Difference between revisions of "Conservapedia talk:Lenski dialog"

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(reply to Larry Farma)
(Reply to comments in archive: "real scientists" don't do such a good job)
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:::::: Your sermon is misplaced.  Taxpayers paid for Lenski's study, and any real scientist should reject the inexplicable withholding the data underlying its conclusions.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
 
:::::: Your sermon is misplaced.  Taxpayers paid for Lenski's study, and any real scientist should reject the inexplicable withholding the data underlying its conclusions.--[[User:Aschlafly|Aschlafly]] 22:22, 27 June 2008 (EDT)
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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.
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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.
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What does "real scientists" mean? If it means practicing academics today, it's sadly wrong. Most [[professor values|professors]] are self-centered, and would see true peer review as impinging on their personal freedom. "Who has time," they think, "to transcribe lab notebooks? I've got more papers to publish!" I bet the majority would even resist your request to Lenski. This liberal attitude towards truth is what leads to claptrap like [[Particle/wave duality theory]] and [[COBE|the theory of cosmic microwave background radiation]]. [[User:Drochld|Drochld]] 09:19, 28 June 2008 (EDT)
  
 
== More replies to archived comments ==
 
== More replies to archived comments ==

Revision as of 07:19, 28 June 2008

Archive 1

The discussion below concerns the letters and response set forth at Conservapedia:Lenski dialog.

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)
...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)
...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)
...(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)
...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)
...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)
...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)
...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)
...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.
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)

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)

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.
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 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.
Genetic variation through sexual reproduction is a variation within the existing genetic information; sexual reproduction does not create new genetic information.
Philip J. Rayment 23:31, 27 June 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)

(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)

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)