Conservapedia talk:Lenski dialog

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Archive 1

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

Contents

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"[1]
So where are all the data Lenski said he analyzed?--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. --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.--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). --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. -- 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.--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. Turbidity checking: 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). Low concentration of glucose in DM25: this is a factual statement about DM25 media, not an observation. Contaminants: 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. Figure 1: 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. Number of Cit clones, and the following comments except the last: 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. Cit+ is not a contaminant: 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. -- 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.--Aschlafly 11:34, 27 June 2008 (EDT)


Regarding the questions highlighted by Aschlafly to which 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.--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.--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?--Aschlafly 22:22, 27 June 2008 (EDT)
Consider rereading the paper and pull out references provided. It's there.--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.--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.--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?--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.--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.--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.--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.--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.--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.--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.--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.--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.--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.--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.--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.--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.--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 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 the theory of cosmic microwave background radiation. 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.--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.--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.--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.--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? —The preceding unsigned comment was added by Falsehood (talk)
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. --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.

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.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:
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.
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.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 here.
We both know the Earth is round, so the trip is still possible, if not extended. This and this are good links on information theory.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?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.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.JPohl 12:08, 30 June 2008 (EDT)
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.
"This and 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.
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. --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. 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 this brief description of "Haldane's Dilemma".
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 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. --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. --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."[2]
"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.
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).
--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 --

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) -- 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).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 falsehoodsDeanWinter 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.--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. 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.--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.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.--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. --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.--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.--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.--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).--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 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 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 � 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? 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?--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.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.--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.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). 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. 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. 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). 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. 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.LarryFarma 16:18, 27 June 2008 (EDT)
Ok, fair enough. Enjoy your time here. :) 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. 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?"?--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")? 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?" --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) ?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. :-)--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. 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. --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.--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. 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.
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.
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.
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. --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.--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.--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%). --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.--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. 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? 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.--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. LarryFarma 13:29, 29 June 2008 (EDT)
I will not stoop to name calling. Goodbye and good luck with your enquiries.--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?" 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. -- Aaronp
In fact, the only contributions that Larry has made have been to this talk page. Can we get a 90/10 block please? 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. 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.
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. 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.
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. 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. --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.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. Philip J. Rayment 22:53, 26 June 2008 (EDT)

Archive Link?

Can a link be provided to the archive for this page? Thanks. --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? --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. 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. 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 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. [3] [4] —The preceding unsigned comment was added by Drochld (talk)

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?--Frey 13:31, 28 June 2008 (EDT)
If they're not believers, and they're not agnostics/doubters, then they're atheists. Atheism = disbelief. 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.--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.--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.--Boreas talk 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. --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. —The preceding unsigned comment was added by Scholl (talk)

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? 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.--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. 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".--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. 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.--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. 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 this specific issue 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. 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.--Aschlafly 09:35, 3 July 2008 (EDT)
Sorry for the late reply, but 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! 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.--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.--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. 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[5] (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. --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 —The preceding unsigned comment was added by KevinF (talk)

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? 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. --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.LowKey 08:06, 5 December 2008 (EST)
Well put, LowKey. FYI, a chart summarizing how the data were undisclosed is here.--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? --transResident Transfanform! 23:09, 2 July 2008 (EDT)
Good point, AutoFire.--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.LowKey 17:56, 4 December 2008 (EST)
http://www.youtube.com/watch?v=-uz1CiDDIq4 According to Dawkins he stopped to confront the interviewers. —The preceding unsigned comment was added by Vuiasl (talk)---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. --₮K/Talk! 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 {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. LowKey 18:35, 8 December 2008 (EST)}, so the "on the spot" objection is invalid on that account alone.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) --₮K/Talk! 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.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 its own. - 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.--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.--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.--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.--Andy Schlafly 13:08, 15 April 2010 (EDT)
So I went ahead and formatted, hope thats alright. Is this the extra information you were looking for? --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?--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. --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?--Andy Schlafly 17:34, 15 April 2010 (EDT)

You can link directly to the PDF.....--ṬK/Admin/Talk 17:30, 15 April 2010 (EDT)

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. --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.--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. --EmersonWhitecp 19:30, 15 April 2010 (EDT)
Andy, by "raw data," do you mean the bacterial cultures? If that is the case, the main reason Lenski isn't providing you with the raw data is because he thinks that you do not have the proper infrastructure to analyse and maintain them.--PRichards 07:45, 16 April 2010 (EDT)
There's a different between raw data and the actual bacteria PRichards. I doubt anyone would ask for the bacterial samples, suggesting otherwise is just an excuse to not supply the data by playing the "expert" card RichardKerry 07:57, 16 April 2010 (EDT)
Right. PRichards, you take liberal denial to new depths, and your British spelling is a giveaway.--Andy Schlafly 16:44, 16 April 2010 (EDT)
andy, answer the question: "by "raw data," do you mean the bacterial cultures?" raw data could mean anything, please be specific. --Johnb 09:18, 24 May 2010 (EDT)
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