favoring Cit+ evolution was not the purpose, and he did not answer.

Was there a research proposal for this whole experiment that started in 1988, and if so, what does that proposal say, if anything, about my questions? [[User:LarryFarma|LarryFarma]] 10:24, 27 June 2008 (EDT)
:I may be missing something here, but why is the supposed "goal" of the experiment important? It's the important thing the result?--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 11:29, 27 June 2008 (EDT)

::British_cons''':''' Suppose a committee is considering this research for an award or a prize and asks the researchers the same questions I asked''':''' (1) Was Cit+ evolution a goal of the experiment? and (2) was favoring Cit+ evolution a purpose of the glucose-cycling? Are the researchers going to answer, “No, it was not a goal — it was just an unforeseen accident. We don’t deserve any credit for it.”

::Also, IMO knowing the goals of the experiment and the purposes of the experimental methodologies are important parts of understanding the experiment. Also, the candor of the researchers is in question here -- as shown above, I did not get straight consistent answers to simple, basic questions.[[User:LarryFarma|LarryFarma]] 12:27, 27 June 2008 (EDT)
:::There are two possibilities. It was the goal. It was not the goal. The result is that they have produced Cit+. If it was the goal then they have demonstrated what they set out to demonstrate. Well done. If it was not the goal then serendipity has favored them. It is no means unusual in science for unexpected results to further the cause of science. Nobody would reject or question them because they were unexpected. Indeed they are even more welcome if they're unexpected because something new has been learned. So again - well done. I don't see the problem.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 12:45, 27 June 2008 (EDT)

::::British_cons''':''' As I said, suppose that a committee is considering this research for an award -- wouldn't this research be much less deserving of an award if Cit+ evolution were just an unforeseen accident? Also, the candor of the researchers is in question here -- as I showed above, I did not get straight consistent answers to simple, basic questions. As I noted above, Cit+ evolution had been observed before, so it seems that repeating it was a likely goal of the experiment. Also, I asked about the purpose(s) of the glucose-cycling and I got no answer to that question. Knowing the goals of the research and the purposes of the experimental methodologies are important parts of understanding the research.[[User:LarryFarma|LarryFarma]] 14:07, 27 June 2008 (EDT)

::::Thudden''':''' ''As I said, suppose that a committee is considering this research for an award -- wouldn't this research be much less deserving of an award if Cit+ evolution were just an unforeseen accident?'' This betrays a unequivocal lack of understanding of scientific process and acclaim. Hundreds of world-altering scientific discoveries have been serendipitous: Pauling and Penicillin, Galvani and neuroelectricity, Nagano's discovery of interferon, Becquerel and Röntgen's discovery of radioactivity and X-rays respectively. If you stumble on something marvellous by accident, you receive identical academic acclaim, perhaps only with added envy.
:::::'''Fleming''' and Penicillin (just for the sake of accuracy). [[User:HSpalding|HSpalding]] 17:56, 8 January 2009 (EST)
::''"If you stumble on something marvellous by accident, you receive identical academic acclaim,"'' I disagree -- IMO things discovered by intelligent searching are more highly regarded. [[User:LarryFarma|LarryFarma]] 06:17, 29 June 2008 (EDT)
::''Thudden: Your disagreement would be more convincing if it was backed up by evidence, or engaged with the contrary evidence provided.
:::"Identical academic acclaim": Fleming won the Nobel Prize, Becquerel won the Nobel Prize, Rontgen won the first ever Nobel Prize for Physics, Nobel Prizes were awarded for the serendipitous discoveries of restriction endonucleases and RNA interference... Not to mention "Eureka!" The list of people who've won the highest acclaim for accidental discoveries is very, very long. [[User:HSpalding|HSpalding]] 17:56, 8 January 2009 (EST)

::::''"Your disagreement would be more convincing if it was backed up by evidence, or engaged with the contrary evidence provided."''
::::It is just my own personal opinion -- I have no opinion poll results on the question. Do you have any opinion poll results to back up your statement?
::::I was especially impressed by the way Neptune was discovered in 1846 -- a mathematician predicted its location on the basis of perturbations of the motion of Uranus, and Neptune was found in one night very close to the predicted spot. Also, Pluto was found on the basis of perturbations in Neptune's motion but the search took much longer.
::::You should sign your comments at the end, not the beginning -- when you sign them at the beginning, it looks like you are addressing someone (that is what I originally thought about your preceding comment). [[User:LarryFarma|LarryFarma]] 15:06, 29 June 2008 (EDT)

(unindent) Rather than dispute this with you YET AGAIN, can we wait until you respond to criticisms of your position on other websites first? You keep repeating this "no straight answers" argument, and people keep pointing out your error, and you've yet to see this argument through to the end anywhere. Conservapedia is already struggling to maintain its current signal-to-noise ratio, please stop forum-shopping here. [[User:Aziraphale|Aziraphale]] 14:17, 27 June 2008 (EDT) ''<-knows where all the good sales are...''

:: Aziraphale said, ''"Rather than dispute this with you YET AGAIN, can we wait until you respond to criticisms of your position on other websites first? "'' I have already spent a helluva lot of time responding to those criticisms on Carl Zimmer's blog and my own blog! (see links in my first comment on this talk page) But I have been kicked off of Carl Zimmer's blog, and my own blog gets only about 50 visits per day. In contrast, this talk page is getting thousands of visits per day, so it is obviously a much better forum for publicizing my views.

::''"You keep repeating this 'no straight answers' argument, and people keep pointing out your error."'' And I keep pointing out the errors in arguments that attempt to point out my alleged error.[[User:LarryFarma|LarryFarma]] 16:18, 27 June 2008 (EDT)

:::Ok, fair enough. Enjoy your time here. :) [[User:Aziraphale|Aziraphale]] 18:05, 27 June 2008 (EDT) ''<-o/~know when to hold 'em... o/~''

::::''"Enjoy your time here."'' I intend to. I never before had such a good opportunity to publicize my views. [[User:LarryFarma|LarryFarma]] 02:21, 28 June 2008 (EDT)
:::::It has been brought to my attention that there may be a problem with your question. You wish to know about the "goal" of the experiment. Is that a reasonable way to ask a question of a scientific experiment? Shouldn't the question be "What hypothesis was being tested?"?--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 10:03, 28 June 2008 (EDT)
::::::How could a random event, Cit+ evolution, be a "hypothesis"? Even Zachary Blount used the term "goal." What is wrong with saying that an experiment has a "goal" (or "goals")? [[User:LarryFarma|LarryFarma]] 15:53, 28 June 2008 (EDT)
:::::::Because according to the [[Scientific method]] the objective of an experiment is to test an hypothesis. Remember that things are not proved in science - only disproved. The objective of an experiment is never to "prove" anything - only to test an hypothesis. If the hypothesis is confirmed then it is strengthened, if it not confirmed it is weakened or discarded. Consequently the fundamental question to ask of an experiment is, "What hypothesis was being tested?" --[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 16:07, 28 June 2008 (EDT)
::::::::How would you describe Cit+ evolution as a hypothesis, even assuming that Cit+ evolution had not been observed before (Cit+ evolution was observed prior to Lenski's experiment) ?[[User:LarryFarma|LarryFarma]] 21:54, 28 June 2008 (EDT)
:::::::::I'm afraid that's for you to figure out. As I've said, the only sensible way for you to ask the question you want answered is to form it as a question about the hypothesis. How you manage that is down to you. :-)--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 02:27, 29 June 2008 (EDT)
::::::::''"I'm afraid that's for you to figure out."'' It's your idea that it must be stated as a hypothesis, so showing how it can be stated as a hypothesis is your responsibility. Anyway, Lenski could not hypothesize about whether Cit+ evolution could occur, because it had been observed prior to the start of his experiment. All he could do was consider Cit+ evolution to be a "goal" of his experiment. [[User:LarryFarma|LarryFarma]] 05:43, 29 June 2008 (EDT)
:::::::::I'm sorry, I thought you were asking for help. Anyway, the article on [[Scientific method]] ''on this wiki'' states that the reason for an experiment is to test an hypothesis - so it's not my opinion but what this Wiki states. I suppose you could edit the article so this it reflects your view of how science works. --[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 06:24, 29 June 2008 (EDT)
:::::::::Reading Lenski's recent paper for comprehension reveals that the hypothesis being tested is that development of the Cit+ strain is a historically contingent process (that is, arising by multiple steps separated over time). The null hypothesis (not supported by the results of the experiments) is that the Cit+ strain arises by a single, exceptionally rare event.--[[User:Brossa|Brossa]] 10:52, 29 June 2008 (EDT)
::::: ''"Reading Lenski's recent paper for comprehension reveals that the hypothesis being tested is that development of the Cit+ strain is a historically contingent process (that is, arising by multiple steps separated over time)."''
:::::I was aware that one of the original goals of the experiment was to test for historical contingency -- that was the reason for freezing the populations at each 500th generation. My questions were about other things: (1) was Cit+ evolution an original goal of the experiment (remember that this whole experiment started in 1988, long before the study in the present paper), (2) was favoring Cit+ evolution a purpose or one of the purposes of the glucose-cycling (giving the bacteria insufficient glucose supplies so as to cause alternating glucose feeding and starvation), and (3) what were other purposes -- if any -- of the glucose-cycling. Zachary Blount did not give a straight answer to the first question and gave no answers at all to the latter two questions. [[User:LarryFarma|LarryFarma]] 13:12, 29 June 2008 (EDT)
:::::::You continue to dwell on the semantics of 'goal' as though it has some particular relevance to the validity of the research presented in Lenski's latest paper. The experiment was started in '88 to track the evolution of a population of E. coli. The purpose of the 'glucose cycling' is to provide the bacteria with an environment that will favor those mutants that are better able to exploit a limited critical resource. The glucose cycling does not inherently favor the development of a Cit+ strain any more than it favors other potential solutions to the problem - like secreting a toxin to kill your competitors, or faster reproduction to outbreed them, or photosynthesis, or cannibalism, or what have you. There is no other purpose to providing the bacteria with a limited supply of glucose. Citrate is present in the growth medium as a chelating agent and buffer - it was not added solely to serve as a potential carbon source, although it is one.<br />
:::::::You seem to believe that the reason that Lenski is getting acclaim for this research is just that has isolated a strain of E. coli that can metabolize citrate under unusual conditions - and your response seems to be that he does not deserve praise for this, since he didn't set out with this particular outcome in mind - it's just an accident, if in fact the Cit+ bacteria exist at all. Or maybe you object because you think Lenski somehow 'stacked the deck' in favor of his bacteria becoming Cit+, so the results aren't 'fair' somehow. Or perhaps you think that after 20 years of failing to develop a Cit+ strain of E. coli through selection, Lenski just gave up, genetically engineered such a strain, and then faked his data. If you could clearly state what your suspicions are, rather than simply repeating that Blount won't answer your questions, it would be simpler to address your concerns.<br/>
:::::::This is utterly beside the point, however, because the importance of this recent paper does not depend on the detail of the strain being Cit+ - it could have been the development of a toxin, or some other event that led the new strain to be markedly, phenotypically different from its ancestors in some way. The importance lies in the work that was done to sketch out the outline of how the new trait developed, and in the re-development of the same trait during a re-running of the experiment from ancestral stock.<br />
:::::::Is it interesting that the trait seen in Lenski's E. coli is the metabolism of citrate under aerobic conditions? Yes. Is it remarkable? Yes, since you can count the number of E. coli strains that can do this on one hand. It's so wild and crazy that it might lead one to question whether the bacteria involved should even be called E. coli anymore - it's that striking a difference from 'normal' E. coli behavior. Was the development of the Cit+ strain an accident? Entirely. Would another Cit+ strain arise if the experiment was completely restarted from 1988? Almost certainly not - Lenski's data suggests that this is a staggeringly unlikely event, dependent on a series of merely overwhelmingly unlikely events. Did Lenski wish to develop a Cit+ strain from the beginning? No man can know the inner mind of another, but I would bet the farm that he didn't see this coming. If I were designing an E. coli breeding scheme with the stated purpose of selecting for a Cit+ mutant, I can think of much, much, much better ways to do it than this experimental protocol. The Cit+ trait is a novelty - an interesting one, one that is remarkable because of its rarity, one that resonates - but the value of the research does not depend upon it. --[[User:Brossa|Brossa]] 17:33, 29 June 2008 (EDT)

::::''"You continue to dwell on the semantics of 'goal' as though it has some particular relevance to the validity of the research presented in Lenski's latest paper. The experiment was started in '88 to track the evolution of a population of E. coli."''
::::I am trying to get answers to some simple, basic questions about the experiment. Is there something wrong with that?
::::Also, the "semantics" -- as you call them -- of "goal" are very important. A lot of people have the mistaken idea that a goal is necessarily an expected result or is necessarily an intended result. Just going around telling people that the Cit+ evolution was not a goal can be very misleading.
:::::If you want to expand the term 'goal' to the point that you include unexpected, unintended results then you rob it of all meaning. By your reasoning, my getting into a fatal car accident is the 'goal' of my driving to the grocery store. If you think that 'goal' is a term of art that describes the entire universe of possible outcomes of an action, you are mistaken. If you want Blount et al to admit that the emergence of a Cit+ mutant was '''possible''', given the experimental protocol, then I think that you already have your answer: yes. Was it expected? No. Was the experiment designed from the beginning to favor Cit+ mutation over some other pathway? No.--[[User:Brossa|Brossa]] 23:22, 29 June 2008 (EDT)
::::''"The purpose of the 'glucose cycling' is to provide the bacteria with an environment that will favor those mutants that are better able to exploit a limited critical resource."''
::::That statement is too vague.
:::::What part is too vague? The alternatives to glucose cycling are: provide so much glucose that cell growth remains exponential up through the time of the next sampling; provide so little glucose that there is no cell division at all; or use a chemostat setup in which the glucose concentration can be maintained at a constant, arbitrary level indefinitely at the cost of vastly increased material and labor costs to the experimenter.--[[User:Brossa|Brossa]] 12:05, 30 June 2008 (EDT)
::::''"The glucose cycling does not inherently favor the development of a Cit+ strain any more than it favors other potential solutions to the problem - like secreting a toxin to kill your competitors, or faster reproduction to outbreed them, or photosynthesis, or cannibalism, or what have you."''
::::The glucose cycling gives an especially big advantage to Cit+ bacteria because they have something to eat after the glucose supply is exhausted whereas their Cit- neighbors do not.
:::::It gives them '''an''' advantage. It's impossible to predict ahead of time how '''big''' an advantage it is, because instead of being unable to metabolize citrate they may merely be terrible at it. If the Cit- cells are better at glucose metabolism than the Cit+ ones are, they may completely swamp out the Cit+ in the early, glucose-dependent phase. Even if the Cit+ cells continue to grow after the glucose is exhausted, they may never completely outcompete the Cit- cells by the time the next population sample is taken. In fact, this appears to be what has happened, as the experiment has shown that two populations of cells originating from the Ara-3 line have reached a temporary equilibrium: a grows-very-fast-on-glucose Cit- population (10%) and a grows-more-slowly-on-glucose-but-keeps-growing-on-citrate Cit+ population (90%). --[[User:Brossa|Brossa]] 12:05, 30 June 2008 (EDT)
::::''"Citrate is present in the growth medium as a chelating agent and buffer -- it was not added solely to serve as a potential carbon source, although it is one."''
::::Yes, I know it is there as a chelating agent -- but I also want to know if Cit+ evolution was a goal (again, a goal does not have to be an expected result and can even be an unlikely result) and if favoring Cit+ evolution was a purpose or one of the purposes of the glucose-cycling (I also would like to know if there were other purposes of the glucose-cycling and exactly how any other purposes work). The fact that Cit+ evolution was observed once previously adds to my hunch that it was a goal. Also, the bacteria already had the ability to metabolize citrate and just needed to evolve a way to pass citrate through the cell wall.
::::''"You seem to believe that the reason that Lenski is getting acclaim for this research is just that has isolated a strain of E. coli that can metabolize citrate under unusual conditions"''
::::Well, he is getting a lot of acclaim for it, isn't he? The paper has been widely ballyhooed all over the Internet. The Internet has several articles and hundreds of comments about it.
:::::He does not deserve acclaim because he is a farmer who has a goose that lays golden eggs, but because he can demonstrate in rough form how the goose came to lay golden eggs when it's grandparents could not. In fact, he has gone back and re-bred the grandparents and gotten golden-egg laying geese again and again, even though none of his other geese, or even the great-grandparents of the golden goose, can breed golden-egg-layers. The real achievement is not having the goose, it's reproducing it against all the odds, and showing that there's something special about the grandparents compared to the greatgrandparents, even though the grandparents appear to be normal. The fact that many folks, including those in the media, can't get past the 'ohmygoshgoldeneggs!!!' phase is not Lenski's fault.--[[User:Brossa|Brossa]] 23:29, 29 June 2008 (EDT)
::::''"If you could clearly state what your suspicions are"''
::::Right now I am just trying to understand the experiment. [[User:LarryFarma|LarryFarma]] 20:46, 29 June 2008 (EDT)

:::::::''"I'm sorry, I thought you were asking for help."'' You call that "help"? All you did was clutter up this talk page with your irrelevant "hypothesis" idea. With friends like you, who needs enemies? [[User:LarryFarma|LarryFarma]] 10:34, 29 June 2008 (EDT)
::::::::When did I call it help? I said that I thought you were asking for it. In any event Brossa seems to have clarified the situation.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 11:38, 29 June 2008 (EDT)
:::::::''"When did I call it help? I said that I thought you were asking for it."''
:::::::And you thought -- or seemed to think -- that you were giving it. I am beginning to suspect that you are just a troll.
:::::::''"In any event Brossa seems to have clarified the situation."''
:::::::No, he has not clarified the situation -- see my above response to him. [[User:LarryFarma|LarryFarma]] 13:29, 29 June 2008 (EDT)
::::::::I will not stoop to name calling. Goodbye and good luck with your enquiries.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 14:07, 29 June 2008 (EDT)

:::::::Well, what did you expect? First you introduced an irrelevant topic, "hypothesis." Then you contradicted yourself by first saying ''"I'm sorry, I thought you were asking for help"'' and then saying ''"When did I call it help?"'' [[User:LarryFarma|LarryFarma]] 15:42, 29 June 2008 (EDT)

::::::::Mods, can we get a ruling on this? LarryFarma is harassing other users, talking far more than he is making valid contributions, and generally being a troll. If he was defending Lenski instead of attacking the paper, he would have been blocked a long time ago. Can someone please comment on this? I believe we can all make our points without name-calling. -- [[User:Aaronp|Aaronp]]
:::::::In fact, the only contributions that Larry has made have been to this talk page. Can we get a 90/10 block please? [[User:Aaronp|Aaronp]]
::::::::Aaronp: Is somebody hassling you? People who don't want to read my comments don't have to read them.
::::::::Also, the 90/10 rule doesn't apply here because I cannot make any contributions to the project page, which is reserved for the exchange of letters between Schlafly and Lenski.
::::::::BTW, I am not attacking the paper -- I am only attacking the lead author's failure to give straight answers to simple, basic questions about it. [[User:LarryFarma|LarryFarma]] 21:17, 29 June 2008 (EDT)
::::::::: Okay, here's my two-bob's worth.
::::::::: LarryFarma, this page was started to question the ''validity'' of Lenski's work and claims. Although I can see how questions about his ''goals'' would be relevant to awarding him a prize, I can't see that they are relevant to the validity of his work. I think that this might be the cause of some of the angst, as some editors are assuming that you are trying to question the work's ''validity'' with an argument that has no bearing on that point.
::::::::: Secondly, Aaronp has a point about the so-called 90/10 rule. It's point is to ensure that editors contribute to the site and don't just argue. That you are unable to contribute to this project page doesn't mean that you can't contribute elsewhere on the site. The rule is not page-specific in that sense. So as Aaronp has called for that rule to be invoked, and as you have only contributed on this talk page, I think that his request is fair. However, I will allow you to make another post or two to wind up your arguments before doing so. Beyond that, I will feel obliged to enforce it.
::::::::: [[User:Philip J. Rayment|Philip J. Rayment]] 21:35, 29 June 2008 (EDT) (Administrator)

::::::''"LarryFarma, this page was started to question the validity of Lenski's work and claims."''

::::::The opening sentence of my first comment questions the validity of Lenski's work:
::::::''"IMO the paper has no credibility because the lead author of the paper, Zachary Blount, has refused to give straight consistent answers to the following simple, basic questions about the experiment:"''

::::::You say,
::::::''"Although I can see how questions about his goals would be relevant to awarding him a prize"''

::::::That is not the issue here -- the issue here is that the lead author of the paper, Zachary Blount, has not given straight answers to my simple, basic questions about the experiment. If I were a peer-reviewer of the paper or in the audience at a presentation of the paper at a scientific conference, would he be dodging my questions? And my questions are not just about goals -- for example, I also would like to know the purposes of the glucose-cycling (alternating glucose feeding and glucose starvation). These things are all part of understanding the experiment. Also, what does the original research proposal -- if there is one -- say about the goals and methodologies of the experiment? Is Lenski willing to release that proposal?

:::::: ''"That you are unable to contribute to this project page doesn't mean that you can't contribute elsewhere on the site."''

::::::I am new to the site and therefore have not had an opportunity to contribute elsewhere on the site. Would you like me to write an article about co-evolution? All I would have to do would just copy-and-paste from my blog's several articles about co-evolution. I have found the issues of co-evolution to be a very effective challenge to evolution theory.

::::::''" I will allow you to make another post or two to wind up your arguments before doing so. Beyond that, I will feel obliged to enforce it."''

::::::Are you willing, then, to censor all future comments that attack my positions? If comments attacking my positions are posted in the future here, then why shouldn't I be allowed to defend myself? In fact, while I was writing this comment, Brossa posted three comments attacking my positions.

::::::Also, how do you intend to "enforce" the 90/10 rule -- by IP address blocking? That is often ineffective and also often unintentionally blocks other Internet users who share the same ISP proxy.

::::::BTW, I am very annoyed that Aaronp hypocritically called me a "troll" while criticizing me for using that name to insult another commenter. [[User:LarryFarma|LarryFarma]] 01:14, 30 June 2008 (EDT)

::::::: Perhaps I wasn't sufficiently clear in some of my comments. The first part of my message was not as an administrator, but just to try and clarify the issues. I didn't mean to suggest that you hadn't addressed the validity of his claims. It was meant simply to point out that some may be misunderstanding the point of your comments. And I'm not saying that the questions you are raising are not legitimate questions to raise.
::::::: It's not true to say that you "have not had an opportunity to contribute elsewhere on the site". You've had opportunity every time you've edited.
::::::: We do allow copying of your own work. There is a template available to note that it is your own work. And of course it can be edited by others, as is the case with all articles.
::::::: If you stop making arguments, your critics will stop disagreeing with you. Yes, it will likely mean that they will get the last word, and that might be unfortunate, but that's not going to be reason to ignore the so-called 90/10 rule.
::::::: I'm not suggesting that you are the only one in the wrong here. Uncivil language happens a fair bit. But that's peripheral to the issue I'm discussing here.
::::::: I've unblocked you, because it wasn't fair for you to be blocked for 90/10 when I'd given you a warning and permission to make one or two more posts, but you used one on responding to me, so that gives you one left to respond to your critics. And fair warning: I've referred to the 90/10 rule as the "so-called" 90/10 rule, because it's not a rule against precisely 90% talk vs. 10% contributions, but a rule against "unproductive activity", with 90/10 being an ''example'' of that. So simply making the odd article edit or posting the odd copied article will not necessarily avoid that rule. It's something that we administrators make a judgement on, and others will make it more readily that I will.
::::::: [[User:Philip J. Rayment|Philip J. Rayment]] 09:51, 30 June 2008 (EDT)

:::::''"I've unblocked you, because it wasn't fair for you to be blocked for 90/10 when I'd given you a warning and permission to make one or two more posts, but you used one on responding to me, so that gives you one left to respond to your critics."''

:::::That reminds me of the following lawyer joke:
:::::Customer: What are your rates?
:::::Lawyer: $100 for three questions.
:::::Customer: Isn't that kind of steep?
:::::Lawyer: Yes. What is your third question?

:::::''"If you stop making arguments, your critics will stop disagreeing with you. Yes, it will likely mean that they will get the last word"''

:::::Almost all of my arguments here have been answers to my critics. What is at stake here is my right to answer critics. And the reason why I have been making more comments here than other commenters is that other commenters have been using tag-team tactics against me. Giving me just one more opportunity to answer attacks is unacceptable because those attacks are continuing and will continue. And how do I know that other commenters here are not violating the 90/10 rule? Am I being singled out because of Aaronp's rude complaint?

:::::''"It's not true to say that you "have not had an opportunity to contribute elsewhere on the site". You've had opportunity every time you've edited."''

:::::I would have liked to make some contributions to Conservapedia articles, but I now have mixed feelings about Conservapedia because of the 90/10 rule, an arbitrary and unfair rule which is being used to prevent me from defending myself here. I gave up on Wikipedia a long time ago because of its arbitrary and unfair rules and practices, and I am now seeing that Conservapedia is no better.

:::::Anyway, we can debate my questions here until doomsday, but nothing can excuse Zachary Blount's failure to give straight answers to those questions. [[User:LarryFarma|LarryFarma]] 15:26, 30 June 2008 (EDT)

::::::While I completely agree with you that the 90/10 rule is somewhat intimidating (I even refrained from removing wikilinks to salted articles from talk pages because I feared that a casual inspection would make those edits look like "talk, talk, talk"!), it should be said that so far, 20 of your 20 edits were on this page. In other words, your contributions outside of this discussion amount to ZERO. This is an encyclopedia project (or at least it says so) and not a discussion forum. Making encyclopedia edits should be your first priority, not an afterthought. If I remember correctly (I have only paid little attention to this trainwreck), people with far better ratios also received 90/10 blocks for making just a few posts here. You on the other hand were given ''edit rights'' just so you could debate here. Look at me, I got more than a 100 edits (according to My Preferences), most of them non-talk, and I still can't edit at night. You have been treated ''extremely'' well, all things considered. It's time that you actually contribute to the site's primary purpose: Building an encyclopedia. --[[User:KevinM|KevinM]] 15:42, 30 June 2008 (EDT)

== removal of content from this page removes context of Lenski's second reply ==
I'm sure it's an oversight but Lenski, in his second letter, made several direct references to the discussion that has been removed from this page. Some of his comments thus appear inappropriately to lack context. I'm sure you did not intend to remove significant parts of this debate, especially when the result seems so one-sided.[[User:AndyMann|AndyMann]] 20:09, 26 June 2008 (EDT)
: Yes, it was an oversight. It was archived, but the archive was not linked to on this page. It has since been linked. [[User:Philip J. Rayment|Philip J. Rayment]] 22:53, 26 June 2008 (EDT)

==Archive Link?==

Can a link be provided to the archive for this page? Thanks. --[[User:DinsdaleP|DinsdaleP]] 20:48, 26 June 2008 (EDT)

Oops. Did my edits delete the earlier sections? If so, I'm sorry. Could someone restore the original? --[[User:Argon|Argon]]
:No, your edits were not a problem. It was the edits of those individuals who decided to use this talk page as an attack forum. [[User:Karajou|Karajou]] 21:02, 26 June 2008 (EDT)

I read this page a while ago - Lensky and ASchaffly's two-and-fro, and have since returned. Why is it that ASchaffly's second letter this time seems to have been edited to be a lot more polite than when I first read it? It makes Lenski's second reply seem unnecessarily rude. When I first read this I felt his tone was justified, now it seems out of place.
:I don't think the letter has been changed at all. [[User:HenryS|HenryS]] 22:54, 21 July 2008 (EDT)

== Whence Lenski? ==

Lenski's article was published in the PNAS, which is from the National Academy of Sciences. Just [http://www.google.com/search?q=%22national+academy+of+sciences%22+god Google their name and "god"] and see why they care so much about "proving" evolution: 93% are atheists! Maybe PNAS isn't a professional organization at all, but a fraternity designed to influence American public policy away from Christian principles. [http://www.stephenjaygould.org/ctrl/news/file002.html] [http://www.answersingenesis.org/docs/3506.asp] {{unsigned|Drochld}}

:I'm a little confused about the terminology of the survey. According to the 1998 figures, 7% had "personal belief", 72% had "personal disbelief", and 21% had "doubt (presumably equivalent to atheism) or agnosticism". I know what atheism and agnosticism are, but what does personal disbelief mean in this case? It sounds like agnosticism, but agnosticism is in a separate category. So what is it? Anyone know?--[[User:Frey|Frey]] 13:31, 28 June 2008 (EDT)
::If they're not believers, and they're not agnostics/doubters, then they're atheists. Atheism = disbelief. [[User:Bugler|Bugler]] 14:10, 28 June 2008 (EDT)
:::I find it doubtful that are more atheists than agnostics. Atheists are 100% certain that God doesn't exist. A good scientist is not 100% certain of anything. I think a survey with more clearly defined choices is called for.--[[User:Frey|Frey]] 23:34, 28 June 2008 (EDT)
::::Actually it is not true to say, ''Atheists are 100% certain that God doesn't exist'' as Conservapedia's article says; [[Weak Atheism]]. Many more scientifically-minded atheists would follow this point of view for the very reasons you state - ''A good scientist is not 100% certain of anything.''--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 12:37, 29 June 2008 (EDT)
:::::I think the distinction to be made here is between personal belief and what can be proven. It is possible to put forward a definition of God that cannot be tested and is therefore neither provable nor falsifiable, however that wouldn't mean an individual couldn't have a personal belief (or disbelief) in God. If I can be forgiven a pop culture reference, I can't prove I don't live in [[The Matrix]] but I have a personal belief that I don't.--<font face = "Verdana">[[User:Boreas|Boreas]]<sup> [[User_Talk:Boreas|'''talk''']]</sup></font> 13:34, 29 June 2008 (EDT)

I'm guessing that 100% of creationist are theists...so? Does this invalidate THEM in any way? No, it does not. I don't see how this line of discussion is pertinent or constructive in any way. --[[User:RobinGoodfellow|RobinGoodfellow]] 14:58, 28 June 2008 (EDT)

I assume that Bugler's ignoring of Gnostics such as myself was not an attempt to polarise the community into more easily distinguishable sects. {{unsigned|Scholl}}

== Qualification ==

It is quite clear why Lenski is annoyed at requests for data and questions about the validity of his work. It is that none of those who are asking have any background in biology (please correct me if I'm wrong) and are as such not qualified to evaluate his work.

If you have questions or doubts about the research, then the *only* way you are going to get any useful result is by finding a biologist who perhaps shares your concerns and asking them to evaluate the research. Do you think, as a historian, that you wouldn't be annoyed by someone with no background in your field questioning your research, having apparently not even thoroughly read it? [[User:Boatie|Boatie]] 08:24, 1 July 2008 (EDT)

: No, Boatie, I'm confident your suggested reason has nothing to do with it. I requested making the data available for review by the public, including experts: "I'd like to review the data myself and ensure availability for others, including experts and my students."[Conservapedia:Lenski dialog] You can reread Lenski's negative response yourself.--[[User:Aschlafly|Aschlafly]] 08:31, 1 July 2008 (EDT)

:: But surely if there are any experts with specific requests then Lenski would provide any additional information that they require, as he has indicated. The fact that he is clearly offended by the initial requests and their implications means that he is now unlikely to cooperate with you, or anyone affiliated with this website, I suspect. [[User:Boatie|Boatie]] 09:28, 1 July 2008 (EDT)

::: Boatie, you're awfully naive if think the withholding of the underlying data from public scrutiny has anything to do with anyone being "offended".--[[User:Aschlafly|Aschlafly]] 09:40, 1 July 2008 (EDT)

:::: I hope you noticed that I didn't resort to petty name-calling. It's not helpful. I didn't suggest that data was being withheld to prevent public scrutiny. Merely I suggested that Lenski is probably not inclined to comply with the demands of a non-expert whose repeated requests may not even be sensible. Note that the report was submitted for peer review, and the paper involved will have since been read by many qualified biologists. [[User:Boatie|Boatie]] 09:46, 1 July 2008 (EDT)

::::: Boatie, you're clueless. People withhold data from public scrutiny for one obvious reason: to prevent the public (including experts) from scrutinizing their work. Feigning offense has nothing to do with it.--[[User:Aschlafly|Aschlafly]] 09:53, 1 July 2008 (EDT)

:::::: That's simply not true, and has been raised plenty of times, Lenski is not necessarily with holding data from any experts, he's only failing to supply to *you*. Find an *actual biologist* with concerns about his work and maybe things will be different. Further name-calling does nothing to help your argument. [[User:Boatie|Boatie]] 10:00, 1 July 2008 (EDT)

:::::: Scientists prefer specifc questions over general ones. In the initial email exchange you had a couple of specific questions that were answered specifically. Asking a general question will only result in "Do you have a question?" Saying "I want to see the data" is not a question. Saying "I want to see the data because I have a question about <i>this specific issue </i>I have" is more likely to get an answer. Prof Lenski has stated multiple times that he would provide samples etc to qualified people if they have questions on his research. Since no one here has demonstrated the required credentials and filed the proper paperwork to obtain a sample of prof lenski's work, this hand waving is all for naught. [[User:Toaster1|Toaster1]] 23:50, 1 July 2008 (EDT)

:::::: Aschlafly, I think you're rather clueless in this matter yourself. I've read the e-mail correspondence and I don't think Lenski is being evasive or deliberately withholding data from you or making claims he cannot back with evidence. When you think he's holding stuff back, you should be specific about what you feel is missing and why you think that is important for the claim and specifically ask for that data. You can run around screaming about something not being true, but that won't help much in the matter at hand. But then again I get the feeling you really don't want the data to be there at all, but rather make sure everyone follows you in believing the data doesn't exist to begin with. You put too much emphasis on the fact Lenski ''must'' be withholding something, without actually stating what it is and why it would disprove his claims. -- (unsigned by User:DeLight) 09:26, 3 July 2008 (EDT)

::::::: We've been extremely specific about which data are being withheld. See [[Richard Lenski]]. And I found Lenski to be quite clear that he's not going to release his underlying data for public review, even though it was publicly funded. Perhaps you think Lenski is perfect and there is no chance of flaws in his work that the public might discover when the underlying data are released, but such a position is obviously absurd.--[[User:Aschlafly|Aschlafly]] 09:35, 3 July 2008 (EDT)

:::::::: Sorry for the late reply, but [[User:DeanS|one of your sysops]] found it necessary to block me following my previous critique. To answer your statement, I don't think Lenski is perfect, I hardly know the man, but I do know what I have read in the correspondence between him and you. I don't agree he's not willing to share his work for public review, because he is willing, yet he has some well-founded conditions that should be met first. This is a lack of willingness to share with ''just anyone'', and rather sensible in science. Do you really think it's wise for all scientists to send samples of their work (especially in biology) to any Tom, Dick and Harry who asks for it, without knowing if they can actually handle the materials safely?
:::::::::Three things about your comment: First, it is a sensible question to ask a scientist for proof of his research when that scientist is getting government funding for his research; second, it is wise for them to send samples of their work; they do send them to other scientists, so why not the general public (unless they have something to hide); and third, you were blocked for a reason, the least of which is a German proxy address to hide your own, which you are not permitted to do so...so bye again! [[User:Karajou|Karajou]] 04:25, 7 July 2008 (EDT)

:::::::::: Just to answer a question you posed Karajou "second, it is wise for them to send samples of their work; they do send them to other scientists, so why not the general public (unless they have something to hide)" scientists are liable for the samples they provide. Thus the reason for MTAs and other inquiries to purpose of use for the samples. Most work and materials discovered or used by a scientist are not owned by the scientist, the institution normally has control over distribution beyond the scope of the grant or funding source. It would be foolish for a scientist to hand out potentially infectious material to anyone who asked for it, thus the reason why a qualified institution must used to receive the samples. I work part time for a company that does biorepository services, LN2 -80 and other long term cold storage. We have to maintain a license with the FDA and CDC for the bacteria and viruses that we hold. So to sum up, if the requestor does not have proper credentials for exploring the sample the scientist is legally obligated to withhold said samples till the requester meets qualification.
::::::::::To keep using the tax funded research claim is misleading. The military is tax funded and most of its operations are not open for public, most work by the CDC and HHS is funded by tax dollars and once again is not available for the general public.--[[User:Able806|Able806]] 10:33, 7 July 2008 (EDT)

==MTA==
Did anyone ask Lenski if a MTA is required by MSU to provide his data? Most MTAs are used for specific materials like cultures and such but a few are now requiring them for actual analysis results. Most universities now require specific permissions to be granted for scientific research due to the fear that such information could be used in inappropriate ways. Perhaps Lenski is bound by the university until a MTA is filed or feels that it is a waste of time to supply data that would only be understood by a few people here, which to my knowledge, care not to spend the time to analyze it. I could be wrong but I know I would not supply my test results to anyone who asked for it without understanding what they intended to do with it. I could be held liable for what they did with the information.

As for the length of time for the peer review, it is obvious that many here do not understand the process nor do they understand the difference of peer review of a publication verses replication of an experiment. Most experiments are not replicated for several years due to the need for funding. Peer review of publications is based on application of sound analysis techniques and clear summery of data analyzed. Not an actual analysis of the data. While I do not review papers, my wife does and it is not at all what has been implied here. I have published in a few journals, each with different standards and different times for the publication to go to press. Lenski's experiment is not complicated and only required minimal tests, therefore it would be expected to be a quick peer review of the publication due to the simplicity. If he performed tests using animals, or followed metabolisms then the peer review should have taken much longer. However, due to the few tests that he performed, all of which are accepted standardized protocol for research microbiologists, the need to dig deeper was not required. So to sum up, few experiments, easy study, and simple conclusion equals fast turn around for publication. If you read the paper, Lenski did not make any claims about anything other than the development of the bacteria's ability to metabolize citrate, pretty simple.--[[User:Able806|Able806]] 10:43, 2 July 2008 (EDT)

== Bad motive redux ==

I was blocked for two weeks for this post:

Let's face the truth, there is no real desire here for Andrew Schlafly or anyone on Conservapedia to get the raw data. The reason that this is even an issue is because placing this demand and getting no response somehow makes Lenski look bad and therefore automatically discredits him and his research and therefore the theory of evolution. The position of Mr. Schlafly is that the Bible is inerrant and the Genesis creation story is true. No amount of scientific data is going to change that. So why argue with him? MAnderson 10:05, 18 June 2008 (EDT)

Mr. Schlafly has since posted these comments:
“At some point, StatsMsn, an open mind requires admitting the possibility that the data have not been made available because there is concern about what an independent reviewer may conclude from it. Are you open-minded enough to admit that possibility? It's a waste of time arguing with a closed mind, and if you won't admit at least that possibility then this discussion is unproductive”.--Aschlafly 09:00, 19 June 2008 (EDT)
"If I'm reading the dates on the front of this particular paper correctly, I think peer review was a mere 15 days or so. Looks to me like a rubber-stamp process for this subject matter despite making claims that were reported as being newsworthy." --Aschlafly 16:47, 19 June 2008 (EDT)
"Don't pretend that Lenski welcomes independent review of the data." --Aschlafly 15:15, 19 June 2008 (EDT)

He has said these things even though the data and even the E. Coli samples are available to qualified researchers. Really my original post was dead on correct! He doesn’t want the data and merely wants to create the appearance of impropriety on the part of Lenski to discredit him. [[User:MAnderson|MAnderson]] 11:16, 2 July 2008 (EDT)

''Don't pretend that Lenski welcomes independent review of the data.'' I don't think MAnderson is claiming that Lenski ''welcomes'' independent review of "the data", nor does he need to ''welcome'' it in order to act properly. He needs to make it available where it will "allow others to replicate and build on work published in PNAS". It is evident that you do not wish to either replicate the experiment (which, if Lenski made it up, would fairly conclusively prove him a fraud) nor do you wish to review it in any meaningful way (which may build on the work by revealing its faults). That is the PNAS requirement. It appears that Dr. Georgia Purdom of "Answers in Genesis" has plenty of data to perform her intended review[http://www.answersingenesis.org/articles/2008/06/14/news-to-note-06142008] (no doubt very negative) of Lenski's research.

''"At some point, StatsMsn, an open mind requires admitting the possibility that the data have not been made available because there is concern about what an independent reviewer may conclude from it"'' Agreed. Can we test that hypothesis? It hasn't been tested so far (unless Dr. Purdom asked for data, in which case its been falsified) because we have not seen any prospective independent reviewer ask for data. You are not a reviewer (independent or otherwise) unless you review and you are not a ''prospective'' reviewer unless you ''seek to review''. Why not develop a plan (with AiG or the Discovery Institute) of just what you are going to do with the data, beyond that already published of course, and ask for the data that lets you do that? Until you have that plan it is abundantly clear that you are not a "reviewer" and have no entitlement to extra (unspecified by you) data. --[[User:Billd|Bill Dean]] 08:50, 3 July 2008 (EDT)

== Why does it matter? ==
Hello Conservapedians-
It seems like you are making a huge fuss about Leski's experiment, as if you do not want it to be true.I mean, of course it should be subject to peer review, but it JUST came to the general public. Give it time. However, why exactly does it matter, anyway?
There are several dozen OTHER recorded examples of the following:
--Speciation
--Beneficial Mutation
--Mutations adding information
So, while important, it is not like Lenski's data shows us anything new.
If you would like examples of such, just ask. I assume, however, that you are already aware of the observations, and
there is something important
{{unsigned|KevinF}}
: It's mainly Aschlafly that pursued this. Many others, including me, disagreed with that course. That was simply the first of several mistakes you made, and the others relate to you having almost no idea of what creationists believe. Do you support the concept of criticising an idea without knowing much about it? Because that is what you are doing. Creationists ''accept'' speciation. They also ''accept'' beneficial mutations. The one that they ''don't'' accept is mutations adding information, because it is ''not'' observed (apart from some questionable claims, such as this one of Lenski's). I won't ask for examples simply because I've been down this road before, of having supposed examples provided, only to have them not stack up when investigated. When Richard Dawkins was asked for examples, ''he was unable to supply any''. And why do you think Lenski's research was cited as answering creationist criticisms? If creationist criticism has been answered so much before, so that this is nothing new, then why make a deal about it as though it ''is'' something new? [[User:Philip J. Rayment|Philip J. Rayment]] 22:44, 2 July 2008 (EDT)

::While Lenski is certainly being quite snarky in his responses, Mr. Aschlafly does not seem to understand that in an experiment like this, the "raw data" isn't something that can be printed out and mailed. The raw data is ''the actual bacterial colonies with the mutation''. Thus, the raw data is completely useless to anyone who does not have a properly equipped biological lab, and indeed is illegal to provide to anyone without a properly equipped biological lab since E. coli bacteria are a potential disease vector. --[[User:JacieCady|JacieCady]] 19:42, 4 December 2008 (EST)
:::No the bacterial colonies are the samples. The raw data are the uninterpreted measurements and observations. This claim is little more than misdirection to justify not providing the data. If I tell you my car can stop on a dime & I know this because I have tested it, my car and a dime are NOT the raw data. The raw data would be the records of the attempts to stop on a dime including records of where the car stopped in relation to the dime. If I was asked for this data and said that I cannot send you my car because you don't have a lock up garage, I am merely dodging the question.[[User:LowKey|LowKey]] 08:06, 5 December 2008 (EST)

:::: Well put, LowKey. FYI, a chart summarizing how the data were undisclosed is [[Lenski|here]].--[[User:Aschlafly|Aschlafly]] 09:37, 5 December 2008 (EST)

:"When Richard Dawkins was asked for examples, ''he was unable to supply any''"—Oh, give me a break. Do you honestly expect someone to be able to come up with such information on the spot? --<sub>[[Special:Contributions/AutoFire|<font color= 'black' face= 'OCR A Extended'>trans</font>]]</sub>[[User:AutoFire|<font color= 'red' face= 'OCR A Extended'>Resident Transfan</font>]]<sup>[[User Talk:AutoFire|<font color= 'black' face= 'OCR A Extended'>form!</font>]]</sup> 23:09, 2 July 2008 (EDT)
::Good point, AutoFire.--[[User:JackH|JackH]] 17:15, 4 December 2008 (EST)
:::He shouldn't have to "come up" with anything "on the spot". He had claimed the existance of examples many times, he should have already known of ''at least one'', but he couldn't. This is like the editor of a car magazine claiming that the new BMW has many improvements over the previous model, but when asked for one can’t supply any. Nobody would claim it was unfair to expect him to come up with one on the spot.[[User:LowKey|LowKey]] 17:56, 4 December 2008 (EST)

::::http://www.youtube.com/watch?v=-uz1CiDDIq4 According to Dawkins he stopped to confront the interviewers. {{Unsigned|Vuiasl}}---22:21, 7 December 2008

*That link goes to a video that supplies no information about the topic. It merely says questions to Dawkins are hoaxes by Creationists, yet doesn't provide one example or proof. --[[User:TK|'''₮K''']]<sup>[[User_Talk:TK|/Talk!]]</sup> 00:56, 8 December 2008 (EST)

:The interview made Dawkins look a fool. Of course he has attempted to explain it away. The CMI website provides plenty of info about this, it even has a timeline showing how much time Dawkins had to come up with something, so even ignoring all of the above "on the spot" is still wildly inaccurate. It was more a case of Dawkins "realising" he might be talking to creationists because evolutionists would have accepted the elephant-hurling without challenge. Also, the interview was ''11 years'' ago and he ''still'' hasn't provided the examples as asked {<small>With the possible exception of Lenski's experiment, which he ''may'' have mentioned. But the [in]validity of that is the subject at hand here in the first place. [[User:LowKey|LowKey]] 18:35, 8 December 2008 (EST)</small>}, so the "on the spot" objection is invalid on that account alone.[[User:LowKey|LowKey]] 18:28, 8 December 2008 (EST)

::*I'm confused here. Everyone should know by now Dawkins is a fraud. As they should all know my opinion of him. That video didn't seem a bit different from the two times I have observed lectures by him, and he wondered off his prepared remarks. Results were the same as for Obama. Poor. (not Ed) --[[User:TK|'''₮K''']]<sup>[[User_Talk:TK|/Talk!]]</sup> 18:39, 8 December 2008 (EST)
:::Ah but everyone should also know that evolution is an invalid conclusion, but millions believe it to be a "fact". Scripture clearly tells us that people are blinded.[[User:LowKey|LowKey]] 18:48, 8 December 2008 (EST)
::::What Dawkins does or doesn't do is hardly of any importance. Evolution doesn't rely on him, or what he does and doesn't do in interviews. It falls flat on [[Counterexamples to Evolution|its own]]. [[User:RodWeathers|- Rod Weathers]] 18:54, 8 December 2008 (EST)

==Hsdebater comment==
I think Schlaffy misses the point of why Lenski didn't give him the experiments. He might think it's a conspiracy to silence him, but I (no offense schlaffy) beleive, like many others it seems on this site, it to be the simple explanation that you're not a scientist, and probably never taken a collegecourse on microbiology, evolutionary biology,and just plain biology.--[[User:Hsdebater|Hsdebater]] 10:55, 15 April 2010 (EDT)

: Please learn how to spell basic words like "believe" (it's not "beleive"), and then realize that I don't think Lenski made all his taxpayer-funded data available for ''any'' public scrutiny, which of course would have included many knowledgeable people.--[[User:Aschlafly|Andy Schlafly]] 11:00, 15 April 2010 (EDT)

::What do you mean i just read his paper in my science class just yesterday, and i have also read it outside of class.--[[User:Hsdebater|Hsdebater]] 13:02, 15 April 2010 (EDT)

::: So you apparently read his ''claims'' ... but where's the data underlying the claims? Despite my repeated requests, and despite the taxpayer funding of the project, I don't think he ever made all his data available for public scrutiny.--[[User:Aschlafly|Andy Schlafly]] 13:08, 15 April 2010 (EDT)

::::So I went ahead and formatted, hope thats alright. [http://www.pnas.org/content/105/23/7899/suppl/DCSupplemental Is this] the extra information you were looking for? --[[User:EmersonWhitecp|EmersonWhitecp]] 17:09, 15 April 2010 (EDT)

:::::I don't see real data in your link or answers to the data requests that have been outstanding for nearly two years at [[Richard Lenski]]. Do you?--[[User:Aschlafly|Andy Schlafly]] 17:23, 15 April 2010 (EDT)

::::::There is a very small link you must click on to get to the 2 page PDF (1.25 more like it) with the data. --[[User:EmersonWhitecp|EmersonWhitecp]] 17:27, 15 April 2010 (EDT)

::::::: (edit conflict) Which specific data requested nearly two years ago in [[Richard Lenski]] do you claim is contained in the mere 1.25-page of text in the pdf?--[[User:Aschlafly|Andy Schlafly]] 17:34, 15 April 2010 (EDT)

You can link directly to the PDF.....--<big>[[User:TK|'''ṬK''']]</big><sub>/Admin</sub><sup>[[User_Talk:TK|/Talk]]</sup> 17:30, 15 April 2010 (EDT)

:[http://www.pnas.org/content/suppl/2008/06/02/0803151105.DCSupplemental/0803151105SI.pdf PDF in question] To be honest I can't figure out what more information you would want than what was in the original paper, your point by point rundown doesn't make sense to me. I was just trying to be helpful, not trying to make a point or anything. --[[User:EmersonWhitecp|EmersonWhitecp]] 17:46, 15 April 2010 (EDT)

::If you want to believe whatever a professor says without verifying it, then you don't need to look at any underlying data. But do you give the Bible at least equal time and trust?

::It took me only a minute or so to look at the first request for data in [[Richard Lenski]] (concerning turbidity), and then search the pdf for "turbid" for me to observe that the actual data are not there.--[[User:Aschlafly|Andy Schlafly]] 19:08, 15 April 2010 (EDT)

:::Sorry I thought you were talking about a different data set. Fig. 1 Is the recreation that they measured. However if you read the paper he said that the turbidity was measured visually, that means that someone looked at it every day to make sure it looked alright, not that someone did a disk test for turbidity which would be impractical in such a small volume. This is standard procedure for liquid culture in a laboratory, something even college sophomores have to learn to do. --[[User:EmersonWhitecp|EmersonWhitecp]] 19:30, 15 April 2010 (EDT)

Conservapedia talk:Lenski dialog

2010-04-15T23:30:52Z

EmersonWhitecp: /* Hsdebater comment */

[http://www.conservapedia.com/Conservapedia_talk:Lenski_dialog/archive1 Archive 1]

The discussion below concerns the letters and response set forth at [[Conservapedia:Lenski dialog]]. See also [[Flaws in Lenski Study]].

== Reply to comments in archive ==

: The comments above by defenders of withholding data have been unsatisfactory, to say the least.

: [[Lenski]] says in his published paper: "Z.D.B. and R.E.L. [Lenski] analyzed data"[http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf]

: So where are all the data [[Lenski]] said he analyzed?--[[User:Aschlafly|Aschlafly]] 00:27, 25 June 2008 (EDT)

::As clearly stated in Professor [[Lenski]]'s second response:

::: ''"Finally, let me now turn to our data. As I said before, the relevant methods and data about the [[evolution]] of the citrate-using bacteria are in our paper. In three places in our paper, we did say 'data not shown', which is common in scientific papers owing to limitations in page length, especially for secondary or minor points. None of the places where we made such references concern the existence of the citrate-using bacteria; they concern only certain secondary properties of those bacteria. We will gladly post those additional data on my website." ''

::If the additional data is not on his website by now, I'm sure it will be soon. --[[User:DinsdaleP|DinsdaleP]] 07:45, 25 June 2008 (EDT)

::: If "the relevant ... data ... are in our paper," as set forth in the above quote of Lenski, then he would not have much data. So don't pretend the data is too voluminous to turn over. The paper is only 8 pages long!

::: In fact, the graphs in the paper suggest to a reader that there is underlying data having greater resolution than a graph can provide, and yet those data have not been disclosed for public scrutiny.--[[User:Aschlafly|Aschlafly]] 19:24, 26 June 2008 (EDT)

:::: The resolution of the graphs are more than sufficient to communicate the results. If the figures didn't provide sufficient clarity for their purpose the authors would have also provided tables. For example, in figure 1 it's clear the culture shifted its growth pattern. In figure 2, one can see that the Cit+ cultures reach a higher density in the media, as indicated by the higher ODs. To a microbiologist, those results indicate that the Cit+ cells can utilize more of the nutrients in the media (in this case, citrate). --[[User:Argon|Argon]] 21:08, 26 June 2008 (EDT)

:::: I'd like to chime in here and give some professional perspective. I am a molecular biologist -- if I asked him to, Prof. Lenski would send me a sample from his bacterial stocks (I have a -80 freezer and know how to work with E. coli). Let's assume for a minute that, like you, I strongly suspected the results of the paper (I do not, but that doesn't matter for this exercise). If this were the case, two of the routes I could take would be to re-analyze Prof. Lenski's data or replicate his experiments. In some cases, data and their analysis are complex, and re-analysis can yield different results than those the original author reached. This is the case for a large-scale association study, for example -- there are tons of data to analyze, and their analysis is not straightforward. In Prof. Lenski's case, however, the data are extremely simple, consisting primarily of 1) OD readings to measure fitness, and 2) colony counts.

:::: OD readings, or optical density readings, are obtained by pipetting a sample of cultured bacteria into a cuvette, sticking that cuvette into a machine, and writing down the number that pops up on a screen. Somewhere in a grad student's notebook (or in his/her computer) is a list of these numbers, and their average and range were presented in the PNAS paper at each generation in Figure 1 (similar data are presented in Figure 2 and Figure 5). So, in other words, the data you see in the paper *are all of the data* save for a second grade computation...which was probably performed by Excel. If you don't believe the data in the paper, then what do you expect to gain from seeing these "raw" data? There is so little to gain that I seriously doubt that PNAS would take such a request seriously.

:::: The meat of the paper, in Table 1, is a presentation of colony counts. These are obtained by another grad student picking up a bacterial culture plate, counting the number of colonies on it, and moving on to the next plate. Again, the raw data are what you see in the paper. What exactly are you expecting here, photographic images of all of the tens of thousands of plates they examined? That is just not done. Why would we go to that level of self-surveillance to please a small, vocal minority of people claiming fraud? The public's interest is not served by spending inordinate amounts of effort and money on this level of surveillance. If the science is correct, his experiment will be replicated.

:::: In sum, as others have tried to explain, there really isn't any more complex data for you to reasonably request. A slightly expanded list of numbers from what's in the paper won't get you anything if you already don't believe the data. And the scientific culture doesn't even come close to expecting photographic evidence of bacterial plates. Your best bet, if you really don't believe the results, is to get an outsider to try and replicate and/or confirm some portion of his results. The easy route would be to ask for a cit+ strain and its ancestor and see if they are indeed cit- and cit+. You could even sequence them to check if the cit+ strain is indeed an ancestor of the cit- strain, but while this would be a perfectly normal approach in a molecular biology lab with impressive resources, the entire concept of evolution is anathema to you, so I can't think of a reasonable criterion you would use to determine ancestry. If you wanted to go the hard route, you could obtain the ancestral strain and grow and measure them for years as Prof. Lenski's lab did.

:::: I hope this has been somewhat instructive for you in explaining why a request for "further data" will not bear fruit beyond the small amount of data that Prof. Lenski says he will make available. And why it is not reasonable to expect further data. I am more than happy to respond to questions or requests for clarification if you would like. -- [[User:Princetonian|Princetonian]] 23:50, 26 June 2008 (EDT)

::::: For starters, most of the opposition to releasing the data has been the false claim that the data are too voluminous to release. You are making the opposite claim, one which is more consistent with Lenski's paper: there is very little important data beyond what is in the 8-page paper. But that doesn't withstand scrutiny either.

::::: The "meat" of the paper is this, and at a minimum the data should be released for it (pp. 2-3 from paper):

:::::: Evolution of Cit Function in Population Ara-3. The LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time. [DATA ON THESE OBSERVATIONS?] Owing to the low concentration of glucose in DM25 medium [DATA?], the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. [DATA?] These contaminated cultures reach much higher turbidity owing to the high concentration of citrate in the medium, which allows the contaminants to reach high density. (When contamination occurs, the affected population is restarted from the latest frozen sample.) [DATA FOR WHEN THAT OCCURRED?] After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).[HIGHER RESOLUTION DATA UNDERLYING FIGURE?] A number [DATA?] of Cit clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all [DATA?] were Ara, T5-sensitive, and T6-resistant, as expected (2) [DATA ABOUT THESE AND OTHER CHARACTERISTICS?]. DNA sequencing also showed [DATA?] that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, and each of these mutations distinguishes this population from all [DATA?] of the others (30). Therefore, the Cit variant arose within the LTEE and is not a contaminant [THIS CONCLUSION NEEDS TO BE CHECKED BY INDEPENDENT REVIEW OF THE ACTUAL DATA, WHICH I DOUBT OCCURRED IN THE BRIEF PEER REVIEW OF THIS PAPER]

::::: Note, by the way, how the opponents of data disclosure seem to have no idea about what data Lenski actually has, which raises further questions about the merits of the conclusion.--[[User:Aschlafly|Aschlafly]] 09:15, 27 June 2008 (EDT)

:::::: I know some people here have claimed that the data are too voluminous to release...I didn't know what they were talking about, which is one reason I chimed in. Anyway, here are point by point responses to each of these cases. <i>Turbidity checking</i>: these data are either in a grad student's notebook somewhere, or were not recorded. I wouldn't at all be surprised if they weren't recorded due to the nature of the data (it's just a visual check of turbidity, and wouldn't be reported in a paper). <i>Low concentration of glucose in DM25</i>: this is a factual statement about DM25 media, not an observation. <i>Contaminants</i>: Same comment as the turbidity checking. Either there's a one-liner in a notebook somewhere ("Flask 25 contaminated, re-grew from stock") or nothing at all, since it's tangential to the experiment. <i>Figure 1</i>: As I already mentioned, the data in Figure 1 are actually comprehensive -- three data points went into each plotted point. They report the range (which give you a max and a min) and they also show you the average, which allows you to impute the third data point. <i>Number of Cit clones, and the following comments except the last</i>: these data are probably recorded in a lab notebook somewhere, since they're rather not tangential to the experiment. In addition, I'm sure they have a frozen stock of each cit+ bacterial clone that they checked, so this is something that could be easily independently verified. <i>Cit+ is not a contaminant</i>: no this would not be a part of the peer review...peer reviewers are not out to find fraud in general. Especially in the inaugural paper of somebody just nominated into the national academy. And the data underlying contamination checking are also extremely simple -- you plate the bacteria on an Ara+ plate and check sensitivity by eye, for example -- so there is no need to verify methodology as long as you trust the source.

:::::: You're basically asking for the lab notebooks of all of the grad students involved in the experiment over the 20 years. The data in these notebooks is going to be, in general, very simple (e.g., the statement "colony grew on Ara-, is a contaminant") since as I mentioned, there is no photographic evidence of this. Additionally, while biotech companies generally have document retention policies as required by law, no such policies exist at the academic level (although specific institutions may have them). A very few labs are run like well-oiled machines -- lab notebooks are kept up-to-date and thorough, and every observation is recorded. This is the ideal, but almost no labs actually achieve it, since most labs are working at 125% speed in an effort to get experiments finished and published.

:::::: If you're really interested in monitoring the quotidien details of these experiments, that falls outside of the scope of what PNAS and professional standards would require Lenski to release, I believe. You're not asking to re-analyze data so much as to oversee the entire experiment for fraud. This would require giving you all of Lenski's graduate students' lab notebooks for an indefinite period of time, which would be quite disruptive, and as I said probably wouldn't even yield the level of data you seem to want. In this case your best bet is to contact MSU and ask for a comprehensive review of Lenski's lab and his notes for this experiment. But without any evidence to point to said fraud, they will certainly deny your request for oversight. Your expectations here just aren't in line with professional standards in the field in the absence of any evidence of fraud. -- [[User:Princetonian|Princetonian]] 10:49, 27 June 2008 (EDT)

::::::: You've confirmed that the strident claims by Lenski defenders here that the data are too voluminous to release were nonsense. We'll see how many of them now admit they were wrong. Let's not hold our breaths!

::::::: But your opposite approach above, which essentially suggests there are no data that can be released, doesn't withstand scrutiny either. Figure 1 is plainly a low-resolution representation of underlying data that must exist. The greater resolution should be released. Similarly, there should be data underlying the essential assertion that a particular sample was not contaminated, while others had been. For example, the paper asserts that "[a] number of Cit clones were isolated." How many were isolated? If those data exist, then it should be released along with the other data. If those data do not exist, then that is even more telling.--[[User:Aschlafly|Aschlafly]] 11:34, 27 June 2008 (EDT)

:::::Regarding the questions highlighted by [[User:Aschlafly|Aschlafly]] to which [[User:Princetonian|Princetonian]] also responded: Many of the techniques questioned are standard procedures that a trained microbiologist would understand. Let's take this apart by question:
:::::'''''...the turbidity of each is checked visually at that time. [DATA ON THESE OBSERVATIONS?]'''''
:::::This is qualitative observation. Every microbiologist does this when they pull their cultures out of the incubator. The evaluation an experimenter asks: Can you see through the test tube or not? Is the culture denser or lighter than the last time you looked? The reported observations are the data.

:::::: Show us the data. Are you suggesting that no record was kept of these observations??? I hope that's not what you mean. But say so if that is your view.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::I described how the observation was performed. How the observations are recorded is up to the lab or technician culturing the cells.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Owing to the low concentration of glucose in DM25 medium [DATA?]'''''
:::::A reference to the description of the media is provided in the paper and is included on Lenksi's web pages. I linked to that page recently in another comment. It is general knowledge among microbiologists that nutrient limited cultures will reach a peak density that depends on the concentration of the limiting nutrient.

:::::: Again, show us the data. What was the concentration of glucose and, more importantly, did it ever change?--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Consider rereading the paper and pull out references provided. It's there.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. [DATA?]'''''
:::::Observation. Either they saw contaminated cultures or not.

:::::: No kidding. The point, obviously, is to disclose the data of what they saw. How many is "occasional"? Show us the records supporting that claim, so we can assess the frequency of contamination compared to alleged evolution. At a minimum, it appears that contamination was significantly more frequent than the alleged evolution.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Contamination is a problem every microbiology lab understands and encounters. What matters and what is particularly relevant to this experiment is the means of detecting and controlling for it. They outline the steps for detecting contaminating and restarting the experiment from uncontaminated stocks in their papers and web pages.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...(When contamination occurs, the affected population is restarted from the latest frozen sample.) [DATA FOR WHEN THAT OCCURRED?]'''''
:::::Not relevant for the results. It's just the researchers describing how they restarted the experiment whenever they suspected a contamination. It does not alter the experimental outcome.

:::::: It is relevant, at a minimum for reasons stated in my above response. Also, did the restarting ever result in repeats of the observed contamination?--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::They controlled for contamination. If their previous stock was contaminated they would likely return to ones before that last stock. Clearly, they would not want to work with contaminated stocks as it would damage the experiment.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).[HIGHER RESOLUTION DATA UNDERLYING FIGURE?]'''''
:::::Higher resolution is not really necessary. The graph provides a ''qualitative'' visualization that starkly reveals that the cultures underwent a change that allowed them to grow to a significantly higher density than previously. They report in the text the actual generation were the change occurred and that seems to line up with the transition in the figure (take out a ruler, if necessary). Their subsequent experiments bracketed the strains from points before, during and after the obvious population transition.

:::::: Your answer here is absurd. Higher resolution in science is always helpful. The precise rate of change among the population would reveal much about what was really occurring. The data must exist to generate the graph. Disclose it rather than obscuring it with a low-resolution graph.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::If one reads the paper, one finds that weakly Cit+ clones arise earlier than the visible transition. Reading the paper one would see that they analyze the emergence times: ''Cit+ clones could be readily isolated from the frozen sample of population Ara-3 taken at generation 33,000. To estimate the time of origin of the Cit+ trait, we screened 1,280 clones randomly chosen from generations 30,000, 30,500, 31,000, 31,500, 32,000, 32,500, and 33,000 for the capacity to produce a positive reaction on Christensen’s citrate agar, which provides a sensitive means to detect even weakly citrate-using cells.'' As for the visible transition: ''After ~33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days''. Note also that they performed 'replay' experiments (which took up the rest of the paper) to specifically analyze the frequency and times when Cit+ strains could be generated. The last half of the paper contains the work that provides information about the possible nature of the mutations and addresses your question.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all [DATA?] were Ara, T5-sensitive, and T6-resistant, as expected (2) [DATA ABOUT THESE AND OTHER CHARACTERISTICS'''''
:::::Derived from observation. The phenotypic markers are described elsewhere and the means of testing them are well known by professional microbiologists. The origin of the strain and its markers can be determined by following the references provided. The strain is also referenced on Lenski's pages here: https://myxo.css.msu.edu/ecoli/strainsource.html Other information about how they tested markers can also be found starting from here (provided by Lenski): https://myxo.css.msu.edu/ecoli/

:::::: Disclose the data so that independent reviewers can assess how reliable the claims are here. The methodology may be "well known" but only disclosure of the data will demonstrate whether the methodology was applied in a flawless manner.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Those are all based on visual observation. Reporting the observation *is* reporting data. Lenksi's group provides information how they performed the tests so that any professional microbiologist would be able to follow the work. The way for someone to test the methodology is to repeat the tests on the strains themselves. Recall that Lenski did say that the strains would be made available to labs. So, for anyone interested in seeing for themselves that "the methodology was applied in a flawless manner", I suggest they go find a friendly microbiologist to request and perform the tests for them.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...DNA sequencing also showed [DATA?] that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations'''''
:::::Report of observation. They sequenced the specified genes and found no difference in base-by-base comparisons. There is no need in this paper to print all sequences side by side as they're the same. The words, "no difference" transmits the same information in less space as showing all the identical sequences side-by-side with the original, previously released sequence. See also the next lines.

:::::: No one suggested that the DNA be published "in this paper," but rather that the data be made publicly available for independent review and verification.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::Again, the sequences are available. If someone wants to confirm that the sequencing was done correctly they can request the strains from Lenski and repeat the sequencing. The protocols are published.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...each of these mutations distinguishes this population from all [DATA?] of the others (30).'''''
:::::See reference (30) from Lenksi's paper. It describes how the genes in those populations were originally sequenced. The ancestral sequences were uploaded into GeneBank, a publically accessible sequence repository, and the identifying mutations were presented in the supplemental table published on the PNAS web site along with the original paper.

:::::: That's spelled "publicly", not "publically", and again disclosure of the data concerning the mutations is necessary to verify the claims made.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::If someone wants to confirm that the sequencing was done correctly they can request the strains from Lenski and repeat the sequencing. The protocols are published and Lenski has stated he would make the strains available.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

:::::'''''...Therefore, the Cit variant arose within the LTEE and is not a contaminant [THIS CONCLUSION NEEDS TO BE CHECKED BY INDEPENDENT REVIEW OF THE ACTUAL DATA, WHICH I DOUBT OCCURRED IN THE BRIEF PEER REVIEW OF THIS PAPER]'''''
:::::The authors reported the actual data in a manner that is readily understood and accepted by microbiologists. The data and analysis is not terribly complex or confusing for someone familiar with the field (and quite a few who aren't expert microbiologists). Andy, I've seen little requested that isn't standard practice & generally understood among microbiologists or not already available if one follows the references provided in the paper.

:::::: You're right that the "data and analysis" are "not terribly complex." Which is why the odd withholding the data merely serves to heighten skepticism towards the claims made.
:::::::YMMV. I've encountered no one on the web or elsewhere and trained in microbiology who thinks the data is being 'oddly' withheld. Most of us manage to locate the references and other sources provided.

:::::: The bottom line is that some think that Lenski's claims must be accepted on faith rather than independent verification of the data. That is not science.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)

:::::Just a word about reading the professional, scientific literature: Scientific papers are by the nature of their medium, mostly brief, to the point and highly condensed. Rather than repeat all the background information that others in the field may already know and encouraged to limit the length by journals with page limits, authors provide references to other papers that contain the previously published information. They also use terms that are well-defined within their profession to shorten the text further. One wouldn't expect a layman with no experience in biology to easily digest the paper. To point is not to obfuscate but to simmer the paper down to essentials that others in the field can readily understand. With some effort to become familiar with the underlying & established techniques & science, determined, non-experts can eventually pick up this information. I'd respectfully suggest to anyone *seriously* interested in the paper but not comfortable with the technical details, that they may want to find a knowledgeable biologist willing to explain. At least they should read the entire paper and the additional papers referenced within. Consider asking DI's research institute or Behe for help with understanding the techniques behind the work.--[[User:Argon|Argon]] 20:11, 27 June 2008 (EDT)

:::::: Your sermon is misplaced. Taxpayers paid for Lenski's study, and any real scientist should reject the inexplicable withholding the data underlying its conclusions.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
:::::::YMMV but in my view, it's like going to a librarian and demanding they provide something made from paper: Books? Magazines? Newspapers? What type of books? What subjects? My opinion is that if someone: doesn't know what one wants, doesn't appear to understand the report, demands to see 'the data' without appearing to know what they're asking for in the first place or how to process the information, I'm not sure how any experimental scientist would comply with that request. Furthermore, I'd find it odd that the requests persist despite the fact that the paper was indeed published in compliance with establish profession standards and the strains were made available (in compliance with journal and university research policy). Again, if someone thinks the work was done incorrectly they can get a lab to request the strains and try to repeat many of the observations. That is why the materials and methods sections exist in papers: To allow others to repeat and confirm the work.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

Unfortunately, there are essentially no real scientists left. Peer review is almost never done with the amount of scrutiny Aschlafly discusses. Reviewers, even for journals with long submission-to-publication times, do not request the original data. When original data are requested, it is by researchers who want to continue the work and write publications of their own on the subject. There just aren't incentives to do thorough reviews.

Aschlafly, I think you're right that review should have been more stringent. I think you're wrong, however, to conclude that an exception was made here. Its true that review time was very short in this case. The total number of man-hours devoted to '''any''' review, however, is seldom more than 40.

What does "real scientists" mean? If it means practicing academics today, it's sadly wrong. Most [[professor values|professors]] are self-centered, and would see true peer review as impinging on their personal freedom. "Who has time," they think, "to transcribe lab notebooks? I've got more papers to publish!" I bet the majority would even resist your request to Lenski. This liberal attitude towards truth is what leads to claptrap like [[Particle/wave duality theory]] and [[COBE|the theory of cosmic microwave background radiation]]. [[User:Drochld|Drochld]] 09:19, 28 June 2008 (EDT)

: With respect to your comments on peer review, note that there were merely 14 days between the time the Lenski manuscript was sent for review and the time it was confirmed for publication. I doubt even 10 good hours of real peer review were devoted to the Lenski manuscript, let alone the 40 you mention. The 14 days included administrative and communication delays, and business and weekend days. It looks like a "rubber stamp" process to me for evaluating this Lenski manuscript, in contrast to other papers published by the same journal. It seems possible to me that there was no meaningful peer review at all for the Lenski manuscript, and it may be worth making inquiries of the Journal on this point alone.--[[User:Aschlafly|Aschlafly]] 09:44, 28 June 2008 (EDT)

::The paper is straightforward and the data clear. Lenski's work is well known within the microbiology community and therefore much of the preceding information is already generally understood (i.e. reviewers don't need to dig through all the references). I can see it sailing through review.--[[User:Argon|Argon]] 10:19, 28 June 2008 (EDT)

::: In other words, you seem to be saying the latest paper was not given a thorough, independent peer review. I agree with that analysis. In fact, it probably "sailed through" without any meaningful peer review at all, despite published journal procedures claiming to require meaningful peer review.--[[User:Aschlafly|Aschlafly]] 11:08, 28 June 2008 (EDT)

::::On the contrary. I see it sailing through review because the experiment is straightforward, clearly reported and very interesting to the field. The techniques are uncontroversial and well understood among microbiologists. Easy reviews proceed faster, plain and simple. That reveals nothing about whether the paper received more, less or the same of scrutiny as the typical paper.

::::Are you familiar with PNAS review policy? I ask because in previous notes you've wondered whether authors submit original (raw?) data in addition to their paper's actual manuscripts. Have you perhaps discussed review policies with other Nation Academy of Sciences members or at least, publishing biologists? It might be more productive than polling anonymous sources on the internet.--[[User:Argon|Argon]] 11:28, 30 June 2008 (EDT)

:::::Aschlafly, the purpose of a Peer Review is not to make sure the entire experiment wasn't a massive fraud - it is to ensure that the work adhered to scientific principles and guidelines. In this case, the work was short and did adhere to principal. Lenski has, as required, laid out how the experiment can be repeated. Are you saying that he risked his entire reputation on results that can be checked and refuted by another lab? {{unsigned|Falsehood}}

::::Aschlafly, peer reviews are not suitable to detect all experiment flaws or outright fraud. Reviewers can't always know whether a lab assistent made a mistake or even if the experiment was done at all. The primary goal is to make sure that the experiment can be repeated so completely independent researchers can verify the results. This is the only good verification. A mistake in the experiment means that the data cannot be trusted. That is true for fraudulent data as well. There are several reasons to repeat an experiment. First of all, a groundbreaking result will nearly always be repeated. Scientists want to be sure they can trust the result and not waste years on related experiments. The second reason is to test yourself. A scientist may want to repeat an important experiment before starting their own related experiments. It may also be done to test a new lab or test setup. Thirdly, indications of fraud are an obvious reason. Fourthly, highly complicated experiments that can easily go wrong may be replicated. Fifthly, new scientists are less trusted and more likely to be checked. Now, this experiment is not particularly likely to be repeated. It is not particularly groundbreaking (evolutionary changes have been observed in many other experiments), complicated and there are no indications of fraud. Of course, you/Conservapedia may want to appeal to colleages of mr. Lenski for a repeat of (parts of) the experiment, but I doubt that they will be swayed by your arguments that seem to boil down to: 'I don't understand the science, but I don't like the result, so there must be a mistake'. It would be wiser to point to an actual lack of evidence or methodology flaw in the paper (if it exists), so an experiment can be drafted to test the significance of that mistake. --[[User:Aapje|Aapje]] 07:29, 8 July 2008 (EDT)

== More replies to archived comments ==

:"''Why do you say that it does not support evolution?''" ([[Conservapedia talk:Lenski dialog/archive1#Questions for Aschlafly , not Bugler]] (Asked by JPohl of me):
See my post (now in the archive) dated 23:05, 16 June 2008 (search for that text).

:"''The current living species of coelacanth are not the same as the ones in fossils''" ([[Conservapedia talk:Lenski dialog/archive1#E. coli in our bowels]]) (in a question by Wandering to me)
:"''Modern coelacanths are anything but unchanged. For example, they're roughly three times as large as their ancient predecessors. Of the two known living species, neither are in the same genus as ancient coelacanths. Your statement is ''blatantly'' false''" (Same section) (by Rspeed in a response to Jimxchue)
How do we know that they are not the same species or genus? "Species" is defined in terms of interfertility, something that cannot be determined for fossils. And size doesn't mean much. Great Danes and Chihuahuas are in the same ''sub''-species, but the ratio of size difference is greater than 1:3.

[[User:Philip J. Rayment|Philip J. Rayment]] 23:14, 26 June 2008 (EDT)

:Hi Philip, I read your post and I don't think it addresses anything other than semantics. The bacteria was standard E Coli, and then after tens of thousands of generations, it started to metabolise citrate, which normally ''distinguishes'' E Coli from other species. That's very clearly the process of changing inherited traits over generations - ie, evolution.[[User:JPohl|JPohl]] 08:45, 27 June 2008 (EDT)
:: I can't help wondering if you skimmed it too quickly and didn't pick which bit I was referring to here. I'll explain it in a different way:
::* According to evolution, there must be millions of information-generating mutations to go from microbes to man.
::* According to creation, mutations do ''not'' produce new genetic information, although ''very rarely'', you might by chance get the odd one.
::Lenski has allegedly found ''one'' information-generating mutation. So which of those two competing predictions does this evidence match the best?
:: I also pointed out two weeks ago on Andy's talk page the following:
{{QuoteBox|It took 31,500 generations before the bacteria acquired a single new ability (even assuming they actually do have some new genetic information). 31,500 generations for humans is around 600,000 to 900,000 years (depending on the average time between generations). Yet humans have supposedly evolved ''hundreds'' if not ''thousands'' of new abilities from their supposed primate forbears in a time span only three to five times that long. So this research can be seen as evidence (not absolute proof, of course) that evolution simply does not occur fast enough for us humans to have evolved, which is therefore ''evidence'' that evolution can't explain our existence.}}
:: [[User:Philip J. Rayment|Philip J. Rayment]] 09:37, 27 June 2008 (EDT)

:::There are some flaws in that logic though:
:::*Simple cells likely first appeared 4 billion years ago. Given how many existed simultaneously (an entire planet at some times v. a few petri dishes) and that simpler living beings have shorter lifespans, going from "microbes to man" (or something as genetically complex as man) is really a matter of time.
:::*31,500 generations is not a minimum number of generations for a rare, complex trait to manifest. That just happened to be the case here. Dumb luck could have had significant mutations develop at any earlier (or later) point.
:::*What definition of "ability" are you using here? All of the bacteria also evolved larger cells - would you count that as an "ability"? According to Lenski's work, "enough bacterial cells had lived and died that all simple mutations must already have occurred several times over"
:::*Bacteria are asexual. Animals and plants reproduce through sex, which causes significantly more genetic variation.[[User:JPohl|JPohl]] 12:18, 27 June 2008 (EDT)

:::: No, going from microbe to man is ''not'' a matter of time. If you are travelling south from Sydney, how long will it take you to reach Brisbane? Answer: It's not a question of how long, because you are going in the wrong direction. The same applies here: you can't go from microbes to man when mutations destroy information rather than create it. See also [http://creationontheweb.com/content/view/431/ here].
::::: We both know the Earth is round, so the trip is still possible, if not extended. [http://www.talkorigins.org/faqs/information/infotheory.html This] and [http://www.talkorigins.org/faqs/information/apolipoprotein.html this] are good links on information theory.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: Yes, perhaps 31,500 generations just ''happened'' to be the case here. As you say, it ''might'' occur sooner, and it ''might'' take longer. But my argument was based on the ''evidence'' of this example, not on what speculation ''might'' allow for. The ''evidence'' is not ''proof'', but the ''evidence'' in this case is ''against'' evolution.
::::: I'm not following your claim here. The mutation happened, and it is proof against evolution?[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: I'm talking about the ability claimed by the research, to metabolise citrate, that apparently requires new genetic information. Being bigger presumably does not require that, else they would have trumpeted that as well.
::::: They didn't trumpet the metabolisation of citrate as "new information", but rather as a complex mutation that dramatically distinguished it from earlier generations. It would be like coming back to Earth in 100,000 years and finding that humans suddenly have two-foot-long third legs.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: Genetic variation through sexual reproduction is a variation ''within'' the existing genetic information; sexual reproduction does not create ''new'' genetic information.
::::: It varies the gene pool, which allows for different types of mutation and more dramatic diversification.[[User:JPohl|JPohl]] 12:08, 30 June 2008 (EDT)
:::: [[User:Philip J. Rayment|Philip J. Rayment]] 23:31, 27 June 2008 (EDT)
:::::: "''We both know the Earth is round, so the trip is still possible, if not extended.''": So? Like all analogies, it's not perfect. Evolution doesn't go around in circles like travelling around the Earth, so that reply is invalid, and the objection remains: mutations go in the wrong direction.
:::::: "''[http://www.talkorigins.org/faqs/information/infotheory.html This] and [http://www.talkorigins.org/faqs/information/apolipoprotein.html this] are good links on information theory.''": No, they are not good links at all. From memory of checking the first one out before, it has little of substance. The second is a disagreement over a particular case, not a general look at information, and has some errors in it that I can identify.
:::::: "''I'm not following your claim here. The mutation happened, and it is proof against evolution?''": I said "evidence", not "proof". If you don't understand the difference, read the relevant sections in my [[Essay: Accuracy vs. neutrality on Conservapedia]]. Creationism ''also'' proposes mutations, so the fact that a mutation happened is not evidence favouring evolution.
:::::: "''They didn't trumpet the metabolisation of citrate as "new information", but rather as a complex mutation that dramatically distinguished it from earlier generations. It would be like coming back to Earth in 100,000 years and finding that humans suddenly have two-foot-long third legs.''": The New Scientist article quoted Jerry Coyne saying "it says you can get these complex traits evolving by a combination of unlikely events, ... That's just what creationists say can't happen.". What creationists say "can't happen" is an ''increase in information''. So if you are claiming that nobody is claiming this to be an increase in information, they you are claiming that Jerry Coyne doesn't know what he's talking about regarding what creationists claim (which could be the case, actually!). As for your example, a short third leg probably doesn't require new information anyway. We already have the information for legs, so failure (mutation) of a switch might result in a third one (it's happened with animals), and another fault (mutation) might cause that third leg to be stunted. So if Lenski's discovery is like this, then it really is the case that it doesn't support evolution, because microbes-to-microbiologist evolution requires ''new'' genetic information.
:::::: "''[Sexual reproduction] varies the gene pool, which allows for different types of mutation and more dramatic diversification.''": That sounds like hand-waving to me, rather than an argument of substance.
:::::: [[User:Philip J. Rayment|Philip J. Rayment]] 10:40, 1 July 2008 (EDT)

:::::Philip,
:::::With due respect, I see a fairly serious problem with the position you're taking. One of the central arguments against evolution is that mutations ''cannot'' produce new information. Now you're arguing that:

:::::''"According to creation, mutations do ''not'' produce new genetic information, although ''very rarely'', you might by chance get the odd one."''

:::::The problem is that, if it can "very rarely" happen "by chance," then the premise that mutations do not produce new genetic information is simply false. Instead, we're faced with a debate over ''how frequently'' mutations produce new genetic information. --[[User:Benp|Benp]] 10:41, 28 June 2008 (EDT)

Philip, I see your point about how the creation of new information through mutation does not necessarily contradict creationism at all. However, it hardly seems like evidence ''for'' it; and extrapolating as you did (trying to claim the timeframe for these bacteria applies equally to the supposed evolution of humans) honestly seems like mostly speculation... Which I admit is often overused by evolutionists as well, but it still isn't a good basis for deciding which theory the evidence favors. [[User:Feebasfactor|Feebasfactor]] 11:27, 28 June 2008 (EDT)

: BenP, it's possible to have both a rule and exceptions to that rule. For all practical purposes, mutations don't create new information. However, that doesn't rule out that, once in a blue moon (actually, far less often), you might actually get ''something'' simple that is new. And yes, I guess that there is then a debate about how frequently mutations produce new genetic information, which is sort of what I've been discussing here, in pointing out that ''in this case'' it took 31,500 generations, and even that assumes that this ''did'' happen, which I think is a long way from being accepted. But the question is not ''really'' how long it takes, but whether or not the extremely rare one is going to be swamped by all the deleterious ones. And especially with more complex creatures, it is easily going to get swamped, especially in creatures with sexual reproduction. That is, even if, once in 30,000 generations, there was the odd information-gaining mutation, then what's the chances that that mutation will get passed on to the next generation? Especially given that this won't be the only mutation being selected for (or against).
: Feebasfactor, why is not not evidence ''for'' creation? If that's the prediction that it best fits, then it ''is'' evidence for it! You're right about the timeframe not applying to humans. Because humans reproduce sexually, and therefore the next generation will not necessarily inherit the mutation, and because natural selection favours ''individuals'', not ''mutations'', then a less-fit ''individual'' will be selected ''against'' even with the odd "good" mutation. So really, it will occur a lot ''slower'' for humans than for bacteria.
: For more information on this, see [http://creationontheweb.com/content/view/4473 this] brief description of "Haldane's Dilemma".
: [[User:Philip J. Rayment|Philip J. Rayment]] 11:27, 29 June 2008 (EDT)

:: It's amusing to me that you cite Haldane's Dilemma, even though it was debunked at the same time it was given that name. As Leigh Van Valen pointed out on page in his paper [http://www.jstor.org/pss/2458906 Haldane's Dilemma, Evolutionary Rates, and Heterosis], significant evolutionary changes occur when the environmental changes cause unadapted organisms have less reproductive success. This holds with evolutionary theory, as there is abundant evidence of large changes occurring in organisms at times where their environment changes and their population is small. Mind you, this is the paper which originated the term "Haldane's Dilemma", so with the exception of J. B. S. Haldane's papers, this is the original source. --[[User:Rspeed|Rspeed]] 16:41, 30 June 2008 (EDT)

: Philip, the massive increase in size is just one (and the most readily visible) aspect of Coelacanthiforme's evolution since the end of the Cretaceous. If you want firm proof, there are significant differences in skeletal structure between the most closely-related ancient and modern species of coelacanth (Macropoma and Latimeria). It is an established fact that modern species of coelacanth are in a separate genus. --[[User:Rspeed|Rspeed]] 15:01, 30 June 2008 (EDT)
:: There have apparently been various ''attempts'' to debunk Haldane's Dilemma, but those attempts have themselves been debunked. In 1992 (well after Van Valen's paper), George C. Williams wrote of Haldane's Dilemma, "In my opinion the problem was never solved, by Wallace or anyone else."[http://saintpaulscience.com/Haldane.htm]
:: "''It is an established fact that modern species of coelacanth are in a separate genus''": Oh? Because you say so? Yet you didn't explain how this can be determined without interfertility tests. No, this "established fact" is by decree, not scientific tests of interfertility.
:: [[User:Philip J. Rayment|Philip J. Rayment]] 11:22, 1 July 2008 (EDT)
::: "Oh? Because you say so?" No, because the scientists who know how to determine taxonomy said so. Your argument is unbelievably weak, by that logic humans could be genetically compatible with T-Rex. Rather than simply dismissing everything that disagrees with the Bible, you should probably do some research from reliable sources. The scientific method exists for a reason.
::: That's fine about someone disagreeing with Van Valen's conclusions, but can you share his reasoning? I found Van Valen's debunking of Haldane's Dilemma to be quite logical and it fits with the data (such as Prof. Lenski's experiment).
::: --[[User:Rspeed|Rspeed]] 20:35, 3 July 2008 (EDT)

==Lead author won't answer simple, basic questions==

IMO the paper has no credibility because the lead author of the paper, Zachary Blount, has refused to give straight consistent answers to the following simple, basic questions about the experiment:

(1) -- whether evolution of citrate-eating (Cit+) E. coli bacteria was a goal of the experiment (I noted that a "goal" does not have to be a sure result), and

(2) -- whether the purpose or one of the purposes of the glucose-cycling (giving insufficient glucose supplies in order to cause alternating glucose feeding and glucose starvation) was to favor the evolution of citrate-eating E. coli bacteria.

Blount's refusal to properly answer these questions is discussed in the following article on my blog --

[http://im-from-missouri.blogspot.com/2008/06/co-author-of-e-coli-paper-dodges.html Co-author of E. coli paper dodges questions]

More details concerning Blount's refusal to properly answer these questions are in the comment thread under the following post on Carl Zimmer's "The Loom" blog (note particularly my most recent comments in that thread) --
[http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php A new step in evolution]

Also, I think Andy Schlafly is wrong to request all of the raw data, because (1) copying all of the raw data to send to him would be a huge job and (2) the raw data might not even be in a form that could be readily understood by someone who did not participate in the research. IMO the citrate-eating bacteria are the best evidence supporting the paper (such as it is).[[User:LarryFarma|LarryFarma]] 18:59, 26 June 2008 (EDT)
: a reading of the blog reveals that Zachary Blount did indeed address the questions that the above poster named and did so clearly. Please read more carefully next time and don't post falsehoods[[User:DeanWinter|DeanWinter]] 19:10, 26 June 2008 (EDT)

:: LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. (I did not find the answer in the paper.) Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population? The details of the data might shed light on how that goal was achieved, if in fact that was the goal. They should turn over the data for public scrutiny so that questions can be resolved.--[[User:Aschlafly|Aschlafly]] 19:33, 26 June 2008 (EDT)
::: Blount's comments on "LarryFarma's" blog make it clear that the evolution of citric eaters was not a goal, but not completely unexpected. The paper, though it was pretty technical for me, seems to indicate that as well. [[User:AndyMann|AndyMann]] 20:15, 26 June 2008 (EDT)

:::: If you're serious, then please provide some quotes and links to back up your statements. Also contribute to entries rather than violating the [[90/10 rule]].--[[User:Aschlafly|Aschlafly]] 20:32, 26 June 2008 (EDT)

:Reply to Aschlafly's comment of 19:33, 26 June 2008 (EDT) --
:''"LarryFarma raises an excellent question about whether a goal of Lenski and Blount's project was to generate citrate-eating E. Coli bacteria. ('''I did not find the answer in the paper.''')"'' (emphasis added) I asked Zachary Blount to clarify his statements about whether evolution of Cit+ (citrate-eating) E. coli bacteria was a goal of the experiment. He answered by asking me to go on a wild goose chase by reading the whole paper, which has 8 pages of fine print -- this is called "bibliography bluffing." And when people balk at going on these wild goose chases, they are accused of not wanting to learn.

:''"Did the researchers figure out, after many years of fruitless attempts, how best to promote the percentage of citrate-eating E. Coli bacteria in a population?"'' As I said, I asked Blount whether favoring Cit+ evolution was the purpose or one of the purposes of the glucose-cycling (giving the bacteria insufficient supplies of glucose so as to create alternating glucose feeding and glucose starvation), and he did not answer.

:''"They should turn over the data for public scrutiny so that questions can be resolved."'' I disagree with you here, for the reasons stated at the end of my first comment in this talk page.[[User:LarryFarma|LarryFarma]] 05:25, 28 June 2008 (EDT)

:: Thanks for your insightful comments and continued efforts to obtain the truth.

:: It has been conceded, finally, by Lenski defenders that the data are not too voluminous to turn over. The underlying data for Figure 1 in the paper for the population expansion during the alleged evolution of the Cit-plus phenotype, for example, could shed light on whether contamination played a role. There is no legitimate reason to withhold the greater resolution from the public, which funded the study.--[[User:Aschlafly|Aschlafly]] 09:15, 28 June 2008 (EDT)

::::People need to stop asking to "turn over the data for public scrutiny" before they've fully read and comprehended the papers and information released to date. E. Coli don't live off of citrate - it's a characteristic of the species - so there was no "goal to promote the percentage that could do it". The fact that a certain population were able to after after thousands of generations of reproduction in a controlled, monitored setting was the key observation, and Lenski's team is still investigating the specifics of when and how that characteristic was enabled. It reflects poorly on an online encyclopedia that the leadership is still questioning whether sufficient data to understand the experiment has been released. The most relevant data from the experiment is the actual bacteria itself, and Lenski has publicly offered to share samples of them with any scientist qualified to handle them, who follows the proper, professional protocols. The Consevapedia community has yet to see a specific, professional response to Professor Lenski's second letter other than a flippant remark about attitude and a continued insistence that data has not been revealed when it clearly has.

::::I'll probably earn another 90/10 block for this, but when you continue to question Lenski's work while admitting that you've only skimmed the related paper, you accomplish nothing but setting a poor example of intellectual honesty for the students who use CP as a trustworthy resource. With all respect, I would ask that instead, you retain the services of a qualified scientist who can engage in a proper review of Lenski's work, whose could then post an ongoing journal of the review process and its findings here on CP. ''That'' would be an appropriate lesson for the students in the proper application of scientific scrutiny to findings that some find questionable. Godspeed. --[[User:DinsdaleP|DinsdaleP]] 20:20, 26 June 2008 (EDT)

::::The development of citrate metabolizers wasn't the main intent (see Lenski's early papers) and it's actually tangential in the overall context of the long-term experiment. Zachary Blount describes the purpose of citrate in the media in his responses at Carl Zimmer's blog, The Loom. http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php (see replies #115 & #270). Citrate was not added to be a carbon nutrient in the media but as a non-metabolizable chelator (the three carboxyl groups of citrate can bind certain cations in solution). The recipe for the medium was taken from other microbiologists who developed the recipe as a general culture medium back in 1949. Lenski's description of the DM25 media is here: https://myxo.css.msu.edu/ecoli/dm25liquid.html. Glucose was the intended carbon source. If you read the Lenski article cited by Blount (Phenotypic and genomic evolution during a 20,000-generation experiment with the bacterium Escherichia coli. -- available here: https://www.msu.edu/~lenski/, you'll see the setup and reasons for performing the experiments (An earlier article at generation 2000 is here: http://myxo.css.msu.edu/lenski/pdf/1991,%20AmNat,%20Lenski%20et%20al.pdf). Basically, Lenksi wanted to see how mutations arise and move through populations over time. Even if the media and growth conditions remain pretty consistent over time, the populations continuously shift and change. That is because for a bacterium in the experiment the 'environment' is not just made up of the flask and media but also the *other cells in the flask* with which it must compete. This results in a continuously shifting competitive environment as mutations arise in lineages. Citrate utilization was just one of the many interesting variations acquired over the course of the experiment. Read his other papers for more details and a fuller understanding of the open-ended experiment's scope.--[[User:Argon|Argon]] 21:16, 26 June 2008 (EDT)

::::: I looked at the blog and found it to be remarkably uninformative. I saw nothing about Blount and Lenski's purpose, nothing that persuasively ruled out non-evolutionary reasons for the citrate-eating bacteria, and nothing to justify the withholding of the data to reveal greater resolution than provided by the figures in the paper.--[[User:Aschlafly|Aschlafly]] 23:00, 26 June 2008 (EDT)

::::::Blogging has limits, which is why I also provided references to Lenski's other papers, including some of those Blount mentioned would be worth reading.--[[User:Argon|Argon]] 20:37, 27 June 2008 (EDT)

::::With regard to 'competent scientists' consider that Behe, in his discussions on this topic has not argued about the 'mechanics' and data presented in Lenski's paper. In his review that can be found on the amazon.com website, he calls Lenksi's work 'fascinating' (and means it in a good way).--[[User:Argon|Argon]] 21:29, 26 June 2008 (EDT)

That was strange -- for several hours I was not able to post here, but now I can. Here is my response to Argon's comment of 21:16, 26 June 2008 (EDT)

Argon said, "The development of citrate metabolizers wasn't the main intent"

I didn't ask if Cit+ (citrate-eating E. coli bacteria) evolution was the "main intent" of the experiment -- I only asked if Cit+ evolution was one of the original "goals." There is a misunderstanding about what the word "goal" means -- a goal does not have to be a sure result. In searches for the Lost Dutchman Mine and the ivory-billed woodpecker, finding them are "goals." A "goal" can be one of many goals, a secondary goal, a longshot goal, or whatever. And "intent" is not part of the definition of "goal" -- "intent" generally means what one plans to do, but one cannot plan to achieve an uncertain result. BTW, the term "citrate metabolizers" is misleading because the bacteria already had the ability to metabolize citrate but did not have the ability to pass it through the cell walls.

Zachary Blount's following statement in comment #115 under the [http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php New step in evolution] post on Zimmer's blog indicates that Cit+ evolution was one of the original goals of the experiment:

''"When Dr. Lenski started, he figured the citrate would provide an opportunity that the populations might or might not figure out a way to exploit, thereby presenting a potential point of divergence between the populations (this is my understanding - I will need to check with him to make certain I understand this properly)."''

Blount then essentially contradicted his above statement by saying that "the intent of the experiment was never to evolve a Cit+ E. coli variant" (comment #115) and that Cit+ evolution was "not a goal" (comment #122).

Also, the following factors suggest that Cit+ evolution was an original goal of the experiment:

(1) Cit+ evolution had been observed once before. Blount reported in comment #115 under the [http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php New step in evolution] post on Zimmer's blog, ''"there has been only one report of a spontaneous Cit+ mutant of E. coli in the past century (Hall, B. 1982. Chromosomal mutation for citrate utilization by Escherichia coli K-12. Journal of Bacteriology, 151: 269 ï¿½ 273.)"). ''

(2) I and others assumed that a purpose of the glucose-cycling (giving the bacteria an insufficient glucose supply so as to create alternating glucose feeding and glucose starvation) was to favor Cit+ evolution. I asked Blount if this was in fact a purpose of the glucose-cycling and he did not answer. I asked what the purpose of the glucose-cycling was if favoring Cit+ evolution was not the purpose, and he did not answer.

Was there a research proposal for this whole experiment that started in 1988, and if so, what does that proposal say, if anything, about my questions? [[User:LarryFarma|LarryFarma]] 10:24, 27 June 2008 (EDT)
:I may be missing something here, but why is the supposed "goal" of the experiment important? It's the important thing the result?--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 11:29, 27 June 2008 (EDT)

::British_cons''':''' Suppose a committee is considering this research for an award or a prize and asks the researchers the same questions I asked''':''' (1) Was Cit+ evolution a goal of the experiment? and (2) was favoring Cit+ evolution a purpose of the glucose-cycling? Are the researchers going to answer, “No, it was not a goal — it was just an unforeseen accident. We don’t deserve any credit for it.”

::Also, IMO knowing the goals of the experiment and the purposes of the experimental methodologies are important parts of understanding the experiment. Also, the candor of the researchers is in question here -- as shown above, I did not get straight consistent answers to simple, basic questions.[[User:LarryFarma|LarryFarma]] 12:27, 27 June 2008 (EDT)
:::There are two possibilities. It was the goal. It was not the goal. The result is that they have produced Cit+. If it was the goal then they have demonstrated what they set out to demonstrate. Well done. If it was not the goal then serendipity has favored them. It is no means unusual in science for unexpected results to further the cause of science. Nobody would reject or question them because they were unexpected. Indeed they are even more welcome if they're unexpected because something new has been learned. So again - well done. I don't see the problem.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 12:45, 27 June 2008 (EDT)

::::British_cons''':''' As I said, suppose that a committee is considering this research for an award -- wouldn't this research be much less deserving of an award if Cit+ evolution were just an unforeseen accident? Also, the candor of the researchers is in question here -- as I showed above, I did not get straight consistent answers to simple, basic questions. As I noted above, Cit+ evolution had been observed before, so it seems that repeating it was a likely goal of the experiment. Also, I asked about the purpose(s) of the glucose-cycling and I got no answer to that question. Knowing the goals of the research and the purposes of the experimental methodologies are important parts of understanding the research.[[User:LarryFarma|LarryFarma]] 14:07, 27 June 2008 (EDT)

::::Thudden''':''' ''As I said, suppose that a committee is considering this research for an award -- wouldn't this research be much less deserving of an award if Cit+ evolution were just an unforeseen accident?'' This betrays a unequivocal lack of understanding of scientific process and acclaim. Hundreds of world-altering scientific discoveries have been serendipitous: Pauling and Penicillin, Galvani and neuroelectricity, Nagano's discovery of interferon, Becquerel and Röntgen's discovery of radioactivity and X-rays respectively. If you stumble on something marvellous by accident, you receive identical academic acclaim, perhaps only with added envy.
:::::'''Fleming''' and Penicillin (just for the sake of accuracy). [[User:HSpalding|HSpalding]] 17:56, 8 January 2009 (EST)
::''"If you stumble on something marvellous by accident, you receive identical academic acclaim,"'' I disagree -- IMO things discovered by intelligent searching are more highly regarded. [[User:LarryFarma|LarryFarma]] 06:17, 29 June 2008 (EDT)
::''Thudden: Your disagreement would be more convincing if it was backed up by evidence, or engaged with the contrary evidence provided.
:::"Identical academic acclaim": Fleming won the Nobel Prize, Becquerel won the Nobel Prize, Rontgen won the first ever Nobel Prize for Physics, Nobel Prizes were awarded for the serendipitous discoveries of restriction endonucleases and RNA interference... Not to mention "Eureka!" The list of people who've won the highest acclaim for accidental discoveries is very, very long. [[User:HSpalding|HSpalding]] 17:56, 8 January 2009 (EST)

::::''"Your disagreement would be more convincing if it was backed up by evidence, or engaged with the contrary evidence provided."''
::::It is just my own personal opinion -- I have no opinion poll results on the question. Do you have any opinion poll results to back up your statement?
::::I was especially impressed by the way Neptune was discovered in 1846 -- a mathematician predicted its location on the basis of perturbations of the motion of Uranus, and Neptune was found in one night very close to the predicted spot. Also, Pluto was found on the basis of perturbations in Neptune's motion but the search took much longer.
::::You should sign your comments at the end, not the beginning -- when you sign them at the beginning, it looks like you are addressing someone (that is what I originally thought about your preceding comment). [[User:LarryFarma|LarryFarma]] 15:06, 29 June 2008 (EDT)

(unindent) Rather than dispute this with you YET AGAIN, can we wait until you respond to criticisms of your position on other websites first? You keep repeating this "no straight answers" argument, and people keep pointing out your error, and you've yet to see this argument through to the end anywhere. Conservapedia is already struggling to maintain its current signal-to-noise ratio, please stop forum-shopping here. [[User:Aziraphale|Aziraphale]] 14:17, 27 June 2008 (EDT) ''<-knows where all the good sales are...''

:: Aziraphale said, ''"Rather than dispute this with you YET AGAIN, can we wait until you respond to criticisms of your position on other websites first? "'' I have already spent a helluva lot of time responding to those criticisms on Carl Zimmer's blog and my own blog! (see links in my first comment on this talk page) But I have been kicked off of Carl Zimmer's blog, and my own blog gets only about 50 visits per day. In contrast, this talk page is getting thousands of visits per day, so it is obviously a much better forum for publicizing my views.

::''"You keep repeating this 'no straight answers' argument, and people keep pointing out your error."'' And I keep pointing out the errors in arguments that attempt to point out my alleged error.[[User:LarryFarma|LarryFarma]] 16:18, 27 June 2008 (EDT)

:::Ok, fair enough. Enjoy your time here. :) [[User:Aziraphale|Aziraphale]] 18:05, 27 June 2008 (EDT) ''<-o/~know when to hold 'em... o/~''

::::''"Enjoy your time here."'' I intend to. I never before had such a good opportunity to publicize my views. [[User:LarryFarma|LarryFarma]] 02:21, 28 June 2008 (EDT)
:::::It has been brought to my attention that there may be a problem with your question. You wish to know about the "goal" of the experiment. Is that a reasonable way to ask a question of a scientific experiment? Shouldn't the question be "What hypothesis was being tested?"?--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 10:03, 28 June 2008 (EDT)
::::::How could a random event, Cit+ evolution, be a "hypothesis"? Even Zachary Blount used the term "goal." What is wrong with saying that an experiment has a "goal" (or "goals")? [[User:LarryFarma|LarryFarma]] 15:53, 28 June 2008 (EDT)
:::::::Because according to the [[Scientific method]] the objective of an experiment is to test an hypothesis. Remember that things are not proved in science - only disproved. The objective of an experiment is never to "prove" anything - only to test an hypothesis. If the hypothesis is confirmed then it is strengthened, if it not confirmed it is weakened or discarded. Consequently the fundamental question to ask of an experiment is, "What hypothesis was being tested?" --[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 16:07, 28 June 2008 (EDT)
::::::::How would you describe Cit+ evolution as a hypothesis, even assuming that Cit+ evolution had not been observed before (Cit+ evolution was observed prior to Lenski's experiment) ?[[User:LarryFarma|LarryFarma]] 21:54, 28 June 2008 (EDT)
:::::::::I'm afraid that's for you to figure out. As I've said, the only sensible way for you to ask the question you want answered is to form it as a question about the hypothesis. How you manage that is down to you. :-)--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 02:27, 29 June 2008 (EDT)
::::::::''"I'm afraid that's for you to figure out."'' It's your idea that it must be stated as a hypothesis, so showing how it can be stated as a hypothesis is your responsibility. Anyway, Lenski could not hypothesize about whether Cit+ evolution could occur, because it had been observed prior to the start of his experiment. All he could do was consider Cit+ evolution to be a "goal" of his experiment. [[User:LarryFarma|LarryFarma]] 05:43, 29 June 2008 (EDT)
:::::::::I'm sorry, I thought you were asking for help. Anyway, the article on [[Scientific method]] ''on this wiki'' states that the reason for an experiment is to test an hypothesis - so it's not my opinion but what this Wiki states. I suppose you could edit the article so this it reflects your view of how science works. --[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 06:24, 29 June 2008 (EDT)
:::::::::Reading Lenski's recent paper for comprehension reveals that the hypothesis being tested is that development of the Cit+ strain is a historically contingent process (that is, arising by multiple steps separated over time). The null hypothesis (not supported by the results of the experiments) is that the Cit+ strain arises by a single, exceptionally rare event.--[[User:Brossa|Brossa]] 10:52, 29 June 2008 (EDT)
::::: ''"Reading Lenski's recent paper for comprehension reveals that the hypothesis being tested is that development of the Cit+ strain is a historically contingent process (that is, arising by multiple steps separated over time)."''
:::::I was aware that one of the original goals of the experiment was to test for historical contingency -- that was the reason for freezing the populations at each 500th generation. My questions were about other things: (1) was Cit+ evolution an original goal of the experiment (remember that this whole experiment started in 1988, long before the study in the present paper), (2) was favoring Cit+ evolution a purpose or one of the purposes of the glucose-cycling (giving the bacteria insufficient glucose supplies so as to cause alternating glucose feeding and starvation), and (3) what were other purposes -- if any -- of the glucose-cycling. Zachary Blount did not give a straight answer to the first question and gave no answers at all to the latter two questions. [[User:LarryFarma|LarryFarma]] 13:12, 29 June 2008 (EDT)
:::::::You continue to dwell on the semantics of 'goal' as though it has some particular relevance to the validity of the research presented in Lenski's latest paper. The experiment was started in '88 to track the evolution of a population of E. coli. The purpose of the 'glucose cycling' is to provide the bacteria with an environment that will favor those mutants that are better able to exploit a limited critical resource. The glucose cycling does not inherently favor the development of a Cit+ strain any more than it favors other potential solutions to the problem - like secreting a toxin to kill your competitors, or faster reproduction to outbreed them, or photosynthesis, or cannibalism, or what have you. There is no other purpose to providing the bacteria with a limited supply of glucose. Citrate is present in the growth medium as a chelating agent and buffer - it was not added solely to serve as a potential carbon source, although it is one.<br />
:::::::You seem to believe that the reason that Lenski is getting acclaim for this research is just that has isolated a strain of E. coli that can metabolize citrate under unusual conditions - and your response seems to be that he does not deserve praise for this, since he didn't set out with this particular outcome in mind - it's just an accident, if in fact the Cit+ bacteria exist at all. Or maybe you object because you think Lenski somehow 'stacked the deck' in favor of his bacteria becoming Cit+, so the results aren't 'fair' somehow. Or perhaps you think that after 20 years of failing to develop a Cit+ strain of E. coli through selection, Lenski just gave up, genetically engineered such a strain, and then faked his data. If you could clearly state what your suspicions are, rather than simply repeating that Blount won't answer your questions, it would be simpler to address your concerns.<br/>
:::::::This is utterly beside the point, however, because the importance of this recent paper does not depend on the detail of the strain being Cit+ - it could have been the development of a toxin, or some other event that led the new strain to be markedly, phenotypically different from its ancestors in some way. The importance lies in the work that was done to sketch out the outline of how the new trait developed, and in the re-development of the same trait during a re-running of the experiment from ancestral stock.<br />
:::::::Is it interesting that the trait seen in Lenski's E. coli is the metabolism of citrate under aerobic conditions? Yes. Is it remarkable? Yes, since you can count the number of E. coli strains that can do this on one hand. It's so wild and crazy that it might lead one to question whether the bacteria involved should even be called E. coli anymore - it's that striking a difference from 'normal' E. coli behavior. Was the development of the Cit+ strain an accident? Entirely. Would another Cit+ strain arise if the experiment was completely restarted from 1988? Almost certainly not - Lenski's data suggests that this is a staggeringly unlikely event, dependent on a series of merely overwhelmingly unlikely events. Did Lenski wish to develop a Cit+ strain from the beginning? No man can know the inner mind of another, but I would bet the farm that he didn't see this coming. If I were designing an E. coli breeding scheme with the stated purpose of selecting for a Cit+ mutant, I can think of much, much, much better ways to do it than this experimental protocol. The Cit+ trait is a novelty - an interesting one, one that is remarkable because of its rarity, one that resonates - but the value of the research does not depend upon it. --[[User:Brossa|Brossa]] 17:33, 29 June 2008 (EDT)

::::''"You continue to dwell on the semantics of 'goal' as though it has some particular relevance to the validity of the research presented in Lenski's latest paper. The experiment was started in '88 to track the evolution of a population of E. coli."''
::::I am trying to get answers to some simple, basic questions about the experiment. Is there something wrong with that?
::::Also, the "semantics" -- as you call them -- of "goal" are very important. A lot of people have the mistaken idea that a goal is necessarily an expected result or is necessarily an intended result. Just going around telling people that the Cit+ evolution was not a goal can be very misleading.
:::::If you want to expand the term 'goal' to the point that you include unexpected, unintended results then you rob it of all meaning. By your reasoning, my getting into a fatal car accident is the 'goal' of my driving to the grocery store. If you think that 'goal' is a term of art that describes the entire universe of possible outcomes of an action, you are mistaken. If you want Blount et al to admit that the emergence of a Cit+ mutant was '''possible''', given the experimental protocol, then I think that you already have your answer: yes. Was it expected? No. Was the experiment designed from the beginning to favor Cit+ mutation over some other pathway? No.--[[User:Brossa|Brossa]] 23:22, 29 June 2008 (EDT)
::::''"The purpose of the 'glucose cycling' is to provide the bacteria with an environment that will favor those mutants that are better able to exploit a limited critical resource."''
::::That statement is too vague.
:::::What part is too vague? The alternatives to glucose cycling are: provide so much glucose that cell growth remains exponential up through the time of the next sampling; provide so little glucose that there is no cell division at all; or use a chemostat setup in which the glucose concentration can be maintained at a constant, arbitrary level indefinitely at the cost of vastly increased material and labor costs to the experimenter.--[[User:Brossa|Brossa]] 12:05, 30 June 2008 (EDT)
::::''"The glucose cycling does not inherently favor the development of a Cit+ strain any more than it favors other potential solutions to the problem - like secreting a toxin to kill your competitors, or faster reproduction to outbreed them, or photosynthesis, or cannibalism, or what have you."''
::::The glucose cycling gives an especially big advantage to Cit+ bacteria because they have something to eat after the glucose supply is exhausted whereas their Cit- neighbors do not.
:::::It gives them '''an''' advantage. It's impossible to predict ahead of time how '''big''' an advantage it is, because instead of being unable to metabolize citrate they may merely be terrible at it. If the Cit- cells are better at glucose metabolism than the Cit+ ones are, they may completely swamp out the Cit+ in the early, glucose-dependent phase. Even if the Cit+ cells continue to grow after the glucose is exhausted, they may never completely outcompete the Cit- cells by the time the next population sample is taken. In fact, this appears to be what has happened, as the experiment has shown that two populations of cells originating from the Ara-3 line have reached a temporary equilibrium: a grows-very-fast-on-glucose Cit- population (10%) and a grows-more-slowly-on-glucose-but-keeps-growing-on-citrate Cit+ population (90%). --[[User:Brossa|Brossa]] 12:05, 30 June 2008 (EDT)
::::''"Citrate is present in the growth medium as a chelating agent and buffer -- it was not added solely to serve as a potential carbon source, although it is one."''
::::Yes, I know it is there as a chelating agent -- but I also want to know if Cit+ evolution was a goal (again, a goal does not have to be an expected result and can even be an unlikely result) and if favoring Cit+ evolution was a purpose or one of the purposes of the glucose-cycling (I also would like to know if there were other purposes of the glucose-cycling and exactly how any other purposes work). The fact that Cit+ evolution was observed once previously adds to my hunch that it was a goal. Also, the bacteria already had the ability to metabolize citrate and just needed to evolve a way to pass citrate through the cell wall.
::::''"You seem to believe that the reason that Lenski is getting acclaim for this research is just that has isolated a strain of E. coli that can metabolize citrate under unusual conditions"''
::::Well, he is getting a lot of acclaim for it, isn't he? The paper has been widely ballyhooed all over the Internet. The Internet has several articles and hundreds of comments about it.
:::::He does not deserve acclaim because he is a farmer who has a goose that lays golden eggs, but because he can demonstrate in rough form how the goose came to lay golden eggs when it's grandparents could not. In fact, he has gone back and re-bred the grandparents and gotten golden-egg laying geese again and again, even though none of his other geese, or even the great-grandparents of the golden goose, can breed golden-egg-layers. The real achievement is not having the goose, it's reproducing it against all the odds, and showing that there's something special about the grandparents compared to the greatgrandparents, even though the grandparents appear to be normal. The fact that many folks, including those in the media, can't get past the 'ohmygoshgoldeneggs!!!' phase is not Lenski's fault.--[[User:Brossa|Brossa]] 23:29, 29 June 2008 (EDT)
::::''"If you could clearly state what your suspicions are"''
::::Right now I am just trying to understand the experiment. [[User:LarryFarma|LarryFarma]] 20:46, 29 June 2008 (EDT)

:::::::''"I'm sorry, I thought you were asking for help."'' You call that "help"? All you did was clutter up this talk page with your irrelevant "hypothesis" idea. With friends like you, who needs enemies? [[User:LarryFarma|LarryFarma]] 10:34, 29 June 2008 (EDT)
::::::::When did I call it help? I said that I thought you were asking for it. In any event Brossa seems to have clarified the situation.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 11:38, 29 June 2008 (EDT)
:::::::''"When did I call it help? I said that I thought you were asking for it."''
:::::::And you thought -- or seemed to think -- that you were giving it. I am beginning to suspect that you are just a troll.
:::::::''"In any event Brossa seems to have clarified the situation."''
:::::::No, he has not clarified the situation -- see my above response to him. [[User:LarryFarma|LarryFarma]] 13:29, 29 June 2008 (EDT)
::::::::I will not stoop to name calling. Goodbye and good luck with your enquiries.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 14:07, 29 June 2008 (EDT)

:::::::Well, what did you expect? First you introduced an irrelevant topic, "hypothesis." Then you contradicted yourself by first saying ''"I'm sorry, I thought you were asking for help"'' and then saying ''"When did I call it help?"'' [[User:LarryFarma|LarryFarma]] 15:42, 29 June 2008 (EDT)

::::::::Mods, can we get a ruling on this? LarryFarma is harassing other users, talking far more than he is making valid contributions, and generally being a troll. If he was defending Lenski instead of attacking the paper, he would have been blocked a long time ago. Can someone please comment on this? I believe we can all make our points without name-calling. -- [[User:Aaronp|Aaronp]]
:::::::In fact, the only contributions that Larry has made have been to this talk page. Can we get a 90/10 block please? [[User:Aaronp|Aaronp]]
::::::::Aaronp: Is somebody hassling you? People who don't want to read my comments don't have to read them.
::::::::Also, the 90/10 rule doesn't apply here because I cannot make any contributions to the project page, which is reserved for the exchange of letters between Schlafly and Lenski.
::::::::BTW, I am not attacking the paper -- I am only attacking the lead author's failure to give straight answers to simple, basic questions about it. [[User:LarryFarma|LarryFarma]] 21:17, 29 June 2008 (EDT)
::::::::: Okay, here's my two-bob's worth.
::::::::: LarryFarma, this page was started to question the ''validity'' of Lenski's work and claims. Although I can see how questions about his ''goals'' would be relevant to awarding him a prize, I can't see that they are relevant to the validity of his work. I think that this might be the cause of some of the angst, as some editors are assuming that you are trying to question the work's ''validity'' with an argument that has no bearing on that point.
::::::::: Secondly, Aaronp has a point about the so-called 90/10 rule. It's point is to ensure that editors contribute to the site and don't just argue. That you are unable to contribute to this project page doesn't mean that you can't contribute elsewhere on the site. The rule is not page-specific in that sense. So as Aaronp has called for that rule to be invoked, and as you have only contributed on this talk page, I think that his request is fair. However, I will allow you to make another post or two to wind up your arguments before doing so. Beyond that, I will feel obliged to enforce it.
::::::::: [[User:Philip J. Rayment|Philip J. Rayment]] 21:35, 29 June 2008 (EDT) (Administrator)

::::::''"LarryFarma, this page was started to question the validity of Lenski's work and claims."''

::::::The opening sentence of my first comment questions the validity of Lenski's work:
::::::''"IMO the paper has no credibility because the lead author of the paper, Zachary Blount, has refused to give straight consistent answers to the following simple, basic questions about the experiment:"''

::::::You say,
::::::''"Although I can see how questions about his goals would be relevant to awarding him a prize"''

::::::That is not the issue here -- the issue here is that the lead author of the paper, Zachary Blount, has not given straight answers to my simple, basic questions about the experiment. If I were a peer-reviewer of the paper or in the audience at a presentation of the paper at a scientific conference, would he be dodging my questions? And my questions are not just about goals -- for example, I also would like to know the purposes of the glucose-cycling (alternating glucose feeding and glucose starvation). These things are all part of understanding the experiment. Also, what does the original research proposal -- if there is one -- say about the goals and methodologies of the experiment? Is Lenski willing to release that proposal?

:::::: ''"That you are unable to contribute to this project page doesn't mean that you can't contribute elsewhere on the site."''

::::::I am new to the site and therefore have not had an opportunity to contribute elsewhere on the site. Would you like me to write an article about co-evolution? All I would have to do would just copy-and-paste from my blog's several articles about co-evolution. I have found the issues of co-evolution to be a very effective challenge to evolution theory.

::::::''" I will allow you to make another post or two to wind up your arguments before doing so. Beyond that, I will feel obliged to enforce it."''

::::::Are you willing, then, to censor all future comments that attack my positions? If comments attacking my positions are posted in the future here, then why shouldn't I be allowed to defend myself? In fact, while I was writing this comment, Brossa posted three comments attacking my positions.

::::::Also, how do you intend to "enforce" the 90/10 rule -- by IP address blocking? That is often ineffective and also often unintentionally blocks other Internet users who share the same ISP proxy.

::::::BTW, I am very annoyed that Aaronp hypocritically called me a "troll" while criticizing me for using that name to insult another commenter. [[User:LarryFarma|LarryFarma]] 01:14, 30 June 2008 (EDT)

::::::: Perhaps I wasn't sufficiently clear in some of my comments. The first part of my message was not as an administrator, but just to try and clarify the issues. I didn't mean to suggest that you hadn't addressed the validity of his claims. It was meant simply to point out that some may be misunderstanding the point of your comments. And I'm not saying that the questions you are raising are not legitimate questions to raise.
::::::: It's not true to say that you "have not had an opportunity to contribute elsewhere on the site". You've had opportunity every time you've edited.
::::::: We do allow copying of your own work. There is a template available to note that it is your own work. And of course it can be edited by others, as is the case with all articles.
::::::: If you stop making arguments, your critics will stop disagreeing with you. Yes, it will likely mean that they will get the last word, and that might be unfortunate, but that's not going to be reason to ignore the so-called 90/10 rule.
::::::: I'm not suggesting that you are the only one in the wrong here. Uncivil language happens a fair bit. But that's peripheral to the issue I'm discussing here.
::::::: I've unblocked you, because it wasn't fair for you to be blocked for 90/10 when I'd given you a warning and permission to make one or two more posts, but you used one on responding to me, so that gives you one left to respond to your critics. And fair warning: I've referred to the 90/10 rule as the "so-called" 90/10 rule, because it's not a rule against precisely 90% talk vs. 10% contributions, but a rule against "unproductive activity", with 90/10 being an ''example'' of that. So simply making the odd article edit or posting the odd copied article will not necessarily avoid that rule. It's something that we administrators make a judgement on, and others will make it more readily that I will.
::::::: [[User:Philip J. Rayment|Philip J. Rayment]] 09:51, 30 June 2008 (EDT)

:::::''"I've unblocked you, because it wasn't fair for you to be blocked for 90/10 when I'd given you a warning and permission to make one or two more posts, but you used one on responding to me, so that gives you one left to respond to your critics."''

:::::That reminds me of the following lawyer joke:
:::::Customer: What are your rates?
:::::Lawyer: $100 for three questions.
:::::Customer: Isn't that kind of steep?
:::::Lawyer: Yes. What is your third question?

:::::''"If you stop making arguments, your critics will stop disagreeing with you. Yes, it will likely mean that they will get the last word"''

:::::Almost all of my arguments here have been answers to my critics. What is at stake here is my right to answer critics. And the reason why I have been making more comments here than other commenters is that other commenters have been using tag-team tactics against me. Giving me just one more opportunity to answer attacks is unacceptable because those attacks are continuing and will continue. And how do I know that other commenters here are not violating the 90/10 rule? Am I being singled out because of Aaronp's rude complaint?

:::::''"It's not true to say that you "have not had an opportunity to contribute elsewhere on the site". You've had opportunity every time you've edited."''

:::::I would have liked to make some contributions to Conservapedia articles, but I now have mixed feelings about Conservapedia because of the 90/10 rule, an arbitrary and unfair rule which is being used to prevent me from defending myself here. I gave up on Wikipedia a long time ago because of its arbitrary and unfair rules and practices, and I am now seeing that Conservapedia is no better.

:::::Anyway, we can debate my questions here until doomsday, but nothing can excuse Zachary Blount's failure to give straight answers to those questions. [[User:LarryFarma|LarryFarma]] 15:26, 30 June 2008 (EDT)

::::::While I completely agree with you that the 90/10 rule is somewhat intimidating (I even refrained from removing wikilinks to salted articles from talk pages because I feared that a casual inspection would make those edits look like "talk, talk, talk"!), it should be said that so far, 20 of your 20 edits were on this page. In other words, your contributions outside of this discussion amount to ZERO. This is an encyclopedia project (or at least it says so) and not a discussion forum. Making encyclopedia edits should be your first priority, not an afterthought. If I remember correctly (I have only paid little attention to this trainwreck), people with far better ratios also received 90/10 blocks for making just a few posts here. You on the other hand were given ''edit rights'' just so you could debate here. Look at me, I got more than a 100 edits (according to My Preferences), most of them non-talk, and I still can't edit at night. You have been treated ''extremely'' well, all things considered. It's time that you actually contribute to the site's primary purpose: Building an encyclopedia. --[[User:KevinM|KevinM]] 15:42, 30 June 2008 (EDT)

== removal of content from this page removes context of Lenski's second reply ==
I'm sure it's an oversight but Lenski, in his second letter, made several direct references to the discussion that has been removed from this page. Some of his comments thus appear inappropriately to lack context. I'm sure you did not intend to remove significant parts of this debate, especially when the result seems so one-sided.[[User:AndyMann|AndyMann]] 20:09, 26 June 2008 (EDT)
: Yes, it was an oversight. It was archived, but the archive was not linked to on this page. It has since been linked. [[User:Philip J. Rayment|Philip J. Rayment]] 22:53, 26 June 2008 (EDT)

==Archive Link?==

Can a link be provided to the archive for this page? Thanks. --[[User:DinsdaleP|DinsdaleP]] 20:48, 26 June 2008 (EDT)

Oops. Did my edits delete the earlier sections? If so, I'm sorry. Could someone restore the original? --[[User:Argon|Argon]]
:No, your edits were not a problem. It was the edits of those individuals who decided to use this talk page as an attack forum. [[User:Karajou|Karajou]] 21:02, 26 June 2008 (EDT)

I read this page a while ago - Lensky and ASchaffly's two-and-fro, and have since returned. Why is it that ASchaffly's second letter this time seems to have been edited to be a lot more polite than when I first read it? It makes Lenski's second reply seem unnecessarily rude. When I first read this I felt his tone was justified, now it seems out of place.
:I don't think the letter has been changed at all. [[User:HenryS|HenryS]] 22:54, 21 July 2008 (EDT)

== Whence Lenski? ==

Lenski's article was published in the PNAS, which is from the National Academy of Sciences. Just [http://www.google.com/search?q=%22national+academy+of+sciences%22+god Google their name and "god"] and see why they care so much about "proving" evolution: 93% are atheists! Maybe PNAS isn't a professional organization at all, but a fraternity designed to influence American public policy away from Christian principles. [http://www.stephenjaygould.org/ctrl/news/file002.html] [http://www.answersingenesis.org/docs/3506.asp] {{unsigned|Drochld}}

:I'm a little confused about the terminology of the survey. According to the 1998 figures, 7% had "personal belief", 72% had "personal disbelief", and 21% had "doubt (presumably equivalent to atheism) or agnosticism". I know what atheism and agnosticism are, but what does personal disbelief mean in this case? It sounds like agnosticism, but agnosticism is in a separate category. So what is it? Anyone know?--[[User:Frey|Frey]] 13:31, 28 June 2008 (EDT)
::If they're not believers, and they're not agnostics/doubters, then they're atheists. Atheism = disbelief. [[User:Bugler|Bugler]] 14:10, 28 June 2008 (EDT)
:::I find it doubtful that are more atheists than agnostics. Atheists are 100% certain that God doesn't exist. A good scientist is not 100% certain of anything. I think a survey with more clearly defined choices is called for.--[[User:Frey|Frey]] 23:34, 28 June 2008 (EDT)
::::Actually it is not true to say, ''Atheists are 100% certain that God doesn't exist'' as Conservapedia's article says; [[Weak Atheism]]. Many more scientifically-minded atheists would follow this point of view for the very reasons you state - ''A good scientist is not 100% certain of anything.''--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 12:37, 29 June 2008 (EDT)
:::::I think the distinction to be made here is between personal belief and what can be proven. It is possible to put forward a definition of God that cannot be tested and is therefore neither provable nor falsifiable, however that wouldn't mean an individual couldn't have a personal belief (or disbelief) in God. If I can be forgiven a pop culture reference, I can't prove I don't live in [[The Matrix]] but I have a personal belief that I don't.--<font face = "Verdana">[[User:Boreas|Boreas]]<sup> [[User_Talk:Boreas|'''talk''']]</sup></font> 13:34, 29 June 2008 (EDT)

I'm guessing that 100% of creationist are theists...so? Does this invalidate THEM in any way? No, it does not. I don't see how this line of discussion is pertinent or constructive in any way. --[[User:RobinGoodfellow|RobinGoodfellow]] 14:58, 28 June 2008 (EDT)

I assume that Bugler's ignoring of Gnostics such as myself was not an attempt to polarise the community into more easily distinguishable sects. {{unsigned|Scholl}}

== Qualification ==

It is quite clear why Lenski is annoyed at requests for data and questions about the validity of his work. It is that none of those who are asking have any background in biology (please correct me if I'm wrong) and are as such not qualified to evaluate his work.

If you have questions or doubts about the research, then the *only* way you are going to get any useful result is by finding a biologist who perhaps shares your concerns and asking them to evaluate the research. Do you think, as a historian, that you wouldn't be annoyed by someone with no background in your field questioning your research, having apparently not even thoroughly read it? [[User:Boatie|Boatie]] 08:24, 1 July 2008 (EDT)

: No, Boatie, I'm confident your suggested reason has nothing to do with it. I requested making the data available for review by the public, including experts: "I'd like to review the data myself and ensure availability for others, including experts and my students."[Conservapedia:Lenski dialog] You can reread Lenski's negative response yourself.--[[User:Aschlafly|Aschlafly]] 08:31, 1 July 2008 (EDT)

:: But surely if there are any experts with specific requests then Lenski would provide any additional information that they require, as he has indicated. The fact that he is clearly offended by the initial requests and their implications means that he is now unlikely to cooperate with you, or anyone affiliated with this website, I suspect. [[User:Boatie|Boatie]] 09:28, 1 July 2008 (EDT)

::: Boatie, you're awfully naive if think the withholding of the underlying data from public scrutiny has anything to do with anyone being "offended".--[[User:Aschlafly|Aschlafly]] 09:40, 1 July 2008 (EDT)

:::: I hope you noticed that I didn't resort to petty name-calling. It's not helpful. I didn't suggest that data was being withheld to prevent public scrutiny. Merely I suggested that Lenski is probably not inclined to comply with the demands of a non-expert whose repeated requests may not even be sensible. Note that the report was submitted for peer review, and the paper involved will have since been read by many qualified biologists. [[User:Boatie|Boatie]] 09:46, 1 July 2008 (EDT)

::::: Boatie, you're clueless. People withhold data from public scrutiny for one obvious reason: to prevent the public (including experts) from scrutinizing their work. Feigning offense has nothing to do with it.--[[User:Aschlafly|Aschlafly]] 09:53, 1 July 2008 (EDT)

:::::: That's simply not true, and has been raised plenty of times, Lenski is not necessarily with holding data from any experts, he's only failing to supply to *you*. Find an *actual biologist* with concerns about his work and maybe things will be different. Further name-calling does nothing to help your argument. [[User:Boatie|Boatie]] 10:00, 1 July 2008 (EDT)

:::::: Scientists prefer specifc questions over general ones. In the initial email exchange you had a couple of specific questions that were answered specifically. Asking a general question will only result in "Do you have a question?" Saying "I want to see the data" is not a question. Saying "I want to see the data because I have a question about <i>this specific issue </i>I have" is more likely to get an answer. Prof Lenski has stated multiple times that he would provide samples etc to qualified people if they have questions on his research. Since no one here has demonstrated the required credentials and filed the proper paperwork to obtain a sample of prof lenski's work, this hand waving is all for naught. [[User:Toaster1|Toaster1]] 23:50, 1 July 2008 (EDT)

:::::: Aschlafly, I think you're rather clueless in this matter yourself. I've read the e-mail correspondence and I don't think Lenski is being evasive or deliberately withholding data from you or making claims he cannot back with evidence. When you think he's holding stuff back, you should be specific about what you feel is missing and why you think that is important for the claim and specifically ask for that data. You can run around screaming about something not being true, but that won't help much in the matter at hand. But then again I get the feeling you really don't want the data to be there at all, but rather make sure everyone follows you in believing the data doesn't exist to begin with. You put too much emphasis on the fact Lenski ''must'' be withholding something, without actually stating what it is and why it would disprove his claims. -- (unsigned by User:DeLight) 09:26, 3 July 2008 (EDT)

::::::: We've been extremely specific about which data are being withheld. See [[Richard Lenski]]. And I found Lenski to be quite clear that he's not going to release his underlying data for public review, even though it was publicly funded. Perhaps you think Lenski is perfect and there is no chance of flaws in his work that the public might discover when the underlying data are released, but such a position is obviously absurd.--[[User:Aschlafly|Aschlafly]] 09:35, 3 July 2008 (EDT)

:::::::: Sorry for the late reply, but [[User:DeanS|one of your sysops]] found it necessary to block me following my previous critique. To answer your statement, I don't think Lenski is perfect, I hardly know the man, but I do know what I have read in the correspondence between him and you. I don't agree he's not willing to share his work for public review, because he is willing, yet he has some well-founded conditions that should be met first. This is a lack of willingness to share with ''just anyone'', and rather sensible in science. Do you really think it's wise for all scientists to send samples of their work (especially in biology) to any Tom, Dick and Harry who asks for it, without knowing if they can actually handle the materials safely?
:::::::::Three things about your comment: First, it is a sensible question to ask a scientist for proof of his research when that scientist is getting government funding for his research; second, it is wise for them to send samples of their work; they do send them to other scientists, so why not the general public (unless they have something to hide); and third, you were blocked for a reason, the least of which is a German proxy address to hide your own, which you are not permitted to do so...so bye again! [[User:Karajou|Karajou]] 04:25, 7 July 2008 (EDT)

:::::::::: Just to answer a question you posed Karajou "second, it is wise for them to send samples of their work; they do send them to other scientists, so why not the general public (unless they have something to hide)" scientists are liable for the samples they provide. Thus the reason for MTAs and other inquiries to purpose of use for the samples. Most work and materials discovered or used by a scientist are not owned by the scientist, the institution normally has control over distribution beyond the scope of the grant or funding source. It would be foolish for a scientist to hand out potentially infectious material to anyone who asked for it, thus the reason why a qualified institution must used to receive the samples. I work part time for a company that does biorepository services, LN2 -80 and other long term cold storage. We have to maintain a license with the FDA and CDC for the bacteria and viruses that we hold. So to sum up, if the requestor does not have proper credentials for exploring the sample the scientist is legally obligated to withhold said samples till the requester meets qualification.
::::::::::To keep using the tax funded research claim is misleading. The military is tax funded and most of its operations are not open for public, most work by the CDC and HHS is funded by tax dollars and once again is not available for the general public.--[[User:Able806|Able806]] 10:33, 7 July 2008 (EDT)

==MTA==
Did anyone ask Lenski if a MTA is required by MSU to provide his data? Most MTAs are used for specific materials like cultures and such but a few are now requiring them for actual analysis results. Most universities now require specific permissions to be granted for scientific research due to the fear that such information could be used in inappropriate ways. Perhaps Lenski is bound by the university until a MTA is filed or feels that it is a waste of time to supply data that would only be understood by a few people here, which to my knowledge, care not to spend the time to analyze it. I could be wrong but I know I would not supply my test results to anyone who asked for it without understanding what they intended to do with it. I could be held liable for what they did with the information.

As for the length of time for the peer review, it is obvious that many here do not understand the process nor do they understand the difference of peer review of a publication verses replication of an experiment. Most experiments are not replicated for several years due to the need for funding. Peer review of publications is based on application of sound analysis techniques and clear summery of data analyzed. Not an actual analysis of the data. While I do not review papers, my wife does and it is not at all what has been implied here. I have published in a few journals, each with different standards and different times for the publication to go to press. Lenski's experiment is not complicated and only required minimal tests, therefore it would be expected to be a quick peer review of the publication due to the simplicity. If he performed tests using animals, or followed metabolisms then the peer review should have taken much longer. However, due to the few tests that he performed, all of which are accepted standardized protocol for research microbiologists, the need to dig deeper was not required. So to sum up, few experiments, easy study, and simple conclusion equals fast turn around for publication. If you read the paper, Lenski did not make any claims about anything other than the development of the bacteria's ability to metabolize citrate, pretty simple.--[[User:Able806|Able806]] 10:43, 2 July 2008 (EDT)

== Bad motive redux ==

I was blocked for two weeks for this post:

Let's face the truth, there is no real desire here for Andrew Schlafly or anyone on Conservapedia to get the raw data. The reason that this is even an issue is because placing this demand and getting no response somehow makes Lenski look bad and therefore automatically discredits him and his research and therefore the theory of evolution. The position of Mr. Schlafly is that the Bible is inerrant and the Genesis creation story is true. No amount of scientific data is going to change that. So why argue with him? MAnderson 10:05, 18 June 2008 (EDT)

Mr. Schlafly has since posted these comments:
“At some point, StatsMsn, an open mind requires admitting the possibility that the data have not been made available because there is concern about what an independent reviewer may conclude from it. Are you open-minded enough to admit that possibility? It's a waste of time arguing with a closed mind, and if you won't admit at least that possibility then this discussion is unproductive”.--Aschlafly 09:00, 19 June 2008 (EDT)
"If I'm reading the dates on the front of this particular paper correctly, I think peer review was a mere 15 days or so. Looks to me like a rubber-stamp process for this subject matter despite making claims that were reported as being newsworthy." --Aschlafly 16:47, 19 June 2008 (EDT)
"Don't pretend that Lenski welcomes independent review of the data." --Aschlafly 15:15, 19 June 2008 (EDT)

He has said these things even though the data and even the E. Coli samples are available to qualified researchers. Really my original post was dead on correct! He doesn’t want the data and merely wants to create the appearance of impropriety on the part of Lenski to discredit him. [[User:MAnderson|MAnderson]] 11:16, 2 July 2008 (EDT)

''Don't pretend that Lenski welcomes independent review of the data.'' I don't think MAnderson is claiming that Lenski ''welcomes'' independent review of "the data", nor does he need to ''welcome'' it in order to act properly. He needs to make it available where it will "allow others to replicate and build on work published in PNAS". It is evident that you do not wish to either replicate the experiment (which, if Lenski made it up, would fairly conclusively prove him a fraud) nor do you wish to review it in any meaningful way (which may build on the work by revealing its faults). That is the PNAS requirement. It appears that Dr. Georgia Purdom of "Answers in Genesis" has plenty of data to perform her intended review[http://www.answersingenesis.org/articles/2008/06/14/news-to-note-06142008] (no doubt very negative) of Lenski's research.

''"At some point, StatsMsn, an open mind requires admitting the possibility that the data have not been made available because there is concern about what an independent reviewer may conclude from it"'' Agreed. Can we test that hypothesis? It hasn't been tested so far (unless Dr. Purdom asked for data, in which case its been falsified) because we have not seen any prospective independent reviewer ask for data. You are not a reviewer (independent or otherwise) unless you review and you are not a ''prospective'' reviewer unless you ''seek to review''. Why not develop a plan (with AiG or the Discovery Institute) of just what you are going to do with the data, beyond that already published of course, and ask for the data that lets you do that? Until you have that plan it is abundantly clear that you are not a "reviewer" and have no entitlement to extra (unspecified by you) data. --[[User:Billd|Bill Dean]] 08:50, 3 July 2008 (EDT)

== Why does it matter? ==
Hello Conservapedians-
It seems like you are making a huge fuss about Leski's experiment, as if you do not want it to be true.I mean, of course it should be subject to peer review, but it JUST came to the general public. Give it time. However, why exactly does it matter, anyway?
There are several dozen OTHER recorded examples of the following:
--Speciation
--Beneficial Mutation
--Mutations adding information
So, while important, it is not like Lenski's data shows us anything new.
If you would like examples of such, just ask. I assume, however, that you are already aware of the observations, and
there is something important
{{unsigned|KevinF}}
: It's mainly Aschlafly that pursued this. Many others, including me, disagreed with that course. That was simply the first of several mistakes you made, and the others relate to you having almost no idea of what creationists believe. Do you support the concept of criticising an idea without knowing much about it? Because that is what you are doing. Creationists ''accept'' speciation. They also ''accept'' beneficial mutations. The one that they ''don't'' accept is mutations adding information, because it is ''not'' observed (apart from some questionable claims, such as this one of Lenski's). I won't ask for examples simply because I've been down this road before, of having supposed examples provided, only to have them not stack up when investigated. When Richard Dawkins was asked for examples, ''he was unable to supply any''. And why do you think Lenski's research was cited as answering creationist criticisms? If creationist criticism has been answered so much before, so that this is nothing new, then why make a deal about it as though it ''is'' something new? [[User:Philip J. Rayment|Philip J. Rayment]] 22:44, 2 July 2008 (EDT)

::While Lenski is certainly being quite snarky in his responses, Mr. Aschlafly does not seem to understand that in an experiment like this, the "raw data" isn't something that can be printed out and mailed. The raw data is ''the actual bacterial colonies with the mutation''. Thus, the raw data is completely useless to anyone who does not have a properly equipped biological lab, and indeed is illegal to provide to anyone without a properly equipped biological lab since E. coli bacteria are a potential disease vector. --[[User:JacieCady|JacieCady]] 19:42, 4 December 2008 (EST)
:::No the bacterial colonies are the samples. The raw data are the uninterpreted measurements and observations. This claim is little more than misdirection to justify not providing the data. If I tell you my car can stop on a dime & I know this because I have tested it, my car and a dime are NOT the raw data. The raw data would be the records of the attempts to stop on a dime including records of where the car stopped in relation to the dime. If I was asked for this data and said that I cannot send you my car because you don't have a lock up garage, I am merely dodging the question.[[User:LowKey|LowKey]] 08:06, 5 December 2008 (EST)

:::: Well put, LowKey. FYI, a chart summarizing how the data were undisclosed is [[Lenski|here]].--[[User:Aschlafly|Aschlafly]] 09:37, 5 December 2008 (EST)

:"When Richard Dawkins was asked for examples, ''he was unable to supply any''"—Oh, give me a break. Do you honestly expect someone to be able to come up with such information on the spot? --<sub>[[Special:Contributions/AutoFire|<font color= 'black' face= 'OCR A Extended'>trans</font>]]</sub>[[User:AutoFire|<font color= 'red' face= 'OCR A Extended'>Resident Transfan</font>]]<sup>[[User Talk:AutoFire|<font color= 'black' face= 'OCR A Extended'>form!</font>]]</sup> 23:09, 2 July 2008 (EDT)
::Good point, AutoFire.--[[User:JackH|JackH]] 17:15, 4 December 2008 (EST)
:::He shouldn't have to "come up" with anything "on the spot". He had claimed the existance of examples many times, he should have already known of ''at least one'', but he couldn't. This is like the editor of a car magazine claiming that the new BMW has many improvements over the previous model, but when asked for one can’t supply any. Nobody would claim it was unfair to expect him to come up with one on the spot.[[User:LowKey|LowKey]] 17:56, 4 December 2008 (EST)

::::http://www.youtube.com/watch?v=-uz1CiDDIq4 According to Dawkins he stopped to confront the interviewers. {{Unsigned|Vuiasl}}---22:21, 7 December 2008

*That link goes to a video that supplies no information about the topic. It merely says questions to Dawkins are hoaxes by Creationists, yet doesn't provide one example or proof. --[[User:TK|'''₮K''']]<sup>[[User_Talk:TK|/Talk!]]</sup> 00:56, 8 December 2008 (EST)

:The interview made Dawkins look a fool. Of course he has attempted to explain it away. The CMI website provides plenty of info about this, it even has a timeline showing how much time Dawkins had to come up with something, so even ignoring all of the above "on the spot" is still wildly inaccurate. It was more a case of Dawkins "realising" he might be talking to creationists because evolutionists would have accepted the elephant-hurling without challenge. Also, the interview was ''11 years'' ago and he ''still'' hasn't provided the examples as asked {<small>With the possible exception of Lenski's experiment, which he ''may'' have mentioned. But the [in]validity of that is the subject at hand here in the first place. [[User:LowKey|LowKey]] 18:35, 8 December 2008 (EST)</small>}, so the "on the spot" objection is invalid on that account alone.[[User:LowKey|LowKey]] 18:28, 8 December 2008 (EST)

::*I'm confused here. Everyone should know by now Dawkins is a fraud. As they should all know my opinion of him. That video didn't seem a bit different from the two times I have observed lectures by him, and he wondered off his prepared remarks. Results were the same as for Obama. Poor. (not Ed) --[[User:TK|'''₮K''']]<sup>[[User_Talk:TK|/Talk!]]</sup> 18:39, 8 December 2008 (EST)
:::Ah but everyone should also know that evolution is an invalid conclusion, but millions believe it to be a "fact". Scripture clearly tells us that people are blinded.[[User:LowKey|LowKey]] 18:48, 8 December 2008 (EST)
::::What Dawkins does or doesn't do is hardly of any importance. Evolution doesn't rely on him, or what he does and doesn't do in interviews. It falls flat on [[Counterexamples to Evolution|its own]]. [[User:RodWeathers|- Rod Weathers]] 18:54, 8 December 2008 (EST)

==Hsdebater comment==
I think Schlaffy misses the point of why Lenski didn't give him the experiments. He might think it's a conspiracy to silence him, but I (no offense schlaffy) beleive, like many others it seems on this site, it to be the simple explanation that you're not a scientist, and probably never taken a collegecourse on microbiology, evolutionary biology,and just plain biology.--[[User:Hsdebater|Hsdebater]] 10:55, 15 April 2010 (EDT)

: Please learn how to spell basic words like "believe" (it's not "beleive"), and then realize that I don't think Lenski made all his taxpayer-funded data available for ''any'' public scrutiny, which of course would have included many knowledgeable people.--[[User:Aschlafly|Andy Schlafly]] 11:00, 15 April 2010 (EDT)

::What do you mean i just read his paper in my science class just yesterday, and i have also read it outside of class.--[[User:Hsdebater|Hsdebater]] 13:02, 15 April 2010 (EDT)

::: So you apparently read his ''claims'' ... but where's the data underlying the claims? Despite my repeated requests, and despite the taxpayer funding of the project, I don't think he ever made all his data available for public scrutiny.--[[User:Aschlafly|Andy Schlafly]] 13:08, 15 April 2010 (EDT)

::::So I went ahead and formatted, hope thats alright. [http://www.pnas.org/content/105/23/7899/suppl/DCSupplemental Is this] the extra information you were looking for? --[[User:EmersonWhitecp|EmersonWhitecp]] 17:09, 15 April 2010 (EDT)

:::::I don't see real data in your link or answers to the data requests that have been outstanding for nearly two years at [[Richard Lenski]]. Do you?--[[User:Aschlafly|Andy Schlafly]] 17:23, 15 April 2010 (EDT)

::::::There is a very small link you must click on to get to the 2 page PDF (1.25 more like it) with the data. --[[User:EmersonWhitecp|EmersonWhitecp]] 17:27, 15 April 2010 (EDT)

::::::: (edit conflict) Which specific data requested nearly two years ago in [[Richard Lenski]] do you claim is contained in the mere 1.25-page of text in the pdf?--[[User:Aschlafly|Andy Schlafly]] 17:34, 15 April 2010 (EDT)

You can link directly to the PDF.....--<big>[[User:TK|'''ṬK''']]</big><sub>/Admin</sub><sup>[[User_Talk:TK|/Talk]]</sup> 17:30, 15 April 2010 (EDT)

:[http://www.pnas.org/content/suppl/2008/06/02/0803151105.DCSupplemental/0803151105SI.pdf PDF in question] To be honest I can't figure out what more information you would want than what was in the original paper, your point by point rundown doesn't make sense to me. I was just trying to be helpful, not trying to make a point or anything. --[[User:EmersonWhitecp|EmersonWhitecp]] 17:46, 15 April 2010 (EDT)

::If you want to believe whatever a professor says without verifying it, then you don't need to look at any underlying data. But do you give the Bible at least equal time and trust?

::It took me only a minute or so to look at the first request for data in [[Richard Lenski]] (concerning turbidity), and then search the pdf for "turbid" for me to observe that the actual data are not there.--[[User:Aschlafly|Andy Schlafly]] 19:08, 15 April 2010 (EDT)

:::That data was in the paper, [http://www.pnas.org/content/105/23/7899/F1.expansion.html Fig. 1] he ran 5 trials and presented the mean and CI95 which is standard for the field. Do you suspect that he miscalculated the mean or standard deviation? I'm not sure what "higher definition" data underlying the figure you might want. --[[User:EmersonWhitecp|EmersonWhitecp]] 19:30, 15 April 2010 (EDT)

Stem cell

2010-04-15T21:59:13Z

EmersonWhitecp: Less peacock, more science

A '''Stem cells''' is a cell that has the ability to differentiate into two or more different types of mature cells within the body.
When a stem cell divides it can divide in such a way as to produce two new daughter stem cells, or one or both of those cells could become more specialized. Stem cells in a mature [[organism]] serve to produce types of cells that are constantly in need of replacement (such as sperm cells) or two repair unexpected damage. Stem cells have a sort of hierarchy of potential, with some having the ability to transform into a broader range of final cell types.

*Broadly speaking, a stem cell is one that – in the course of [[cell division]] and increase in the numbers of cells – is able to reproduce itself and also mature into various specialized types of cells. The stem cell with the greatest potential (totipotential) is the fertilized [[egg cell]], which is capable of developing into a complete organism. [http://www.21stcenturysciencetech.com/articles/winter01/stem_cell.html]

==Controversy over human embryonic stem cell research==
Wolfgang Lillge, M.D. wrote:
*The question of stem cells is currently the dominant subject in the debate over [[biotechnology]] and [[human genetics]]: Should we use [[embryonic stem cells]] or [[adult stem cells]] for future medical therapies? [http://www.21stcenturysciencetech.com/articles/winter01/stem_cell.html]

==See also==

*[[Stem cell research]]

[[category:Biology]]

HeLa cells

2010-04-15T21:52:49Z

EmersonWhitecp: To test the vaccine you would need immune cells.

'''Hela Cells''' are the first human [[cell line]] maintained in a laboratory. They were derived from cervical cancer cells obtained from cancer patient Henrietta Lacks. They were taken without permission<ref>As discarded medical waste, there is no legal obligation to obtain patient consent. Therefore, no law was broken.</ref> and were delivered to a George Gay, the then head of the cell culture laboratory at Johns Hopkins Hospital. He was successful in cultivating and propagating the cell line. Most notably, these cells were used in the development of Jonas Salk's polio vaccine.<ref>[http://helacells.com/ HelaCells.com]</ref>

==References and notes==
{{reflist}}

[[Category:Medicine]]
[[Category:Biology]]

Conservapedia talk:Lenski dialog

2010-04-15T21:46:48Z

EmersonWhitecp: /* Hsdebater comment */

Conservapedia talk:Lenski dialog

2010-04-15T21:27:02Z

EmersonWhitecp: /* Hsdebater comment */

Talk:Richard Lenski

2010-04-15T21:19:59Z

EmersonWhitecp: Archived as per my topic yesterday

[http://conservapedia.com/index.php?title=Talk:Richard_Lenski/archive1 Archive 1]

Talk:Richard Lenski/archive1

2010-04-15T21:15:06Z

EmersonWhitecp: Created page with '==Formatting== I borrowed a template from another wiki which might make the data section a bit easier to comprehend. I will include it here pending approval of senior sysops. [[U…'

==Formatting==
I borrowed a template from another wiki which might make the data section a bit easier to comprehend. I will include it here pending approval of senior sysops. [[User talk:MargeryCampbell|Marge]] 12:03, 28 June 2008 (EDT)

Looks great. Please install in the entry as desired.--[[User:Aschlafly|Aschlafly]] 12:55, 28 June 2008 (EDT)
:Okay, I've moved it. I've also cut it from this page for economy's sake. [[User talk:MargeryCampbell|Marge]] 13:07, 28 June 2008 (EDT)
::Actually it makes the article look amaturish. For starters you have written in capitals and you have not explained why the missing data is significant which is the point of the side-by-side template to do a full rebuttle. [[User:DanielB|DanielB]] 19:44, 28 June 2008 (EDT)

:::I agree. A discussion specifying what one expects from the 'missing' data and what usefulness such information would likely shed is necessary.--[[User:Argon|Argon]] 12:57, 30 June 2008 (EDT)
::::I agree that it is necessary to establish exactly what is being asked for in the terse comments on the right hand side, sadly such a discussion could get the majority of the contributors banned for the 90/10 rule. I myself have not contributed much to this question recently as a result of this rule. Could the powers that be explicitly suspend this rule on this issue so that the question may be freely discussed? --[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 13:12, 30 June 2008 (EDT)

== Listing fields ==

I'm not a parodist, though I did make a mistake on what a CV is.

== Suggestion: Disagreements with E Coli paper should go to a new section? ==

Shouldn't this be a brief bio of Lenski, and a link to the controversy over the paper, including the discussions and the emails, be part of that page instead of here? It looks pretty bad putting it on the main page. 18:11, 30 June 2008 (EDT)
On the other hand, after doing some research, I don't think it's standard for faculty to put degree fields in a list of their degrees.

I googled "MSU biology", then went over the "Faculty List A-G". Here is what I found:

No list of degrees: 2
List with fields: 3
List without fields: 12

Finally, Oberlin is a liberal college, and they do focus mostly on liberal arts. [[User:Drochld|Drochld]] 14:26, 29 June 2008 (EDT)

==Template / formatting==
Out of interest, I help to administer a private wiki where I work, and think this template is quite nice. Might I ask where you found it, and what (if any) associated copyright restrictions there are on it? [[User:Henry8th|Henry8th]] 15:49, 29 June 2008 (EDT)

: Really, "Henry8th"??? That's an amazing coincidence you describe: you just happen to administer a "private wiki" at "work". Before wasting people's time with your silliness, how about convincing us a bit more of the earnestness of comment, as in providing the wiki version number, the type of your employer and the location of your "work". I'm sure the wiki developers who freely donate their efforts for use by all would be thrilled to learn of your profitable use.--[[User:Aschlafly|Aschlafly]] 16:33, 29 June 2008 (EDT)
:: We run Mediawiki 1.6.7 (yes, I know we're incredibly out of date, but we can't upgrade to a newer one as that would require PHP5, whereas we need that server running PHP4 to support other older software). I make it a habit not to disclose too much personal information on the internet, I'm afraid, but I'm a PhD student at a UK university and I help to administer a wiki run by my research group. By "private" I mean "accessible only to people within my research group"; we find that a wiki is an efficient way for us to edit documents collaboratively. [[User:Henry8th|Henry8th]] 16:47, 29 June 2008 (EDT)
:: The copyright policy here says "Conservapedia grants a non-exclusive license to you to use any of the content (other than images) on this site with or without attribution".[[User:JPohl|JPohl]] 11:53, 30 June 2008 (EDT)
:::However, since it was admitted above that the template is not CP's creation, it should first be established whether or not the template was used in a correct way (and if any attributions are needed) before others borrow it from here. [[User:ZTak|ZTak]] 12:06, 30 June 2008 (EDT)
::::I would ask the same question as ZTak above. Firstly, from a legal point of view I would want to be absolutely sure that any code I might upload to a server at my university was properly licensed (we have regular software audits, of course). Secondly, from an ethical point of view I would like to make sure that I can properly credit the original author of the template. As someone whose work involves writing computer programs, I certainly wouldn't appreciate it if someone took software I'd written and didn't attribute authorship correctly. [[User:Henry8th|Henry8th]] 14:36, 30 June 2008 (EDT)

== Fact checking could use some work on the omissions section ==

I strongly encourage editors to confirm that the topics on this entry's 'omissions' section page really refer to "data not provided" and do not reflect the lack of understanding of the research. At a bare minimum it is necessary to completely read the actual article. 'Skimming' it quickly is not fair to the goals of this wiki or Lenksi's lab. To at least be diligent, I recommend that the authors of the "omissions" section go to Lenksi's lab web page here (https://www.msu.edu/~lenski/), and peruse (read, not skim) the many papers related to the Long-Term Evolution project that are referenced in the current paper.--[[User:Argon|Argon]] 11:57, 30 June 2008 (EDT)

== I do not understand why my last edit was reversed ==

It seems to be common practice (and therefore not "odd") to not list what fields faculty majored in, and Oberlin is very liberal. [[User:Drochld|Drochld]] 12:34, 30 June 2008 (EDT)

I'm not certain what 'liberal' has to do with anything and "odd" has pejorative overtones. Rather than worry about 'oddness' why not investigate the degrees? In his graduate program Lenski studied insects and evolution and around 1983, worked with Bruce Levin, moving into the study of microbial evolution.--[[User:Argon|Argon]] 12:51, 30 June 2008 (EDT)

== This man is nothing but a farce ==

Why must we, the children of God, even acknowledge this liberal atheist (as if there is any other form of an atheist) on our glorious site? We are only feeding his overinflated ego by doing so. --[[User:Dexter111344|Dexter111344]] 12:52, 30 June 2008 (EDT)

== A problem with: "Lenski is best known for his claim to have observed [[evolution]] of [[E. coli]] in a long-term laboratory study," ==

This recent study is but one of many papers by Lenksi ''et al'' regarding the evolution of bacterial populations in continuous culture. He is best known professionally for his ''in vitro'' experiments studying the population dynamics of genetic adaptations in bacteria and other studies in microbial evolution.--[[User:Argon|Argon]] 13:14, 30 June 2008 (EDT)

== don't clutter this entry with meaningless edits???? ==

The topic of the page is 'Richard Lenski'. I added additional bibliographic information about Lenski's professional awards and they are reversed as "meaningless edits"? And the 'odd' comment remains despite the fact that it's common to leave the subjects of the degrees out of web pages?--[[User:Argon|Argon]] 13:43, 30 June 2008 (EDT)
:Yes, various links to things such as [[data]] as well. I thought data was central to the question at hand? Why not link to it (such as it is)? And a mention of his work with virtual organisms seems relevant - especially as it's mentioned again at the end.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 13:47, 30 June 2008 (EDT)

And now I'm a "Lenski supporter"? Anyone who actually read the paper and referenced the pertinent section of the article that clearly specified the glucose concentration used is a supporter? I think that addition of 'Lenksi supporter' is needlessly inflammatory. Furthermore, with regard to the question: WHERE IS THE DATA MEASURING OR CONFIRMING THE 25 MG/LITER GLUCOSE? DID THAT CONCENTRATION EVER CHANGE?", I also wrote: "A weighed amount of glucose is mixed into the medium. The paper states that the concentration listed was used in the media throughout the continuous subculturing experiment." and that got removed. Resubmitted.--[[User:Argon|Argon]] 18:14, 30 June 2008 (EDT)

== shouldn't we move the E Coli paper discussion to a separate page? ==

It looks really cheezy to have this right on Lenski's biography, very unprofessional.
Just have a link and move all that discussion to something like Lenski_E_Coli_controversy,
don't erase a thing. [[User:Encinocathy|Cathy]] 18:11, 30 June 2008 (EDT)

== Wrong format for a debate ==

Ignoring all the other issues with this "article", the side-by-side table is really not made for a discussion. Maybe move that part to a debate page? It's quite silly to see an encyclopedia article doing a question-and-answer session with anonymous participants. --[[User:KevinM|KevinM]] 18:18, 30 June 2008 (EDT)
:Agreed. It's silly to post the page without doing the basic research. Better to corral the innuendos into debate pages.--[[User:Argon|Argon]] 18:20, 30 June 2008 (EDT)
::Also, we have yet to discovere the proper attribution for the side-by-side table, and as such it should be taken down or it might constitute a violation of copyright. [[User:ZTak|ZTak]] 18:25, 30 June 2008 (EDT)
:::Given that [[User:MargeryCampbell|Marge]] said she took the template from elsewhere, it would presumably be straightforward for her to tell us where she found it. Given that information I'd happily aid the project by checking out this other wiki's copyright policy before reporting back here. [[User:Henry8th|Henry8th]] 18:45, 30 June 2008 (EDT)
:My issue is mostly about using a left/right table when the left side is basically just the intro section while the right side is suddenly filled with a weird pseudo-debate that goes back and forth. It would be better to do it like this:
==Visual Inspection==
===Lenski's Paper===
(quote)
===Discussion===
(back and forth; not as debate, but in more encyclopedic "A claims B, to which C points out D." style)

==Study Omissions==
(quote)
:And so on. It would make the article more readable. And it would have the added benefit of NOT USING SO MANY ALL-CAPS SENTENCES, BECAUSE DESPITE WHAT SOME SITES SAY, CAPSLOCK IS NOT THE CRUISE CONTROL FOR COOL. --[[User:KevinM|KevinM]] 19:12, 30 June 2008 (EDT)

:Furthermore, it would help review the status of claims rather than deleting them outright: Here's a most recent example: ''(removed least important point, which was obscuring more important ones)" Aschlafly. Revision as of 19:34, 30 June 2008''
:I think it is an important point in two senses: 1) If the level of glucose was not growth limiting then Cit+ mutants might not have been discovered. It is an important feature of the experiment in this instance. 2) It's clear that the glucose concentration was indeed disclosed. How about creating a section titled "Data someone repeatedly claimed was undisclosed but was actually found by looking" and move the deleted test there?--[[User:Argon|Argon]] 20:24, 30 June 2008 (EDT)

== Atheist Lobbying Organization ==

Should this remain in the article, given that it was inserted by an identified (and subsequently banned) parodist? --[[User:Benp|Benp]] 20:52, 30 June 2008 (EDT)

: Anything wrong with the cites for it? By the way, not every block is proper. If in error, and I don't know if this one was, the block is reversed.--[[User:Aschlafly|Aschlafly]] 20:57, 30 June 2008 (EDT)

::There's nothing wrong with the cites, per se; they just don't quite cover the assertion. The cited sources do a good job of establishing that the PNAS is largely atheistic (something which is pretty well-known anyway.) They don't really cover any "lobbying" activities, though. --[[User:Benp|Benp]] 21:04, 30 June 2008 (EDT)

::: OK, based on what you said, how about taking out the "lobbying" reference only? As to the rest, it's informative: most people don't know how atheistic the PNAS is.--[[User:Aschlafly|Aschlafly]] 21:05, 30 June 2008 (EDT)

::::Will do. --[[User:Benp|Benp]] 21:06, 30 June 2008 (EDT)

== Maybe need to add another section ==

It would probably be better to split the biographic information from the discussion of the letters exchanged with A. Schlafly. Perhaps a section titled: "Interactions with Andrew Schlafly" (or "site owner") would better hold that aspect.--[[User:Argon|Argon]] 21:05, 30 June 2008 (EDT)

== e-mail ==

For public interest, could we at CP view the e-mail regarding the template here? If the claim in the e-mail has merit and further measures are pursued, it does not seem fair that the whole site should be punished for one man's refusal to remove the template. Perhaps we could see the e-mail and discuss whether or not the claim is valid. [[User:ZTak|ZTak]] 22:04, 30 June 2008 (EDT)

==Professor?==
''Is'' Lenski an actual professor? I know there are plenty of people who exaggerate their status ad pretend they're something they're not. I wouldn't be surprised at all if he's one of them, given what we know of him so far. Have we seen his credentials? [[User:TonyT|TonyT]] 08:26, 1 July 2008 (EDT)

:TonyT I was about to give you a serious response, but then I realized that you have to be joking so thanks for making me laugh. [[User:Rellik|Rellik]] 15:30, 2 July 2008 (EDT)
::He has been blocked as a parodist already, so don't bother responding. I'm thinking of removing this nonesense. [[User:HenryS|HenryS]] 15:37, 2 July 2008 (EDT)
:::So has 'Rellik'. Isn't it sad to see two trolls having a conversation? [[User:Bugler|Bugler]] 16:35, 2 July 2008 (EDT)

==Digital Organisms==
Lenski is famous for two things. His work with his work E. coli and his work with digital organisms. The work with digital organisms is the work referred to in a somewhat unclear way at the bottom of the page. I have twice tried to mention this other important aspect of his work and twice been reverted. This time the edit was called "Liberal Claptrap"!! One would have thought that, in an article about Richard Lenski, mention of what he ''actually does'' would be important and not "Liberal Claptrap".--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 09:13, 1 July 2008 (EDT)
:If I get no response, presumably I can assume it was reverted in error and I can put it back in?--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 11:47, 1 July 2008 (EDT)

::What did he do with [[E. coli]], and what is a "[[digital organism]]"? --[[User:Ed Poor|Ed Poor]] <sup>[[User talk:Ed Poor|Talk]]</sup> 15:39, 2 July 2008 (EDT)

:::Ed, I think British is talking about the twenty or so years Lenski has been experimenting with and growing up 12 E. coli cell lines. This last bit with the citrate mutation is one entry among twenty years. -- [[User:Aaronp|Aaronp]]
::::Richard Lenski is a well known scientist. He is well-known for his 20-year project on [[E. coli]]. (I must say that I don't know how to respond to Mr Poor's question, "What did he do with E. coli" as the entire Lenski debate has been about his work with E. coli.) He is '''also''' well known for his work with [[Digital organisms]]. The final part of the existing article sort of talks about this in a rather confusing manner. Given that he is well-known for '''both''' these two things and that the article is about him, I had thought it would be a good idea to mention them both.--[[User:British_cons|British_cons]] [[User_talk:British_cons|(talk)]] 08:23, 3 July 2008 (EDT)

== Release data to other [[evolutionists]]? ==

The paper says that only two people analyzed the data: Lenski and a grad student whom I presume acts under his direction and control.--[[User:Aschlafly|Aschlafly]] 15:59, 2 July 2008 (EDT)

He says in his email that he will release the E. coli samples to a competent scientist who asks for them. How is that no agreeing to release the data to other evolutionists? -- [[User:Aaronp|Aaronp]]

:Lenski does say that in his email. He didn't say that he wouldn't release the data to a competent scientist that held creationist views. Really at this point a competent scientist with creationist credentials needs to step forward. [[User:MAnderson|MAnderson]] 16:13, 2 July 2008 (EDT)

::Can we be more clear about "data" and "samples"? The point is whether anyone but his cronies has tried to [[replication of results|replicate]] his results, or even to check whether his data and methods are sound. [[Peer review]] is not enough; that just means his article is worth publication; it doesn't mean he has discovered something which now automatically goes into the standard biology textbooks. --[[User:Ed Poor|Ed Poor]] <sup>[[User talk:Ed Poor|Talk]]</sup> 16:17, 2 July 2008 (EDT)

Peer review = check to see if his methods are sound. You may also note that the experiment took a while, and was published last month. It would be implausible for anyone to have tried to replicate the findings at this point. [[User:Murray|Murray]] 18:09, 2 July 2008 (EDT)

:: I took a quick look and could not find any promise by Lenski that he would release his '''''data''''' (which the paper says he analyzed) to anyone. Can you quote where you think Lenski promises to release his "data"? As to releasing samples to a "competent" scientist, Lenski places so many conditions on that it is doubtful to me that he would view any potential critic as "competent". Regardless, it's clear to me that Lenski will not submit to public scrutiny of the data that the paper says he analyzed.--[[User:Aschlafly|Aschlafly]] 16:19, 2 July 2008 (EDT)

:::Well lets take what you've said as a given Ed. The data and samples are still available to a competent scientist. I am going to contact this Bohlin guy from Probe Ministries to see if he is interested or can find someone who is. I'll report back. [[User:MAnderson|MAnderson]] 16:23, 2 July 2008 (EDT)

:::: You're embarking on a fool's errand, MAnderson. It's clear to me that Lenski won't release his data to anyone independent. I'm not even sure Lenski has any meaningful data to support his claims.--[[User:Aschlafly|Aschlafly]] 16:27, 2 July 2008 (EDT)

:::::Good to see that someone is actually trying, after a week or so of no action. Andy, with how many biologists have you discussed this paper's methodology?--[[User:Argon|Argon]] 19:35, 2 July 2008 (EDT)

:::::: Looks like someone likes this fool's errand of trying to persuade Lenski to turn over his federally funded data. But don't hold your breath, Argon.--[[User:Aschlafly|Aschlafly]] 20:55, 2 July 2008 (EDT)
:::::::Think positive! Have you had any luck finding a microbiologist or similarly qualified researcher with whom you can discuss this paper as it is or the rest of Lenski's work? How about Doug Axe, with the DI's Biology Institute?--[[User:Argon|Argon]] 21:47, 2 July 2008 (EDT)

:::::Note that the strains are the ultimate standard for reproducing the work. It would take less than a week for competent microbiologist to confirm that the strains have the markers specified. Sequencing of the specified regions could also be performed in about a week. In other words, all this could be accomplished in about half of the time this 'debate' has gone on. Running the strains through the replay experiments is also easy and would confirm the results. One can express an opinion about whether Lenski would share the strains as he says (a condition to which he is bound under the journal's rules), but that is pure speculation until someone actually makes the attempt.--[[User:Argon|Argon]] 19:49, 2 July 2008 (EDT)

:::::: Argon, I did ask Lenski to turn over the data, and so can you. He refused, and I'm confident he'll continue to say "no" to any independent scrutiny of his claims.--[[User:Aschlafly|Aschlafly]] 20:55, 2 July 2008 (EDT)
:::::::That misses the point. If you don't trust his report in the paper why would you trust the data he sends you? The *strains* are the key to the paper. They either are or aren't as he says they are. You can't fudge a strain that is supposed to have been grown in continuous culture with an established lineage. Reproducibility of the methods with the materials is what verifies this work. (Actually, so does the whole genome sequencing which is planned in the next stage of the research). The strains *are* available and the requirements Lenski set for sending them are standard for the field. There are thousands of labs that could meet the criteria.
:::::::As I mentioned earlier: Verification of the strain markers could be accomplished in a week. Add another week for sequencing. I'd suggest either finding a sympathetic researcher to give you some help or wait until the whole genome sequencing gets reported later.--[[User:Argon|Argon]] 21:32, 2 July 2008 (EDT)

::Maybe so, in any case I sent this email to Dr. Bohlin, a qualified biologist and creationist.

::Dear Mr. Bohlin,

::Some people at conservapedia.com are concerned that a paper published by Richard Lenski describing a beneficial mutation occurring in E.coli may deserve closer scrutiny. Mr. Lenski has said that he is willing to release his data and samples of the E. coli to a competent scientist for further research and review. You seem to have the proper credentials to make this request. Are you interested or are you aware of other scientist that are at your level and share your personal beliefs that might be interested? I think that everyone at conservapedia would appreciate your input.

::Sincerely,

::Mike Anderson
::Conservapedia contributor

::[[User:MAnderson|MAnderson]] 16:32, 2 July 2008 (EDT)

::: Can't hurt to try, and your efforts deserve praise, MAnderson. I hope for a sensible result from your inquiry, but unfortunately do not expect it.--[[User:Aschlafly|Aschlafly]] 17:16, 2 July 2008 (EDT)
::: Mike, aside from the question of whether you persuade Dr. Bohlin to request and analyze the raw data or strains, perhaps you might ask if he finds any irregularities with methods described.--[[User:Argon|Argon]] 19:31, 2 July 2008 (EDT)

::::Here is the response that I got from Dr. Ray Bohlin of Probe Ministries:

::::Dear Mike,

::::I appreciate your notice of my qualifications but as President of Probe Ministries, I no longer work in a laboratory or have access to one and therefore I am unable to follow up on your gracious request. I have a feeler out to some other scientists but at the moment they are already quite busy with other projects. However, you may not be aware of Mike Behe's excellent response on his author page at Amazon.com. The text is below. Perhaps you could contact Mike about using his response.

::::Respectfully,

::::Ray Bohlin, PhD
::::President
::::Probe Ministries
::::www.probe.org
::::rbohlin@probe.org

::::He provided the response by Prof. Behe but I am not including it because it is lengthy and people can view it on Amazon. My only editorial comment is to note that Prof. Behe in his rebuttal does not in any way conclude that Prof. Lenski’s research is flawed or that his data is incomplete or hidden. He just feels that the experiments results do not support the theory of evolution. [[User:MAnderson|MAnderson]] 08:48, 7 July 2008 (EDT)
::::::Can you provide the link to Prof. Behe's response? [[User:Karajou|Karajou]] 23:06, 10 July 2008 (EDT)

::::Here is the link http://www.amazon.com/gp/blog/A3DGRQ0IO7KYQ2/ref=cm_blog_dp_artist_blog [[User:MAnderson|MAnderson]] 09:08, 11 July 2008 (EDT)

:::::What's going on? Hasn't anyone at conservapedia gotten on the phone and even tried to recruit an christian scientist to follow up on this? Why not?? [[User:MAnderson|MAnderson]] 22:51, 10 July 2008 (EDT)

== Andy Schlafly, please send a letter to Lenski asking him if he is an [[atheism|atheist]] ==

Andy Schlafly, please send a letter to Lenski asking him if he is an [[atheism|atheist]]. [[User:Conservative|Conservative]] 17:34, 2 July 2008 (EDT)

:Why? [[User:MAnderson|MAnderson]] 17:40, 2 July 2008 (EDT)

: Have you read his writing on a discussion about [https://myxo.css.msu.edu/lenski/history/science_and_religion.pdf science and religon] and [https://myxo.css.msu.edu/lenski/history/science_church_and_state.pdf on science, church and state]. --[[User:Rutm|Rutm]] 17:52, 2 July 2008 (EDT)

::I meant why is it relevant to his scientific work? [[User:MAnderson|MAnderson]] 17:55, 2 July 2008 (EDT)

:::Lenski says that with better words than I can in the second pdf I linked above. --[[User:Rutm|Rutm]] 20:23, 2 July 2008 (EDT)
::::Clearly, he's not a 'Dawkins-ite'.--[[User:Argon|Argon]] 21:35, 2 July 2008 (EDT)
::::::One of the links Rutm cited has Lenski stating he told someone it was none of their business what worldview he holds. It would not surprise me if he was one of the many closet atheists who cannot defend their [[atheism]]. Christianity on the other hand has Jesus stating: "Whosoever therefore shall confess me before men, him will I confess also before my Father which is in heaven. But whosoever shall deny me before men, him will I also deny before my Father which is in heaven. - Matthew 10:32-33 [[User:Conservative|Conservative]] 22:49, 3 July 2008 (EDT)

:::::::I knew the reason why. I just wanted you to say it. Basically because Lenski is or might be an atheist, he is immediately discredited. I don't see things that way at all which is why I am perfectly happy to have a dedicated Christian scientist review the data. I assume that honor exist among scientist of all stripes and that the goal of scientist is to fairly judge scientific research. [[User:MAnderson|MAnderson]] 08:53, 7 July 2008 (EDT)
MAnderson, you are extraordinarily naive if you imagine that scientists espousing [[Atheistic]] or [[Liberal]] views somehow turn those views 'off' when conducting research. If one's entire world outlook is distorted in such a way, it affects everything one does - consciously or otherwise. [[User:Bugler|Bugler]] 10:38, 7 July 2008 (EDT)

:Bugler - do you believe avowedly Christian scientists can turn their beliefs off when conducting research? [[User:StanleyAccrington|StanleyAccrington]] 13:46, 7 July 2008 (EDT)

:: In reply to both Bugler and Stan, I guess I prefer to believe that people are basically good and will at least try to take the high road when given the chance. If that is being naive then so be it. Have a great day! [[User:MAnderson|MAnderson]] 17:11, 7 July 2008 (EDT)

:::As a scientist myself, it's patently obvious that anybody who is unable to turn off personal feelings/beliefs and not have them affect their interpretation of data is, by definition, a bad scientist. Data doesn't lie. They are observed facts. If you allow bias to creep into the mix, you're carrying out poor science. [[User:Wisdom89|Wisdom89]] 17:54, 7 July 2008 (EDT)

::::You're being too naive if you think every scientist in the world is completely honest and wouldn't (mis?)interpret the data in a way that wouldn't contradict his worldview. Just look at the Global Warming crowd. [[User:WilliamH|WilliamH]] 18:21, 7 July 2008 (EDT)

:::::We can debate about human nature here if you want, however, that would get us no where. No one said anything about all scientists. Obviously there are exceptions to every rule. We're human. It's ludicrous for me to have to preface my statements with such trivia. So, implying that the ''majority'' of scientists are swayed by their personal beliefs is horribly cynical. A spiritual/religious scientist and an atheist scientist are on equal footing when it comes to data analysis. [[User:Wisdom89|Wisdom89]] 20:08, 7 July 2008 (EDT)

::::::Good to see we agree that atheist scientists can become blinded by their own prejudices and produce misleading conclusions (although we disagree on many other things.) So why is it that one shouldn't be suspicious when the scientist in question is being evasive about the requests for data? [[User:WilliamH|WilliamH]] 15:38, 8 July 2008 (EDT)

''A spiritual/religious scientist and an atheist scientist are on equal footing when it comes to data analysis.'' That is precisely ''not'' the case. Faith in God is natural and right: it is, if you like, the 'default' condition of mankind. Atheism is a perversion of belief; it takes a wilful step into ignorance and defiance of God. Once that step is taken, all values of truth and objectivity fly out of the window. Atheists cannot practice science; the need to 'prove' and 'justify' their terrible howling void of non-belief means that they can only practice pseudo-science. [[User:Bugler|Bugler]] 15:44, 8 July 2008 (EDT)
:I honestly hope you don't ever become a scientist. I say this not to slight you, but because your view on how it should/does function is horribly skewed. [[User:Wisdom89|Wisdom89]] 16:30, 8 July 2008 (EDT)

== An Interesting Lenski Quote ==

From the first of the two papers Rutm linked:

<blockquote>
I think the same facts of evolution--with the perpetual struggle for existence and genetic rewards for selfishness--could just as easily be used to support a religion that both Dr. Hefner and I would find repugnant.
</blockquote>

Is it me, or is Dr. Lenski admitting that evolution can be used to support some extremely nasty philosophies? --[[User:Benp|Benp]] 21:30, 2 July 2008 (EDT)
:I believe he's saying one could '''*attempt*''' to use it justify practically anything. But more likely, one would probably be committing something akin to a naturalistic fallacy in so doing.--[[User:Argon|Argon]] 21:42, 2 July 2008 (EDT)

== Statistical Significance ==
The 2 instances in the little table that imply that statistical significance or lack thereof should be reported look a bit silly. The first phrase refers to the statement by Blount et al. that "A number of Cit+ clones were isolated..." on p7900. Asking how many is all well and good. But it appears the researchers decided how many to isolate, and it is nonsensical to ask about significance. The second phrase refers to the end of the sentence: "all were Ara-, T5-sensitive, and T6-resistant, as expected." It is potentially a bit more relevant here, but still doesn't make a lot of sense to simply ask generally about statistical significance - compared to what? Calculating significance is a way of testing the probability of sampling error, if that helps. [[User:Murray|Murray]] 11:01, 3 July 2008 (EDT)

== Visual Inspection ==
The methodology here is what's important, and they clearly write that the "LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time." The observations for which you are requesting data seem to be the kind of observations that aren't recorded, because they do not need to be. I'll give you an example from my experiences in the lab: when I perform an electrophoresis gel run, I have to make an agarose gel. Every time I do so I follow the recipe taped to our microwave: 40mL TAE buffer, 400mg Agarose. It's a given in our lab that all our gels are 1%, unless otherwise stated. Likewise, it seems likely that somebody working in Lenski's lab will, when checking for turbidity, do so by holding up a tube of culture, observe, "Yep, that's turbid," and continue on with the procedure as outlined in their protocol. If Lenski's lab is more diligent than the one in which I work, then we are still dealing with the kind of data that never leave a graduate student's notebook. Again, what data do you want, a table containing the exact same information every day ''(June 6, 1999 - Checked turbidity of cultures. They were turbid. June 7, 1999 - Checked turbidity of cultures. They were turbid. June 8, 1999 - Che...)''? Or would only scans of graduate students' notebook pages suffice? --[[User:Codyc|Codyc]] 20:54, 5 July 2008 (EDT)

== "Lenksi's biographical sketch does not exhibit any background or experience in mathematics or statistics. " ==

This dirt-digging is getting ridiculous, IMO. Prof. Lenski got his doctoral degree in Zoology. His thesis was "Effects of competition and disturbance on ground beetle populations". That area and evolutionary biology are math intensive with a substantial emphasis in statistics. His second and third papers are: Lenski, R. E., and P. M. Service. 1982. '''The ''statistical analysis'' of population growth rates calculated from schedules of survivorship and fecundity'''. Ecology 63:655-662. and Service, P. M., and R. E. Lenski. 1982. '''Aphid genotypes, plant phenotypes, and genetic diversity: a ''demographic analysis of experimental data'''''. Evolution 36:1276-1282. Did the person who wrote the headline comment even read any of Lenski's works? I would suppose not.--[[User:Argon|Argon]] 14:00, 13 July 2008 (EDT)

== uhhh ==

How would you obtaining E. Coli samples help? I don't think any of the editors or sysops here have the qualifications or the equipment to do anything with them. [[User:Jirby|Jirby]] 11:55, 20 August 2008 (EDT)
perhaps if the sysops presented the entire paper then they could have a more concrete basis for their disagreements and put their questions into full context rather than raising arguments that leave the reader blind to the whole situation. For instance you could have the paper and then say we disagree with this and here's why blah blah blah, instead of pulling random sentences from the paper without context and dissecting them. Because when you think about it critically it only undermines the sysops's arguments with the research. [[User:superstudent|superstudent]] 10:16 22 September 2008

== Lenski's Position ==
I put in the title of the chair that he holds. The information is in his biographical sketch. Why was it changed? I thought a completely accurate description of Lenski was the point of this, or am I wrong? Does mentioning that he's the Hannah Distinguished Professor of Microbial Ecology, as it says on his web page somehow violate a tenate of Conservapedia? The information can be found on his homepage and verified by looking at the web page of the University. Without any idea of why we should not mention his possession of a named professorship, I'm going to put that back in. If this is wrong to do, please tell me. [[User:ArnoldFriend|ArnoldFriend]] 23:05 25 September EDT

==Lenski's Atheism==
This article mentions Lenski's "...unabashed atheism", but provides no citation. I read his two pieces on religion and science (https://myxo.css.msu.edu/lenski/history/science_and_religion.pdf and https://myxo.css.msu.edu/lenski/history/science_church_and_state.pdf), as well as his responses to Aschlafly's letters. Nothing in those documents backs up the atheism claim. Is there something else that supports it? Should this claim be removed? --[[User:Martib|Martib]] 22:49, 15 November 2008 (EST)

==Lenski's Position II==
Why the removal of the mention of his position again? I figured that having a named professorship was something noteworthy in the article. (Noteworthy in what way is up to the reader. I view it as more of a black mark on MSU's case than in favor of Lenski, especially given his refusal to actually disclose his data. If this should be explicit in the entry, please tell me and I'll do my best to put it in.) For the moment, I'm not touching the page, but I am confused as to why an edit I made close to a month ago was changed back now. [[User:ArnoldFriend|ArnoldFriend]] 21:14, 17 November 2008 (EST)

: The academic titles are silly and misleading, particularly when there is no explanation of the process behind the title. He's a professor, and that does have a well-established meaning. Beyond that someone has to make a case for explaining the significance of an additional title before including it.--[[User:Aschlafly|Aschlafly]] 21:23, 17 November 2008 (EST)

:: Ok, that makes sense. Sorry if I came across as harsh, I was just a confused by having one of my edits called "senseless liberal puffery," (which was not its intention). [[User:ArnoldFriend|ArnoldFriend]] 22:00, 17 November 2008 (EST)

::: The John Hannah Distinguished professorships are '''endowed''' professorships that were created in 1966 by the Board of Trustees to honor John Hannah and his 25 years of service to the university. They are teching and research positions. The professorships are “dedicated to the encouragement of continued outstanding scholarship, creative activity, and teaching.” [from MSU ] [[User:Markr|Markr]] 17:07, 18 November 2008 (EST)

== Apologies... ==

I just completely edited the page, posted a paragraph full of nought but my opinion and luckily it was promptly changed... I was very angry upon reading that reprort and its article on Conservapedia and broke a Conservapedia Commandment... I'm sorry.

:You may wish to recreate your account with a real name if you are going to contribute positively instead of just vandalizing articles. [[User:Sulli|Sulli]] 20:12, 12 January 2009 (EST)

== Quite Funny ==

Wow, this is actually quite funny. I wonder did anyone from Conservapedia happen to gain access to the data and specimens that were requested? That would have been hilarious! I can just imagine one of you discovering that the evidence backed up Professor Lenski's claims, only to immediately claim that it was a liberal-athiest conspiracy designed to undermine Creationism.

"Oh, but his research was state-funded, so obviously it is the bastard liberal government meddling with the research findings to brainwash good, faithful Americans into believing the blasphemous theory of Evolution! Well the jokes on them because Darwin repented on his deathbed, booyah!"

Just brilliant. Keep it up guys and gals, you're just the best. --[[User:RyanMcLaughlin|Ryan McLaughlin]] 15:19, 18 November 2009 (EST)

== I'm going to archive this all tomorrow ==

Because it really needs it. --[[User:EmersonWhitecp|EmersonWhitecp]] 15:08, 14 April 2010 (EDT)

Conservapedia talk:Lenski dialog

2010-04-15T21:09:48Z

EmersonWhitecp: /* Why does it matter? */

Human Immunodeficiency Virus

2010-04-14T21:17:55Z

EmersonWhitecp: rewrote a bit, rmv false scientific doubt

The '''Human Immunodeficiency Virus''' ('''HIV''') is the virus that causes [[AIDS]] (Formerly known as Gay Related Immunodeficiency syndrome or "[[gay plague]]"). The Virus infects and slowly kills human CD4+ helper T-Cells. With Treatment the progression of HIV infection to AIDS is slowed considerably, but may still progress. As T-cell counts fall a number of opportunistic infections can take hold and normally benign organisms can become deadly.

A French team of researchers has been given primary credit for the discovery, although the American scientist [[Gallo]] apparently discovered it independently.

A handful of scientists have disagreed with the [[scientific consensus|mainstream]] about the existence of the virus, and dispute still goes on about whether HIV is the sole or even main cause of AIDS.<ref>http://www.duesberg.com/</ref>

==History==
In 1983, Barre-Sinoussi, Chermann, and Montagnier (at the Pasteur Institute in Paris) isolated a retrovirus from lymph node cells of a patient with lymphadenopathy; accordingly, this virus was designated lymphadenopathy-associated virus (LAV). Lymphadenopathy-associated virus was shown to replicate and cause cytopathology in cultures of human peripheral blood lymphocytes. A year after the report on LAV, Gallo and co-workers (at the National Institutes of Health, Bethesda, MD) described the isolation of a cytopathic T-lymphotropic retrovirus, designated human T-lymphotropic virus type III (HTLV-III), from peripheral blood lymphocytes of patients with acquired immunodeficiency syndrome (AIDS)<ref>Gallo RC, Salahuddin SZ, Propovic M, et al. Frequent detection and isolation of cytopathic retroviruses (HTLV-II) from patients with AIDS and at risk for AIDS. ''Science'' 1984;224:500-503.</ref> Although this HTLV-III isolate was later shown to be a contaminant of virus from the Pasteur Institute<ref>Bryant ML, Yamamoti J, Luciw P, Munn R, Marx P, Higgins J, Pedersen N, Levine A, gardner MB, Molecular comparison of retroviruses associated with human and simian AIDS. ''Hematol Oncol'' 1985;3:187-197.</ref><ref>Chang SYP, Bowman BH, Weiss JB, Garcia RE, White TJ. The origin of HIV-1 isolate HTLV-IIIB. ''Nature'' 1993;363:466-469.</ref><ref>Wain-Hobson S, Vartanian JP, Henry M, Chenciner N, Cheynier R, Delassus S, Martins LP, Sala M, Nugeyre MT, Guetard D. LAV revisited: origins of the early HIV-1 isolates from Institut Pasteur. ''Science'' 1991;252:961-965.</ref>, subsequent isolates of HTLV-III were unique<ref>Hahn BH, Gonda MA, Shaw GM, Popovic M, Hoxie JA, Gallo RC, Wong-Staal F. Genomic diversity of the acquired immune deficiency syndrome virus HTLV-III: different viruses exhibit greatest divergence in their envelope genes. Proc Natl Acad Sci USA 1985;82:4813-4817.</ref>. Also, in 1984, Levy and co-workers (at the University of California, San Francisco) cultured an AIDS-associated retrovirus (ARV) from peripheral blood mononuclear cells of an AIDS patient<ref>Levy JA, Hoffman AD, Kramer SM, Landis JA, Shimabukuro JM, Oshiro LS. Isolation of lymphocytopathic retroviruses from San Francisco patients with AIDS. Science 1984;225:840-842</ref>. Molecular cloning and sequence analysis revealed that the genomes of LAV and HTLV-III were nearly identical, exhibiting 1% to 2% divergence. In contrast, the genome of the ARV-2 isolate displayed up to 15% differences in nucleotide sequences in pairwise alignments with the genomes of either LAV or HTLV-III. Electron microscopy demonstrated that these viruses from AIDS patients were morphologically similar to members of the lentivirus genus of the family ''Retroviridae''. Furthermore, comparison of genome sequences also supported the notion that the human retroviruses associated with AIDS were related, albeit distantly, to lentiviruses of other animals.

== Transmission ==

HIV is primarily spread by sexual contact and intravenous drug use. Most early infections in the US were via homosexual sex, and to a lesser extent via intravenous drug use and blood transfusions; most current infections in the world are via heterosexual contact and vertical transmission from mother to child. Mothers infected with HIV transmit the virus to their baby ''in utero'', during childbirth. Mother-to-child transmission can be significantly reduced by the proper use of antiretroviral agents.

Until recently, it was thought that breastfeeding increased the risk of HIV transmission from mother to child. However, research in KwaZulu Natal <ref>''The Lancet'', March 30th 2007</ref> showed that babies of mothers with HIV who receive a mixture of milk and solid foods are 11 times more likely to become infected than those who are exclusively breastfed. Those given formula milk as well as breast milk are nearly twice as likely to become HIV positive. Even in countries with high HIV prevalence, it is calculated that exclusive breastfeeding could prevent 13% of deaths in children under five years-old.

The KwaZulu Natal study involved around 2,700 babies born between 2001 and 2005. Major efforts were made to encourage and support women in breastfeeding by sending counsellors to their homes twice a week. The success of the strategy surprised the researchers. The authors say exclusive breastfeeding "ordinarily protects the integrity of the intestinal mucosa, which thereby presents a more effective barrier to HIV".

Less commonly, contact with infected blood causes HIV transmission. This can occur in health care providers (HCPs) or others exposed to infectious bodily fluids. Transmission is facilitated by breaks in the skin or direct contact with [[Mucosal membranes|mucosal tissues]], such as those found in the eyes, mouth, anus, or vagina. Early in the epidemic, blood transfusions were a significant source of HIV transmission.

Other less likely means of transmission exist, though are rare. There are no confirmed cases from contact with the saliva, sweat or tears of an infected person.

Early on in the epidemic, there was much confusion about the transmission of HIV. After decades of study, this has been clarified. HIV can be found in various body fluids, however its highest concentrations are found in semen, blood, and vaginal secretions. It can also be found in breast milk, but recent research <ref>The Lancet, March 30th 2007</ref> shows that exclusive breastfeeding tends to protect against HIV transmission.

As summarized by the [[Centers for Disease Prevention and Control]]<ref>www.cdc.gov</ref>:

<blockquote>An exposure that might place HCP at risk for HIV infection is defined as a percutaneous injury (e.g., a needlestick or cut with a sharp object) or contact of mucous membrane or nonintact skin (e.g., exposed skin that is chapped, abraded, or afflicted with dermatitis) with blood, tissue, or other body fluids that are potentially infectious. In addition to blood and visibly bloody body fluids, semen and vaginal secretions also are considered potentially infectious. Although semen and vaginal secretions have been implicated in the sexual transmission of HIV, they have not been implicated in occupational transmission from patients to HCP.</blockquote>

===Potentially Infectious Fluids===
''The risk for transmission of HIV infection from these fluids is unknown; the potential risk to HCP from occupational exposures has not been assessed by epidemiologic studies in health-care settings.''

*cerebrospinal fluid
*synovial fluid
*pleural fluid
*peritoneal fluid
*pericardial fluid
*amniotic fluid.

===Non-infectious Fluids===
''The following fluids are not considered potentially infectious '''unless''' they are visibly bloody; the risk for transmission of HIV infection from these fluids and materials is low.''

*feces
*nasal secretions
*saliva
*sputum
*sweat
*tears
*urine
*vomitus

<blockquote>Any direct contact (i.e., contact without barrier protection) to concentrated virus in a research laboratory or production facility requires clinical evaluation. For human bites, clinical evaluation must include the possibility that both the person bitten and the person who inflicted the bite were exposed to bloodborne pathogens. Transmission of HIV infection by this route has been reported rarely.</blockquote>

===Data===
'''Per-contact risk of HIV transmission:'''

:URA with a known seropositive partner: 0.82 percent
:URA with a partner of unknown serostatus, 0.27 percent (95% CI: 0.06, 0.49 percent)
:Unprotected insertive anal intercourse: 0.06 percent.
:Receptive oral sex: 0.04 percent.
(URA=unprotected receptive anal intercourse)
''AIDSWEEKLY Plus; Monday, August 9, 1999''

''"The overall, unadjusted probability of HIV-1 transmission per coital act is 0·0011 in this Ugandan population, and greater infectivity of predominant HIV-1 viral subtypes is unlikely to account for the explosive HIV-1 epidemic in sub-Saharan Africa. Transmission probability per act varies greatly with the HIV-1 viral load of the HIV-1-infected partner, which suggests that interventions to reduce viral load could reduce transmission.15,28 Younger age and genital ulceration also increased the probability of transmission per act."'' THE LANCET, Volume 357: Pages 1149-1153,
14 April 2001.

== Infection ==

After exposure, the virus invades and replicates in immune cells near the site of infection. It quickly spreads to regional lymph nodes and via the blood stream to the rest of the body. During this stage the patient may experience ''Acute Retroviral Syndrome'', a vague flu-like illness. The patient is often [[Asympotomatic carrier|asymptomatic]] for the first 5-10 years after infection. By that time, untreated, progression to AIDS in inevitable, except in a small subset of patients.

== Treatment ==

Treatment issues are complicated by issues of poverty and education. In communities with adequate resources, HIV infection is treatable with Highly Active Retroviral Therapy ([[HAART]]). This therapy effectively prevents progression to AIDS in many patients, however there are many side effects to treatment, and resistance is a serious issue.

== Prevention ==

Prevention is an issue complicated by issues of poverty and education. Sexual transmission can be effectively prevented by avoiding sexual contact ([[abstinence]]), or by regular, proper use of latex condoms. A large percentage of those infected are unaware of their disease status, which complicates prevention. Spouses are often infected without their knowledge of their partner's status.

Occupational infection can be prevented with the use of universal precautions and by post-exposure prophylaxis<ref>Guidelines for the Management of Occupational Exposures to HIV and Recommendations for Postexposure Prophylaxis. MMWR Recomm Rep. 2005;54:1-17.</ref>.

Currently, no [[vaccine]] is available, and it is not clear if a vaccine will be available any time in the near future.

== References ==
<references/>

Mandell, Bennett, & Dolin: Principles and Practice of Infectious Diseases, 6th ed., Copyright © 2005 Churchill Livingstone, An Imprint of Elsevier

THE LANCET, Volume 357: Pages 1149-1153,
14 April 2001.

AIDSWEEKLY Plus; Monday, August 9, 1999

THE LANCET, 30 March 2007, reported in ''The Guardian'', 30 March 2007 [http://www.guardian.co.uk/aids/story/0,,2046416,00.html]

[[Category: Medicine]]
[[Category:Diseases]]
[[Category: Viruses]]

Complementary and Alternative Medicine

2010-04-14T20:54:58Z

EmersonWhitecp: $120 million a year is spent testing and retesting things that we already know don't work.

Complementary and Alternative Medicine (CAM) consists of medical treatments and therapies outside of what is traditionally taught in medical school or recognized for reimbursement by government health programs.

In the [[United States]], 36% of adults are using some form of CAM and spend $36 billion to $47 billion on CAM therapies in 1997.<ref>http://nccam.nih.gov/news/camsurvey_fs1.htm</ref> The numbers of uninsured Americans increases by about 1 million persons per year, and the amount spent on CAM is likely much higher today. If CAM is defined to include megavitamin therapy and prayer specifically for health reasons, 62% of Americans use CAM.

The US National Institutes of Health sponsor the National Center for Complementary and Alternative Medicine NCCAM which spends $120 Million dollars a year researching CAM. To date they have found no major treatments and the vast majority of subjects that they research come up unproductive repeatedly.

CAM Practices include the following:

*Biologically based treatments using substances found in nature, such as herbs, special diets, or vitamins in non-conventional doses, such as massive amounts of Vitamin C.

*Manipulative and body-based practices that utilize movement of body parts.

*Mind-body medicine emphasizing the potential of the mind to affect bodily function and symptoms.

*Holistic medical approaches that focus on all of one's life, as physicians did in ancient times.

*Non-western treatments, such as Chinese acupuncture.

== References ==

<references/>

[[Category:Medicine]]

Talk:Richard Lenski

2010-04-14T19:08:30Z

EmersonWhitecp: /* I'm going to archive this all tomorrow */ new section

HeLa cells

2010-04-14T18:35:15Z

EmersonWhitecp: Saw user HeLa join, figured I'd write a little about HeLa cells

'''Hela Cells''' are the first human [[cell line]] maintained in a laboratory and were derived from an ovarian tumor biopsy from Henrietta Lacks. They were taken with out permission and were delivered to a colleague of her doctor at Johns Hopkins who was attempting to generate a human cell line, he was successful in maintaining the cell line.

Acquired Immunodeficiency Syndrome

2010-04-14T01:58:46Z

EmersonWhitecp: /* Dissent */

'''Acquired Immune Deficiency Syndrome''' (usually referred to as '''AIDS''') is a collection of uncurable diseases and symptoms often believed to be caused by long-term infection with the[[HIV| Human Immunodeficiency Virus]].

== Diagnosis ==

According to the CDC's 1993 guidelines, <ref>http://www.cdc.gov</ref><ref>http://www.merckmedicus.com/ppdocs/us/hcp/content/merck/hiv/hivaids/aidsdefi.htmAIDS is defined </ref>as follows:
HIV infection ''plus'' any of the following:
*[[CD4]] count less than 200 or
*CD4 percentage less than 14% of total lymphocytes or
*Any of the following illnesses: pulmonary TB, recurrent pneumonia, invasive cervical cancer.
*Expanded definition including 23 clinical conditions published elsewhere<ref>http://www.cdc.gov/MMWR/preview/mmwrhtml/00018871.htm</ref>

The World Health Organization uses a different staging method for HIV disease. <ref>http://www.aids-ed.org/aetc/aetc?page=cm-105_disease</ref>

== History ==

The illness was first recognized in the early 1980s<ref>New England Journal of Medicine, Volume 344:1764-1772 June 7, 2001 Number 23</ref> as homosexual men presented to their doctors with a rare lung disease called ''Pneumocystis carinii'' pneumonia (PCP)<ref>Pneumocystis pneumonia -- Los Angeles. MMWR Morb Mortal Wkly Rep 1981;30:250-252)</ref>. Early on, the "[[gay disease]]" took on a variety of names, including "gay cancer" and "Gay-related immune deficiency" (GRID). The [[Centers for Disease Control]] noticed an increase in requests for drugs needed to treat this illness and launched an epidemiological investigation.

Although the first cases of the disease probably go back to the 1950s, the epidemic was not recognized until the early 1980s.[http://www.avert.org/his81_86.htm] The early epidemic occurred in two main branches; in the US and other developed countries, and in sub-Saharan Africa. In the US, the early epidemic was primarily spread by homosexual sex, intravenous drug use, and blood transfusions (prior to the introduction of testing). In Africa, transmission was almost exclusively by heterosexual sex. Currently, most new infections worldwide are spread by promiscuous heterosexual sex and prostitution.

<blockquote>
"We owe it to Ryan to make sure that the fear and ignorance that chased him from his home and his school will be eliminated. We owe it to Ryan to open our hearts and our minds to those with AIDS. We owe it to Ryan to be compassionate, caring and tolerant toward those with AIDS, their families and friends. It's the disease that's frightening, not the people who have it."
—Former U.S. President Ronald Reagan, April 11, 1990 in regards to the case of Ryan White.
</blockquote>

== Natural History ==

After infection with [[HIV]], the virus quickly replicates in lymphatic tissue and travels through the blood to infect most areas of the body. The largest consequence of this is the "hijacking" of certain immune cells, especially so-called T-Helper, or CD-4, cells. Early in the infection, the immune system holds the infection at bay, often causing "Acute Retroviral Syndrome", a flu-like illness. Patients often have swollen lymph nodes. After approximately 8-10 years of infection, the immune system begins to lose its battle. This is primarily seen in the loss of numbers of CD4 cells, however the changes are somewhat more complex. When the CD4 cell level drops low enough, AIDS becomes apparent.
The first symptoms of the illness are generally night sweats, weight loss, and oral thrush.

== Opportunistic Infections (OIs) ==

The hallmark of AIDS is the appearance of ''opportunistic infections'', meaning infections with organisms that do not usually cause human disease, unless given the right "opportunity". This opportunity is the reduction in cell-mediated immunity, first seen in patients with certain cancers or on anti-rejection drugs for organ transplantation.
These infections include:

*[[Candida albicans]]. Caused by the candida fungi, resulting in thrush (mouth) and vaginal yeast infections. Most common HIV-related fungus infection.
* Cryptoccoccal Menigitis. A yeast-like fungus infection that usually involves the brain and lungs, although it can affect almost any organ. Most often occurs when a person's CD4+ T cell count falls below 100 cells per cubic millimeter of blood.
*Cryptococcus neoformans (a cause of meningitis).
*[[Cytomegalovirus]]. Virus can affect the entire body, but it commonly affects the eye's retina, causing blurry vision and in severe cases, blindness. Most likely to occur when a person’s CD4+ T cell count falls below 100.
*Epstein Barr virus (leads to a type of lymphoma).
*Human herpesvirus-8 (causes Kaposi's sarcoma). Results in reddish purple lesions that usually appear on the skin.
* Liver Disease. One of the leading causes of death among AIDS patients,
*Mycobacterium avium complex (atypical mycobacterium). Bacterial infection that can cause persistent fever, night sweats, fatigue, weight loss, anemia, abdominal pain, dizziness, diarrhea and weakness. Most likely occurs when the CD4+T cell count falls below 50.
*[[Mycobacterium tuberculosis]] (TB).
*Pneumocystis jiroveci, previously [[Pneumocystis carinii]]. Condition occurs when a fungus infects the lungs. Symptoms may include night sweats and fatigue, fever, cough, difficulty breathing, weight loss. Most likely to occur when the CD4+ T cell count falls below 200.
* Progressive Multifocal Leukoencephalopathy (PML) Rare disorder of the nervous system caused by a common human polyomavirus, JC virus. Can occur when the CD4+T cell count falls below 200.
* Recurrent Pneumonia. Most likely to occur when the CD4+ T cell count falls below 200
*Staphylococcus aureus (primarily causes skin infections).
*Streptococcus pneumoniae (the primary cause of pneumonia in AIDS patients).
*[[Toxoplasma gondii]]. Condition occurs when a parasite infects the brain. Symptoms include confusion or delusional behavior, severe headaches, fever, seizures and coma. Most likely occurs when the CD4+ T cell count falls below 100.<ref>[http://www.ucsfhealth.org/adult/medical_services/infect/hiv/infections.html Infections Associated with AIDS, UCSF Medical Center.</ref>

== Dissent ==
Among the world's medical professionals and biologists, there is general agreement that HIV causes AIDS. In this, those of Koch's postulates that apply to viral diseases have been clearly fulfilled, and basic science research has shown the same. Specific drugs have been developed that treat HIV infection and AIDS, helping show the causal relationship. That being said, there is a vocal minority of people, scientists and non-scientists alike, who do not believe that HIV causes AIDS. Foremost among these is Dr. Peter Duesberg. Details about these "re-thinkers" and their arguments can be found at several websites, but not in any reliable peer-reviewed journals: <ref>[http://www.reviewingaids.org/awiki/index.php/Main_Page]</ref>

== See also ==
* [[Mortality]]
* [[Homosexuality]]

==External links==
*[http://newsbusters.org/blogs/robert-knight/2007/12/01/some-questions-media-wont-ask-today-about-aids Some Questions the Media Won't Ask Today About AIDS], Robert Knight, [[NewsBusters]], December 1, 2007
* [http://www.ucsfhealth.org/adult/medical_services/infect/hiv/infections.html Infections Associated with AIDS], University of California, San Francisco

==References==
{{reflist}}

[[Category:Diseases]]
[[Category:Syndromes]]
[[Category:Demography]]
[[Category:AIDS| ]]

Acquired Immunodeficiency Syndrome

2010-04-14T01:57:11Z

EmersonWhitecp: /* Definition */

'''Acquired Immune Deficiency Syndrome''' (usually referred to as '''AIDS''') is a collection of uncurable diseases and symptoms often believed to be caused by long-term infection with the[[HIV| Human Immunodeficiency Virus]].

== Diagnosis ==

According to the CDC's 1993 guidelines, <ref>http://www.cdc.gov</ref><ref>http://www.merckmedicus.com/ppdocs/us/hcp/content/merck/hiv/hivaids/aidsdefi.htmAIDS is defined </ref>as follows:
HIV infection ''plus'' any of the following:
*[[CD4]] count less than 200 or
*CD4 percentage less than 14% of total lymphocytes or
*Any of the following illnesses: pulmonary TB, recurrent pneumonia, invasive cervical cancer.
*Expanded definition including 23 clinical conditions published elsewhere<ref>http://www.cdc.gov/MMWR/preview/mmwrhtml/00018871.htm</ref>

The World Health Organization uses a different staging method for HIV disease. <ref>http://www.aids-ed.org/aetc/aetc?page=cm-105_disease</ref>

== History ==

The illness was first recognized in the early 1980s<ref>New England Journal of Medicine, Volume 344:1764-1772 June 7, 2001 Number 23</ref> as homosexual men presented to their doctors with a rare lung disease called ''Pneumocystis carinii'' pneumonia (PCP)<ref>Pneumocystis pneumonia -- Los Angeles. MMWR Morb Mortal Wkly Rep 1981;30:250-252)</ref>. Early on, the "[[gay disease]]" took on a variety of names, including "gay cancer" and "Gay-related immune deficiency" (GRID). The [[Centers for Disease Control]] noticed an increase in requests for drugs needed to treat this illness and launched an epidemiological investigation.

Although the first cases of the disease probably go back to the 1950s, the epidemic was not recognized until the early 1980s.[http://www.avert.org/his81_86.htm] The early epidemic occurred in two main branches; in the US and other developed countries, and in sub-Saharan Africa. In the US, the early epidemic was primarily spread by homosexual sex, intravenous drug use, and blood transfusions (prior to the introduction of testing). In Africa, transmission was almost exclusively by heterosexual sex. Currently, most new infections worldwide are spread by promiscuous heterosexual sex and prostitution.

<blockquote>
"We owe it to Ryan to make sure that the fear and ignorance that chased him from his home and his school will be eliminated. We owe it to Ryan to open our hearts and our minds to those with AIDS. We owe it to Ryan to be compassionate, caring and tolerant toward those with AIDS, their families and friends. It's the disease that's frightening, not the people who have it."
—Former U.S. President Ronald Reagan, April 11, 1990 in regards to the case of Ryan White.
</blockquote>

== Natural History ==

After infection with [[HIV]], the virus quickly replicates in lymphatic tissue and travels through the blood to infect most areas of the body. The largest consequence of this is the "hijacking" of certain immune cells, especially so-called T-Helper, or CD-4, cells. Early in the infection, the immune system holds the infection at bay, often causing "Acute Retroviral Syndrome", a flu-like illness. Patients often have swollen lymph nodes. After approximately 8-10 years of infection, the immune system begins to lose its battle. This is primarily seen in the loss of numbers of CD4 cells, however the changes are somewhat more complex. When the CD4 cell level drops low enough, AIDS becomes apparent.
The first symptoms of the illness are generally night sweats, weight loss, and oral thrush.

== Opportunistic Infections (OIs) ==

The hallmark of AIDS is the appearance of ''opportunistic infections'', meaning infections with organisms that do not usually cause human disease, unless given the right "opportunity". This opportunity is the reduction in cell-mediated immunity, first seen in patients with certain cancers or on anti-rejection drugs for organ transplantation.
These infections include:

*[[Candida albicans]]. Caused by the candida fungi, resulting in thrush (mouth) and vaginal yeast infections. Most common HIV-related fungus infection.
* Cryptoccoccal Menigitis. A yeast-like fungus infection that usually involves the brain and lungs, although it can affect almost any organ. Most often occurs when a person's CD4+ T cell count falls below 100 cells per cubic millimeter of blood.
*Cryptococcus neoformans (a cause of meningitis).
*[[Cytomegalovirus]]. Virus can affect the entire body, but it commonly affects the eye's retina, causing blurry vision and in severe cases, blindness. Most likely to occur when a person’s CD4+ T cell count falls below 100.
*Epstein Barr virus (leads to a type of lymphoma).
*Human herpesvirus-8 (causes Kaposi's sarcoma). Results in reddish purple lesions that usually appear on the skin.
* Liver Disease. One of the leading causes of death among AIDS patients,
*Mycobacterium avium complex (atypical mycobacterium). Bacterial infection that can cause persistent fever, night sweats, fatigue, weight loss, anemia, abdominal pain, dizziness, diarrhea and weakness. Most likely occurs when the CD4+T cell count falls below 50.
*[[Mycobacterium tuberculosis]] (TB).
*Pneumocystis jiroveci, previously [[Pneumocystis carinii]]. Condition occurs when a fungus infects the lungs. Symptoms may include night sweats and fatigue, fever, cough, difficulty breathing, weight loss. Most likely to occur when the CD4+ T cell count falls below 200.
* Progressive Multifocal Leukoencephalopathy (PML) Rare disorder of the nervous system caused by a common human polyomavirus, JC virus. Can occur when the CD4+T cell count falls below 200.
* Recurrent Pneumonia. Most likely to occur when the CD4+ T cell count falls below 200
*Staphylococcus aureus (primarily causes skin infections).
*Streptococcus pneumoniae (the primary cause of pneumonia in AIDS patients).
*[[Toxoplasma gondii]]. Condition occurs when a parasite infects the brain. Symptoms include confusion or delusional behavior, severe headaches, fever, seizures and coma. Most likely occurs when the CD4+ T cell count falls below 100.<ref>[http://www.ucsfhealth.org/adult/medical_services/infect/hiv/infections.html Infections Associated with AIDS, UCSF Medical Center.</ref>

== Dissent ==
Among the world's medical professionals and biologists, there is general agreement that HIV causes AIDS. In this, Koch's postulates have been clearly fulfilled, and basic science research has shown the same. Specific drugs have been developed that treat HIV infection and AIDS, helping show the causal relationship. That being said, there is a vocal minority of people, scientists and non-scientists alike, who do not believe that HIV causes AIDS. Foremost among these is Dr. Peter Duesberg. Details about these "re-thinkers" and their arguments can be found at several websites, but not in any reliable peer-reviewed journals: <ref>[http://www.reviewingaids.org/awiki/index.php/Main_Page]</ref>

== See also ==
* [[Mortality]]
* [[Homosexuality]]

==External links==
*[http://newsbusters.org/blogs/robert-knight/2007/12/01/some-questions-media-wont-ask-today-about-aids Some Questions the Media Won't Ask Today About AIDS], Robert Knight, [[NewsBusters]], December 1, 2007
* [http://www.ucsfhealth.org/adult/medical_services/infect/hiv/infections.html Infections Associated with AIDS], University of California, San Francisco

==References==
{{reflist}}

[[Category:Diseases]]
[[Category:Syndromes]]
[[Category:Demography]]
[[Category:AIDS| ]]

Supreme Court Candidates, 2010

2010-04-14T00:43:38Z

EmersonWhitecp: Well I'll be ... here are the names mentioned in that article, I suspect that this article by slate might harbor some names worth mentioning

[[U.S. Supreme Court]] Justice [[John Paul Stevens]], the only decorated veteran on the U.S. Supreme Court, has announced his resignation and thereby created an election year vacancy.

Here are leading contenders to be nominated to fill his seat, with an analysis of each.

== Elena Kagan ==

Elena Kagan is currently [[Solicitor General]] of the United States, confirmed in 2009 by a vote of 61-31.<ref>[http://senate.gov/legislative/LIS/roll_call_lists/roll_call_vote_cfm.cfm?congress=111&session=1&vote=00107 On the Nomination (Confirmation Elena Kagan, of Massachusetts, to be Solicitor General)], United States Senate</ref> She was born in 1960.

Elena Kagan would be the "first openly gay justice."<ref>http://newledger.com/2010/04/obamas-top-ten-supreme-court-picks/</ref>

Elena Kagan served as Dean of Harvard Law School, where she supported a censorship and banning of participation by the United States Armed Forces in recruitment that is made available to hundreds of other employers. She signed onto a law brief in 2004 urging the [[U.S. Supreme Court]] to overturn the [[Solomon Amendment]], which placed as a condition of receipt of federal funds by institutions (including Harvard Law School) that they not discriminate against recruitment by the U.S. Armed Forces. ''Rumsfeld v. FAIR'', Docket No. 04-1152, 2004 U.S. Briefs 1152. The U.S. Supreme Court rejected her argument by a vote of 8-0. But Harvard University continues to ban [[ROTC]] to this day.<ref>http://talk.collegeconfidential.com/service-academy-parents/724749-interesting-article-about-rotc.html</ref>

Marjorie Dannenfelser, the leader of the Susan B. Anthony List, explained that:<ref>http://www.lifenews.com/nat4932.html</ref>
{{cquote|In the past Kagan has been a strong supporter of the pro-abortion agenda. She has vigorously opposed the de-funding of taxpayer-funded clinics which promote abortions, despite the fact that a majority of Americans do not want their tax dollars to fund abortion providers.}}

Elena Kagan testified, at her confirmation hearing for the position of Solicitor General, in favor of the use of foreign law to interpret the [[U.S. Constitution]].<ref>http://www.politico.com/news/stories/0309/20283.html</ref>

Elena Kagan's "senior thesis at Princeton raises some eyebrows, in that it apparently laments the non-existence of a viable socialist movement in the U.S."<ref>http://www.examiner.com/x-2581-St-Louis-Gun-Rights-Examiner~y2010m4d10-How-Justice-Stevens-retirement-might-benefit-gun-rights</ref>

Elena Kagan's first oral argument before the U.S. Supreme Court was defending the federal campaign finance law in ''Citizens United v. FEC''. The Court rejected her argument and invalidated the law as unconstitutional.

== Diane Wood ==

Diane Wood is a judge on the [[Seventh Circuit|Court of Appeals for the Seventh Circuit]]. Born in 1950, she is a former clerk of Justice [[Harry Blackmun]], the author of ''[[Roe v. Wade]]''.

In a decision reversed by the U.S. Supreme Court, Diane Wood held that activities protesting abortion clinics constituted illegal racketeering, subjecting pro-lifers to the very harsh penalties designed to combat organized crime. ''National Organization for Women v. Scheidler'', 267 F.3d 687 (7th Cir. 2001), ''rev'd'', 537 U.S. 393 (2003). She is probably the candidate most favored by pro-[[abortion]] groups.

Diane Wood ruled against the [[Second Amendment]], to the consternation of gun rights advocates, in Justice v. Town of Cicero, 577 F.3d 768 (7th Cir., Aug. 14, 2009):<ref>http://volokh.com/2010/04/09/diane-wood-on-the-second-amendment/</ref>

:Judge Wood upheld the handgun registration ordinance of Cicero, Illinois. The opinion accurately explained that under the then-current law of the Circuit, the Second Amendment was not incorporated in the Fourteenth. Surprisingly, Judge Wood then asserted that even if the Second Amendment were incorporated, the registration requirement is constitutional. ... Accordingly, it is plausible to infer from her unreasoned opinion a disregard for Second Amendment rights.

Diane Wood "is clearly ready to invent a constitutional right to same-sex marriage."<ref>http://bench.nationalreview.com/post/?q=MDZjZThkOGE4YzA0NjU1N2E2Yjg0MTM1ZWQxNTc1OWM=</ref>

== Merrick Garland ==

Merrick Garland is a judge on the [[D.C. Circuit|Court of Appeals for the D.C. Circuit]]. He did a Supreme Court clerkship with the [[liberal]] Justice [[William Brennan]]. He was born in 1952.

[[Conservative]] Senator [[Trent Lott]] led a floor fight to oppose Garland's nomination to the D.C. Circuit in 1997, and 23 senators voted against his confirmation.<ref>http://www.senate.gov/legislative/LIS/roll_call_lists/roll_call_vote_cfm.cfm?congress=105&session=1&vote=00034</ref>

Merrick Garland has reportedly ruled or made statements against [[Second Amendment]] rights.

==Sidney Thomas==

==Janet Napolitano==

==Jennifer Granholm==

==Leah Ward Sears==

== References ==

<references/>

[[Category:United States Supreme Court]]
[[Category:politics]]

==External links==
[http://www.slate.com/id/2250251/ Slate short list]
[http://thecaucus.blogs.nytimes.com/2010/04/12/white-house-dashes-chatter-of-clinton-as-supreme-court-nominee/ it won't be Hillary]

Supreme Court Candidates, 2010

2010-04-14T00:31:11Z

EmersonWhitecp: I've heard Clintons name a whole lot.

[[U.S. Supreme Court]] Justice [[John Paul Stevens]], the only decorated veteran on the U.S. Supreme Court, has announced his resignation and thereby created an election year vacancy.

Here are leading contenders to be nominated to fill his seat, with an analysis of each.

== Elena Kagan ==

Elena Kagan is currently [[Solicitor General]] of the United States, confirmed in 2009 by a vote of 61-31.<ref>[http://senate.gov/legislative/LIS/roll_call_lists/roll_call_vote_cfm.cfm?congress=111&session=1&vote=00107 On the Nomination (Confirmation Elena Kagan, of Massachusetts, to be Solicitor General)], United States Senate</ref> She was born in 1960.

Elena Kagan would be the "first openly gay justice."<ref>http://newledger.com/2010/04/obamas-top-ten-supreme-court-picks/</ref>

Elena Kagan served as Dean of Harvard Law School, where she supported a censorship and banning of participation by the United States Armed Forces in recruitment that is made available to hundreds of other employers. She signed onto a law brief in 2004 urging the [[U.S. Supreme Court]] to overturn the [[Solomon Amendment]], which placed as a condition of receipt of federal funds by institutions (including Harvard Law School) that they not discriminate against recruitment by the U.S. Armed Forces. ''Rumsfeld v. FAIR'', Docket No. 04-1152, 2004 U.S. Briefs 1152. The U.S. Supreme Court rejected her argument by a vote of 8-0. But Harvard University continues to ban [[ROTC]] to this day.<ref>http://talk.collegeconfidential.com/service-academy-parents/724749-interesting-article-about-rotc.html</ref>

Marjorie Dannenfelser, the leader of the Susan B. Anthony List, explained that:<ref>http://www.lifenews.com/nat4932.html</ref>
{{cquote|In the past Kagan has been a strong supporter of the pro-abortion agenda. She has vigorously opposed the de-funding of taxpayer-funded clinics which promote abortions, despite the fact that a majority of Americans do not want their tax dollars to fund abortion providers.}}

Elena Kagan testified, at her confirmation hearing for the position of Solicitor General, in favor of the use of foreign law to interpret the [[U.S. Constitution]].<ref>http://www.politico.com/news/stories/0309/20283.html</ref>

Elena Kagan's "senior thesis at Princeton raises some eyebrows, in that it apparently laments the non-existence of a viable socialist movement in the U.S."<ref>http://www.examiner.com/x-2581-St-Louis-Gun-Rights-Examiner~y2010m4d10-How-Justice-Stevens-retirement-might-benefit-gun-rights</ref>

Elena Kagan's first oral argument before the U.S. Supreme Court was defending the federal campaign finance law in ''Citizens United v. FEC''. The Court rejected her argument and invalidated the law as unconstitutional.

== Diane Wood ==

Diane Wood is a judge on the [[Seventh Circuit|Court of Appeals for the Seventh Circuit]]. Born in 1950, she is a former clerk of Justice [[Harry Blackmun]], the author of ''[[Roe v. Wade]]''.

In a decision reversed by the U.S. Supreme Court, Diane Wood held that activities protesting abortion clinics constituted illegal racketeering, subjecting pro-lifers to the very harsh penalties designed to combat organized crime. ''National Organization for Women v. Scheidler'', 267 F.3d 687 (7th Cir. 2001), ''rev'd'', 537 U.S. 393 (2003). She is probably the candidate most favored by pro-[[abortion]] groups.

Diane Wood ruled against the [[Second Amendment]], to the consternation of gun rights advocates, in Justice v. Town of Cicero, 577 F.3d 768 (7th Cir., Aug. 14, 2009):<ref>http://volokh.com/2010/04/09/diane-wood-on-the-second-amendment/</ref>

:Judge Wood upheld the handgun registration ordinance of Cicero, Illinois. The opinion accurately explained that under the then-current law of the Circuit, the Second Amendment was not incorporated in the Fourteenth. Surprisingly, Judge Wood then asserted that even if the Second Amendment were incorporated, the registration requirement is constitutional. ... Accordingly, it is plausible to infer from her unreasoned opinion a disregard for Second Amendment rights.

Diane Wood "is clearly ready to invent a constitutional right to same-sex marriage."<ref>http://bench.nationalreview.com/post/?q=MDZjZThkOGE4YzA0NjU1N2E2Yjg0MTM1ZWQxNTc1OWM=</ref>

== Merrick Garland ==

Merrick Garland is a judge on the [[D.C. Circuit|Court of Appeals for the D.C. Circuit]]. He did a Supreme Court clerkship with the [[liberal]] Justice [[William Brennan]]. He was born in 1952.

[[Conservative]] Senator [[Trent Lott]] led a floor fight to oppose Garland's nomination to the D.C. Circuit in 1997, and 23 senators voted against his confirmation.<ref>http://www.senate.gov/legislative/LIS/roll_call_lists/roll_call_vote_cfm.cfm?congress=105&session=1&vote=00034</ref>

Merrick Garland has reportedly ruled or made statements against [[Second Amendment]] rights.

==Hillary Clinton==
[[Hillary Clinton]] is a favorite of many liberals within the Obama camp. She is far more liberal than any justice currently sitting on the bench.

== References ==

<references/>

[[Category:United States Supreme Court]]
[[Category:politics]]

Mitochondrion

2010-04-14T00:22:38Z

EmersonWhitecp: Cleaned up a little, reworded a bit

'''Mitochondria''' (singular: '''mitochondrion'''), are rod-shaped [[organelle]]s that are responsible for the lions share of energy metabolism within a cell, converting [[oxygen]] and nutrients into Carbon dioxide and water and synthesizing [[adenosine triphosphate|ATP]] in the process. ATP is the chemical energy "currency" of the cell that powers the cell's metabolic activities. This process is called [[aerobic respiration]] and is the reason animals breathe oxygen.

The number of mitochondria present in a [[cell]] depends upon the metabolic requirements of that [[cell]], and may range from a single large mitochondrion to thousands of the [[organelle]]s. Mitochondria, which are found in nearly all [[eukaryote]]s, including plants, animals, fungi, and protists, are large enough to be observed with a light microscope and were first discovered in the 1800s.

==Etymology==
The name of the [[organelle]]s was coined to reflect the way they looked to the first scientists to observe them, stemming from the Greek words for "thread" and "granule." For many years after their discovery, mitochondria were commonly believed to transmit hereditary information. It was not until the mid-1950s when a method for isolating the organelles intact was developed that the modern understanding of mitochondrial function was worked out.

==Structure==
The elaborate structure of a mitochondrion is very important to the functioning of the [[organelle]]. Two specialized membranes encircle each mitochondrion present in a cell, dividing the organelle into a narrow intermembrane space and a much larger internal matrix, each of which contains highly specialized proteins. The outer membrane of a mitochondrion contains many channels formed by the protein [[porin]] and acts like a sieve, filtering out molecules that are too big. Similarly, the inner membrane, which is highly convoluted so that a large number of infoldings called [[cristae]] are formed, also allows only certain molecules to pass through it and is much more selective than the outer membrane. To make certain that only those materials essential to the matrix are allowed into it, the inner membrane utilizes a group of transport proteins that will only transport the correct molecules. Together, the various compartments of a mitochondrion are able to work in harmony to generate [[ATP]] in a complex multi-step process.

[[Image:Mitochondriafigure1.jpg]]

Mitochondria are generally oblong [[organelle]]s, which range in size between 1 and 10 micrometers in length, and occur in numbers that directly correlate with the cell's level of metabolic activity. The organelles are quite flexible, however, and time-lapse studies of living cells have demonstrated that mitochondria change shape rapidly and move about in the cell almost constantly. Movements of the [[organelle]]s appear to be linked in some way to the [[microtubule]]s present in the cell, and are probably transported along the network with motor proteins. Consequently, mitochondria may be organized into lengthy traveling chains, packed tightly into relatively stable groups, or appear in many other formations based upon the particular needs of the cell and the characteristics of its microtubular network.

==Mitochondrial DNA==
The mitochondrion is different from most other [[organelle]]s because it has its own circular [[DNA]] (similar to the [[DNA]] of [[prokaryote]]s) and reproduces independently of the cell in which it is found; an apparent case of [[endosymbiosis]]. Evolutionists hypothesize that millions of years ago small, free-living [[prokaryote]]s were engulfed, but not consumed, by larger [[prokaryote]]s, perhaps because they were able to resist the digestive enzymes of the host organism. The two organisms developed a symbiotic relationship over time, the larger organism providing the smaller with ample nutrients and the smaller organism providing [[ATP]] molecules to the larger one. Eventually, according to this view, the larger organism developed into the [[eukaryotic cell]] and the smaller organism into the mitochondrion.

Mitochondrial [[DNA]] is localized to the matrix, which also contains a host of enzymes, as well as [[ribosome]]s for [[protein synthesis]]. Many of the critical metabolic steps of [[cellular respiration]] are catalyzed by enzymes that are able to diffuse through the mitochondrial matrix. The other proteins involved in respiration, including the enzyme that generates [[ATP]], are embedded within the mitochondrial inner membrane. Infolding of the [[cristae]] dramatically increases the surface area available for hosting the enzymes responsible for [[cellular respiration]].

==Similarities to Chloroplasts==
Mitochondria are similar to plant [[chloroplast]]s in that both [[organelle]]s are able to produce energy and metabolites that are required by the host cell. As discussed above, mitochondria are the sites of respiration, and generate chemical energy in the form of [[ATP]] by metabolizing sugars, fats, and other chemical fuels with the assistance of molecular oxygen. [[Chloroplast]]s, in contrast, are found only in plants and algae, and are the primary sites of [[photosynthesis]]. These [[organelle]]s work in a different manner to convert energy from the sun into the biosynthesis of required organic nutrients using carbon dioxide and water. Like mitochondria, [[chloroplast]]s also contain their own [[DNA]] and are able to grow and reproduce independently within the cell.

==Mitochondria Inheritance==
In most animal species, mitochondria appear to be primarily inherited through the maternal lineage, though some recent evidence suggests that in rare instances mitochondria may also be inherited via a paternal route. Typically, a sperm carries mitochondria in its tail as an energy source for its long journey to the egg. When the sperm attaches to the egg during fertilization, the tail falls off. Consequently, the only mitochondria the new organism usually gets are from the egg its mother provided. Therefore, unlike [[nuclear DNA]], [[mitochondrial DNA]] doesn't get shuffled every generation. However, the mt genome has a higher rate of mutation, and consists of only some sixteen thousand base pairs. Hence, it is often more useful to gauge the "genetic distance" between two persons (since sequencing after DNA isolation is much quicker and it provides a finer genetic comb). It is also useful for the study of human [[evolution]]. [[Mitochondrial DNA]] is also used in forensic science as a tool for identifying corpses or body parts, and has been implicated in a number of genetic diseases, such as [[Alzheimer's disease]] and [[diabetes]].

Evolutionary biologists posit the existence of a mitochondrial [[Eve]], the most recent progenitor of all our mitochondrial DNA. That is, this individual is the single individual from whom all persons existing today have a totally matrilineal line of descent. Given two persons A and B, mitochondrial Eve E is "the mother of the mother of ... the mother of A," as well as "the mother of the mother of ... the mother of B" for some numbers n(A) and n(B) of iterations of "the mother of", where n(A) need not equal n(B). This theory does not imply that Eve was the *only* female human existing in her time, just that if a modern human A can trace his ancestry to a contemporary of Eve, F, then any line of desent from F to A must include a male. Evolutionists believe that mitochondrial Eve existed some 160,000 years ago in [[Africa]]. Analogously, the Y chromosome is passed only patrilineally, so her male counterpart is referred to as Y-chromosomal [[Adam]].

==Ethnic Differences==
Because of this slower mutation rate within mitochondrial DNA, human lineages can be more directly traced back through these inherited genes. ''Computational Cell Biology'' by Christopher Fall and Eric Marland indicates that this more-direct linkage allows for a correlation to be drawn between descent and certain traits, such as intelligence:

"The lineal descent of this genetic material makes it possible to more directly trace genetic links and indicates a strong correlation with traits, most interestingly intelligence. This indicates a link between genetic strains that can be measured objectively, although many researchers view such endeavors with distaste in fears of encouraging racist prejudices."<ref>Fall, Christopher, et. al. Computational Cell Biology. Boone, NC: Appalachian State University Press, 2002. 314.</ref>

==References==
<references/>

[[Category:Cellular Biology]]

Richard Lenski

2010-04-14T00:01:35Z

EmersonWhitecp: The experiment is still ongoing, also captured implies that he is holding onto something, you capture an animal, not a force

'''Richard Lenski''' is a professor of microbial [[ecology]] at [[Michigan State University]].<ref>Richard Lenski Biographical Sketch [http://myxo.css.msu.edu/BioSketch.html]</ref><ref>Richard Lenski Homepage [https://www.msu.edu/~lenski/]</ref> He holds a B.A. from Oberlin College (but does not disclose his field of study in his biographical sketch), and a [[doctorate]] in zoology<ref>Purpose in Evolution symposium Participants [http://www.templeton.org/humble_approach_initiative/Purpose_in_Evolution/part6.html]</ref> from the [[University of North Carolina]].<ref>[https://www.msu.edu/~lenski/]</ref>
When Lenski started graduate school at UNC in 1977, his father, professor Gerhard Lenski, was the Chair of the Division of Social Sciences at the same school. <ref>http://hirr.hartsem.edu/ency/lenski.htm</ref>

Richard Lenski is best known for his 20-year E. coli experiment in which he claims to have observed [[evolution]] in progress, saying that bacteria made minor changes in the long-term laboratory study while insisting that it was not due to contamination.

The 2008 paper he co-authored was [[peer review]]ed in 14 days, sparking obvious questions regarding potential problems <ref>See [[Conservapedia talk:Lenski dialog]].</ref> about the thoroughness of the review. The statistical analysis in Lenski's paper has been criticized for having serious flaws.<ref>See [[Flaws in Richard Lenski Study]].</ref>

When Richard Lenski received a public request for the [[data]] underlying for his published claims, he did not provide the actual data even though his study was taxpayer-funded and even though the request was made in part to enable review of the data by students of the requestor.<ref>[[Conservapedia:Lenski dialog]].</ref>

Undisclosed or obscured data for Lenski's 2008 paper are noted below (pp. 2-3 from paper, superscripts omitted):<ref>For those wishing to review the paper personally it may be found at [http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf this link] from Lenski's website.</ref><ref>A Lenski defender has asserted that this table format is copyrighted under [[GFDL]], which imposes overly complex rules for reuse.</ref>

<includeonly>
{{DEFAULTSORT:{{PAGENAME}}}}
</includeonly>
__NOTOC__
<TABLE width=100% cellspacing=2 cellpadding=2>
<TR><TD width=50% valign=top bgcolor=#003366 align=center><font color="#f6f7ff" size="+1">Undisclosed Data</font>
</TD><TD width=50% valign=top bgcolor=#000000 align=center><font color="#f6f7ff" size="+1">Some Questions about the missing data</font></TD></TR></table>

====Visual inspection====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
Evolution of Cit Function in Population Ara-3. The LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time. ...
</TD><TD width=50% valign=top>
Data on these observations?

</TD></TR></table>

====Turbidity====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
...the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment.
</TD><TD width=50% valign=top>
Data? When and how many?
</TD></TR></table>

====Contaminants???====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
These contaminated cultures reach much higher turbidity owing to the high concentration of [[citrate]] in the medium, which allows the contaminants to reach high density. (When contamination occurs, the affected population is restarted from the latest frozen sample.)
</TD><TD width=50% valign=top>
Data for when that occurred, and how often?

A Richard Lenski defender says, "If interested in a thorough review, contact the group directly, with a legitimate request for data. Otherwise, the disclaimer is a more than adequate description of the sample handling process."

In fact, two requests were made directly to Lenski for data, without success. His [[Conservapedia:Lenski dialog#Second_Reply|second response]] was rude and insulting.
</TD></TR></table>

====The Numbers Please?====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).
</TD><TD width=50% valign=top>
Higher resolution data underlying figure not provided despite request.
</TD></TR></table>

====More missing Numbers====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
A number...
</TD><TD width=50% valign=top>
Data? How many? Statistically significant?
</TD></TR></table>

====Trust us====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
of Cit clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all
</TD><TD width=50% valign=top>
Data? How many? Statistically significant?
</TD></TR></table>

====Missing Characteristics====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
...were Ara, T5-sensitive, and T6-resistant, as expected (2)
</TD><TD width=50% valign=top>
Data about these and other characteristics?

A Richard Lenski defender says, "Interested parties should consult the literature on these topics. It is not within the scope of this paper to address the significance of these markers."

What is missing from disclosure are the data that the markers were actually observed in a reliable and conclusive manner in this study.
</TD></TR></table>

====DNA====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
DNA sequencing also showed...
</TD><TD width=50% valign=top>
DATA??

A Richard Lenski defender says, "The inclusion of this data would be considerably more extensive than appropriate for the inclusion in this paper."

No one asked for the data to be printed in the paper. What is missing is disclosure of the data on the website, or upon public request.
</TD></TR></table>

====More missing data====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
...that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, ...
</TD><TD width=50% valign=top>
Data about these and other characteristics?

A Lenski defender cites to general information unrelated to this study: Available in other publications,
pykF <ref>[http://www.ihop-net.org/UniPub/iHOP/gs/519955.html "IHOP-pykF"]</ref> and
nadR <ref>[http://www.ihop-net.org/UniPub/iHOP/mgi/447129.html "IHOP-nadR"]</ref>.

A Richard Lenski supporter also cites an earlier claim (perhaps also unsupported by public release of the data) by Lenski's group: See also the reference for the sequence identification which Blount ''et al.'' list as reference #30 in their paper: Woods, R., D. Schneider, C. L. Winkworth, M. A. Riley, and R. E. Lenski. 2006. Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. PNAS, USA 103:9107-9112.<ref>http://www.pnas.org/cgi/content/abstract/0602917103v1</ref>.
</TD></TR></table>

====More missing data====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
...and each of these mutations distinguishes this population from all the others (30).
</TD><TD width=50% valign=top>
Data distinguishing "This population from all the others"?
</TD></TR></table>

====Fast Tracked====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
Therefore, the Cit variant arose within the LTEE and is not a contaminant.
</TD><TD width=50% valign=top>
The astoundingly short 14-day [[peer review | PEER REVIEW]] period, measured from the day the paper was sent out for review to the day of formal contribution by Lenski after acceptance, raises questions as to whether there was any meaningful peer review of this at all.
</TD></TR></table>

====Sample Sizes?====
<TABLE width=100% cellspacing=10>
<TR><TD width=50% valign=top>
Cit<sup>+</sup> cells constituted [about] 0.5% of the population at generation 31,500, then 15% and 19% in the next two samples, but only [about] 1.1% at generation 33,000.
</TD><TD width=50% valign=top>
What were the sample sizes and where are the actual data for this sampling?
</TD></TR></table>

Lenski's paper was published in the Proceedings of the [[National Academy of Sciences]], a professional society of scientists with a strong bias towards [[atheism]] and [[evolutionism]]. <ref>http://www.stephenjaygould.org/ctrl/news/file002.html</ref> <ref>http://www.answersingenesis.org/docs/3506.asp</ref>

Lenski's work has been criticized in the past also. In a paper Lenski published in ''Nature'' in May 8, 2003 entitled "The Evolutionary Origin of Complex Features," he described a computer simulation that contained no actual biology. In fact, the discussion section of the paper stated:

:"Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires ...."

Dr. William Dembski explained, "In other words, the computer programmers built into the simulation what they thought evolution needed to make it work. The validity of this study therefore depends on whether the simulation faithfully models biological reality."<ref>http://www.designinference.com/documents/2003.09.UncDiss_Intro_Contribs.pdf</ref>

Others have commented on Lenski's work while taking it at face value.<ref>[[Michael Behe]] wrote, in ''[[The Edge of Evolution]]'', "I had argued that the extreme rarity of the development of chloroquine resistance in malaria was likely the result of the need for several mutations to occur before the trait appeared. Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations." Behe also said, "If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did."[http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O]</ref>

==See Also==

*[[Conservapedia:Lenski dialog]] (letters requesting data, and Lenski's responses)
*[[Conservapedia talk:Lenski dialog]] (discussion of Lenski controversy<ref>See [[Liberal style]] point 1</ref>)
*[[Letter to PNAS]]
*[[Significance of E. Coli Evolution Experiments]]
[[Category:Biology]]
[[Category:Scientists]]
[[Category:Academics]]
[[Category:Conservapedia Dealings with PNAS and Lenski]]
[[Category:Evolution]]
[[Category:Deceit]]

{{evolution}}

==References==
<references/>

{{DEFAULTSORT:Lenski, Richard}}

Escherichia coli

2010-04-13T22:46:18Z

EmersonWhitecp: External links

[[Image:E coli at 10000x original.jpg|right|thumb|350px|E. coli bacteria magnified 10000 times.]]
'''Escherichia coli''' ('''E. coli''') is a bacterium.

''E. coli'' is the head of the large [[bacteria]]l family, ''Enterobacteriaceae'', the enteric bacteria, which are faculatively [[anaerobic]] [[Gram-negative]] rods that live in the [[intestine|intestinal tracts]] of animals in health and disease. The Enterobacteriaceae are among the most important bacteria medically. A number of genera within the family are human intestinal pathogens (e.g. ''Salmonella'', ''Shigella'', ''Yersinia''). Several others are normal colonists of the human gastrointestinal tract (e.g. ''Escherichia'', ''Enterobacter'', ''Klebsiella''), but these bacteria, as well, may occasionally be associated with diseases of humans.

In humans the bacterium, which can be transmitted by foods, animal contact, and drinking water, can cause bloody diarrhea, and also lead to hemolytic uremic syndrome (HUS), a life threatening disease. Although other generic strains of E. coli are thought to be harmless to humans, the O157:H7 strain is particularly virulent and dangerous. USDA began an [[E. coli O157:H7]] testing plan in 1994. As part of the Hazard Analysis and Critical Control Point (HACCP) rule,all meat and poultry slaughter plants are required to test carcasses regularly for generic E. coli in order to verify that their sanitary systems are effectively controlling fecal contamination.
''E. coli'' has been described as the workhorse of molecular biology. It is routinely used in laboratories as a tool for the manipulation of DNA and for producing proteins, as well as being a model organism for the study of cellular processes.
== See also ==

*[[American Medical Association]]
*[[Doctor]]
*[[Bacteria]]
*[[USDA]]
[[category:biology]]
[[category:diseases]]

==References==
[http://www.fsis.usda.gov/Fact_Sheets/E_coli/index.asp E. Coli factsheet]

==External Links==
[http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki Ecoliwiki]
[http://www.genome.wisc.edu/ E. coli genome project]

Escherichia coli

2010-04-13T21:40:43Z

EmersonWhitecp: Undo revision 768988 by TK (Talk) Redlink fixed

[[Image:E coli at 10000x original.jpg|right|thumb|350px|E. coli bacteria magnified 10000 times.]]
'''Escherichia coli''' ('''E. coli''') is a bacterium.

''E. coli'' is the head of the large [[bacteria]]l family, ''Enterobacteriaceae'', the enteric bacteria, which are faculatively [[anaerobic]] [[Gram-negative]] rods that live in the [[intestinal tract]]s of animals in health and disease. The Enterobacteriaceae are among the most important bacteria medically. A number of genera within the family are human intestinal pathogens (e.g. ''Salmonella'', ''Shigella'', ''Yersinia''). Several others are normal colonists of the human gastrointestinal tract (e.g. ''Escherichia'', ''Enterobacter'', ''Klebsiella''), but these bacteria, as well, may occasionally be associated with diseases of humans.

In humans the bacterium, which can be transmitted by foods, animal contact, and drinking water, can cause bloody diarrhea, and also lead to hemolytic uremic syndrome (HUS), a life threatening disease. Although other generic strains of E. coli are thought to be harmless to humans, the O157:H7 strain is particularly virulent and dangerous. USDA began an [[E. coli O157:H7]] testing plan in 1994. As part of the Hazard Analysis and Critical Control Point (HACCP) rule,all meat and poultry slaughter plants are required to test carcasses regularly for generic E. coli in order to verify that their sanitary systems are effectively controlling fecal contamination.
''E. coli'' has been described as the workhorse of molecular biology. It is routinely used in laboratories as a tool for the manipulation of DNA and for producing proteins, as well as being a model organism for the study of cellular processes.
== See also ==

*[[American Medical Association]]
*[[Doctor]]
*[[Bacteria]]
*[[USDA]]
[[category:biology]]
[[category:diseases]]

==References==
[http://www.fsis.usda.gov/Fact_Sheets/E_coli/index.asp E. Coli factsheet]

E. coli O157:H7

2010-04-13T21:33:16Z

EmersonWhitecp: Created page with ''''''E. coli'' O157:H7''' is a virulent strain of ''E. coli'' with multiple genes coding for virulence. It expresses a Shiga like A/B5 toxin that behaves in a manner simi…'

'''''E. coli'' O157:H7''' is a virulent strain of ''[[E. coli]]'' with multiple genes coding for virulence. It expresses a Shiga like [[A/B5 toxin]] that behaves in a manner similar ricin within the body. It also codes for special [[Pili]] known as H7 pili which enables it to attach to the Jejunum, an area of the GI tract that E. coli typically does not attach to.

Escherichia coli

2010-04-13T21:26:30Z

EmersonWhitecp:

[[Image:E coli at 10000x original.jpg|right|thumb|350px|E. coli bacteria magnified 10000 times.]]
'''Escherichia coli''' ('''E. coli''') is a bacterium.

''E. coli'' is the head of the large [[bacteria]]l family, ''Enterobacteriaceae'', the enteric bacteria, which are faculatively [[anaerobic]] [[Gram-negative]] rods that live in the [[intestinal tract]]s of animals in health and disease. The Enterobacteriaceae are among the most important bacteria medically. A number of genera within the family are human intestinal pathogens (e.g. ''Salmonella'', ''Shigella'', ''Yersinia''). Several others are normal colonists of the human gastrointestinal tract (e.g. ''Escherichia'', ''Enterobacter'', ''Klebsiella''), but these bacteria, as well, may occasionally be associated with diseases of humans.

In humans the bacterium, which can be transmitted by foods, animal contact, and drinking water, can cause bloody diarrhea, and also lead to hemolytic uremic syndrome (HUS), a life threatening disease. Although other generic strains of E. coli are thought to be harmless to humans, the O157:H7 strain is particularly virulent and dangerous. USDA began an [[E. coli O157:H7]] testing plan in 1994. As part of the Hazard Analysis and Critical Control Point (HACCP) rule,all meat and poultry slaughter plants are required to test carcasses regularly for generic E. coli in order to verify that their sanitary systems are effectively controlling fecal contamination.
''E. coli'' has been described as the workhorse of molecular biology. It is routinely used in laboratories as a tool for the manipulation of DNA and for producing proteins, as well as being a model organism for the study of cellular processes.
== See also ==

*[[American Medical Association]]
*[[Doctor]]
*[[Bacteria]]
*[[USDA]]
[[category:biology]]
[[category:diseases]]

==References==
[http://www.fsis.usda.gov/Fact_Sheets/E_coli/index.asp E. Coli factsheet]

Gram-negative

2010-04-13T21:25:10Z

EmersonWhitecp: Created page with ''''Gram-negative''' bacteria are bacteria that have a phospholipid bilayer on the outside of the cell, protecting the peptidoglycan cell wall. Because Of this outer layer Cr…'

'''Gram-negative''' [[bacteria]] are bacteria that have a phospholipid bilayer on the outside of the cell, protecting the peptidoglycan cell wall. Because Of this outer layer Crystal violet dye will not saturate the peptidoglycan layer when [[Gram stain|Gram staining]] and decolorization will wash away any purple coloration, allowing safranin counter stain to show through. Gram negative bacteria respond differently to many Antibiotics. Because the outer membrane is semipermeable the bacterial cells can keep Beta-Lactamases within the zone and can easily degrade antibiotics such as [[Penicillin]].

[[E. coli]] are the most heavily studied model organism, and are found almost universally in the intestines of mammals.

Essay:The Logic of Hell

2010-04-13T19:14:42Z

EmersonWhitecp: I don't see a name on this, so I figure I can add to it, hope that's alright.

Jesus emphasized [[Hell]] more often than [[Heaven]]. The most powerful sermon of the 18th century was [[Jonathan Edwards]]' "Sinners in the Hands of an Angry God." Yet today rarely, if ever, does anyone hear any serious mention of [[Hell]]. As [[Hell]] has disappeared from discourse, crime and resultant injustices have predictably filled the social vacuum.

Talk of Hell was phased out in the self esteem movement, where parents and leaders began to worry more about the happiness of those in their charge than the productivity or satisfaction. Unsurprisingly happiness has not become more common, but dissatisfaction has risen.

The '''logic of Hell''' is simple: God can and does punish those who offend, ignore, irritate, or exclude Him. There is no denying His power to do so, and there is no logical reason to expect Him not to. Even the most civilized societies impose harsh punishments on wrongdoers, and it is only logical to do so. Indeed, the more civilized a society, often the harsher its punishment of those who inflict injustice (such as crime) on others or themselves. A just society is simply impossible without harsh punishment for wrongdoing, and it is logically absurd to deny the very real existence of [[Hell]].

== See also ==

*[[Logic]]
*[[Dante's Inferno]]

[[Category:Religion Essays]]