Lenski correspondence

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===First letter, June 13, 2008===
{{quotebox|Dear Professor Lenski,

Skepticism has been expressed on Conservapedia about your claims, and the significance of your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study. Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations. In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000. A recent article about your claims appears in New Scientist here: http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Submission guidelines for the Proceedings of the National Academy of Science state that "(viii) Materials and Data Availability. To allow others to replicate and build on work published in PNAS, authors must make materials, data, and associated protocols available to readers. Authors must disclose upon submission of the manuscript any restrictions on the availability of materials or information." Also, your work was apparently funded by taxpayers, providing further reason for making the data publicly available.

Please post the data supporting your remarkable claims so that we can review it, and note where in the data you find justification for your conclusions.

I will post your reply, or lack of reply, on www.conservapedia.com. Thank you.

Andy Schlafly, B.S.E., J.D. Conservapedia
}}

===First reply, June 13, 2008===
{{quotebox|Dear Mr. Schlafly:

I suggest you might want to read our paper itself, which is available for download at most university libraries and is also posted as publication #180 on my website. Here's a brief summary that addresses your three points.

1) "...your claims, that E. Coli bacteria had an evolutionary beneficial mutation in your study." We (my group and scientific collaborators) have already published several papers that document beneficial mutations in our long-term experiment. These papers provide exact details on the identity of the mutations, as well as genetic constructions where we have produced genotypes that differ by single mutations, then compete them, demonstrating that the mutations confer an advantage under the environmental conditions of the experiment. See papers #122, 140, 155, 166, and 178 referenced on my website. In the latest paper, you will see that we make no claim to having identified the genetic basis of the mutations observed in this study. However, we have found a number of mutant clones that have heritable differences in behavior (growth on citrate), and which confer a clear advantage in the environment where they evolved, which contains citrate. Our future work will seek to identify the responsible mutations.

2. "Specifically, we wonder about the data supporting your claim that one of your colonies of E. Coli developed the ability to absorb citrate, something not found in wild E. Coli, at around 31,500 generations." You will find all the relevant methods and data supporting this claim in our paper. We also establish in our paper, through various phenotypic and genetic markers, that the Cit+ mutant was indeed a descendant of the original strain used in our experiments.

3. "In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000." We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not "appear out of the blue", in any case. We do show that what we call a "potentiated" genotype had evolved by generation 20,000 that had a greater propensity to produce Cit+ mutants. We also show that the dynamics of appearance of Cit+ mutants in the potentiated genotypes are highly suggestive of the requirement for two additional mutations to yield the resulting Cit+ trait. Moreover, we found that Cit+ mutants, when they first appeared, were often rather weak at using citrate. At least the main Cit+ line that we studied underwent an additional mutation (or mutations) that refined that ability and led to a large improvement in growth on citrate. All these issues and the supporting methods and data are covered in our paper.

Sincerely,

Richard Lenski
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===Second letter, June 18, 2008===

{{quotebox|Dear Prof. Lenski,

This is my second request for your data underlying your recent paper, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli," published in PNAS (June 10, 2008) and reported in New Scientist ("Bacteria make major evolutionary shift in lab," June 9, 2008).
http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf
http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html

Your work was taxpayer-funded, and PNAS represents that its authors will make underlying data available. I'd like to review the data myself and ensure availability for others, including experts and my students. Others have expressed interest in access to the data in addition to myself, and your website seems well-suited for public release of these data.

If the data are voluminous, then I particularly request access to the data that was made available to the peer reviewers of your paper, and to the data relating to the period during which the bacterial colony supposedly developed Cit+. As before, I'm requesting the organized data themselves, not the graphs and summaries set forth in the paper and referenced in your first reply to me. Note that several times your paper expressly states, "data not shown."

Given that this is my second request for the data, a clear answer is requested as to whether you will make the key underlying data available for independent review. Your response, or lack thereof, will be posted due to the public interest in this issue. Thank you.

Andy Schlafly, B.S.E., J.D.
www.conservapedia.com
cc: PNAS, New Scientist publications
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===Second reply, June 23, 2008===
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Dear Mr. Schlafly:
 
I tried to be polite, civil and respectful in my reply to your first email, despite its rude tone and uninformed content.  Given the continued rudeness of your second email, and the willfully ignorant and slanderous content on your website, my second response will be less polite.  I expect you to post my response in its entirety; if not, I will make sure that is made publicly available through other channels.
 
'''I offer this lengthy reply because I am an educator as well as a scientist.  It is my sincere hope that some readers might learn something from this exchange, even if you do not.''' 
 
First, it seems that '''reading might not be your strongest suit''' given your initial letter, which showed that you had not read our paper, and given subsequent conversations with your followers, in which you wrote that you ''still'' had not bothered to read our paper.  You wrote: “I did skim Lenski’s paper …”  If you have not even read the original paper, how do you have any basis of understanding from which to question, much less criticize, the data that are presented therein?
 
Second, '''your capacity to misinterpret and/or misrepresent facts is plain''' in the third request in your first letter, where you said:  “In addition, there is skepticism that 3 new and useful proteins appeared in the colony around generation 20,000.”  That statement was followed by a link to a news article from ''NewScientist'' that briefly reported on our work.  I assumed you had simply misunderstood that article, because there is not even a  mention of proteins anywhere in the news article.  As I replied, “We make no such claim anywhere in our paper, nor do I think it is correct. Proteins do not ‘appear out of the blue’, in any case.”  So where did your confused assertion come from?  It appears to have come from one of your earlier discussions, in which an acoltye ''[sic]'' (Able806, who to his credit at least seems to have attempted to read our paper) wrote:

:"I think it might be best to clarify some of Richard's work. He started his E.Coli project in 1988 and has been running the project for 20 years now; his protocols are available to the general public. The New Scientist article is not very technical but the paper at ''PNAS'' is. The change was based on one of his colonies developing the ability to absorb citrate, something not found in wild E.Coli. This occurred around 31,500 generations and is based on the development of 3 proteins in the E.Coli genome. What his future work will be is to look at what caused the development of these 3 proteins around generation 20,000 of that particular colony." 

As further evidence of your inability to keep even a few simple facts straight, you later wrote the following: “It [my reply] did clarify that his claims are not as strong as some evolutionists have insisted.”  But no competent biologist would, after reading our paper with any care, insist (or even suggest) that “3 new and useful proteins appeared in the colony around generation 20,000” or any similar nonsense.  It is only in your letter, and in your acolyte’s confused interpretation of our paper, that I have ever seen such a claim.  Am I or the reporter for ''NewScientist'' somehow responsible for the confusion that reflects your own laziness and apparent inability to distinguish between a scientific paper, a news article, and a confused summary posted by an acolyte on your own website?   
 
Third, it is apparent to me, and many others who have followed this exchange and your on-line discussions of how to proceed, that '''you are not acting in good faith''' in requests for data.  From the posted discussion on your web site, it is obvious that you lack any expertise in the relevant fields.  Several of your acolytes have pointed this out to you, and that your motives are unclear or questionable at best, but you and your cronies dismissed their concerns as rants and even ''expelled'' some of them from posting on your website.  [ http://rationalwiki.com/wiki/Expelled:_No_Intelligence_Allowed]  Several also pointed out that I had very quickly and straightforwardly responded that the methods and data supporting the evolution of the citrate-utilization capacity are already provided in our paper.  One poster in your discussions, Aaronp, wrote:

:“I read Lenski's paper, and as a trained microbiologist, I thought that it was both thorough and well done. His claims are backed by good data, namely that which was presented in the figures. I went through each of the figures after Aschlafly said that they were uninformative. Actually, they are basic figures that show the population explosion of the bacterial cultures after the Cit+ mutation occurred. These figures show that the cultures increased in size and mass at a given timepoint, being able to do so because they had evolved a mechanism to utilize a new nutrient, without the assistance of helper plasmids. … Lenksi’s paper, while not the most definite I’ve seen, is still a very well-researched paper that supports its claims nicely.” 

(As far as I saw, Aaronp is the only poster who asserted any expertise in microbiology.)  As further evidence of the absence of good-faith discussion about our research, in the discussion thread that began even before you sent your first email to me, I counted the words “fraud” or “fraudulent” being used more than 10 times, including one acolyte, TonyT, who says bluntly that I am “clearly a fraudulent hack.”  In the discussion thread that also includes comments after my first reply, the number of times those same words are used has increased to 20, with the word “hoax” also now entering the discussion.  A few posters wisely counseled against such slander but that did not deter you.  I must say, it is surprising that someone with a law degree would make, and allow on his website, so many nasty comments that implicitly and even explicitly impugn my integrity, and by extension that of my collaborators, without any grounds whatsoever and reflecting only your dogmatic adherence to certain beliefs.
 
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'''. 
 
It is my impression that you seem to think we have only paper and electronic records of having seen some unusual ''E. coli''.  If we made serious errors or misrepresentations, you would surely like to find them in those records.  If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess.  But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants.  '''In other words, it’s not that we claim to have ''glimpsed'' “a unicorn in the garden” – we have a whole population of them ''living'' in my lab!'''  [ http://en.wikipedia.org/wiki/The_Unicorn_in_the_Garden]  And lest you accuse me further of fraud, I do not literally mean that we have ''unicorns'' in the lab.  Rather, I am making a literary allusion.  [ http://en.wikipedia.org/wiki/Allusion]
 
One of your acolytes, Dr. Richard Paley, actually grasped this point.  He does not appear to understand the practice and limitations of science, but at least he realizes that we have the bacteria, and that they provide “the real data that we [that’s you and your gang] need”.  Here’s what this Dr. Paley had to say:

:“I think there’s a great deal of misunderstanding here from the critics of Mr. Schlafly and obfuscation on the part of Prof. Lenski and his supporters. The real data that we need are not in the paper. Rather they are in the bacteria used in the experiments themselves. Prof. Lenski claims that these bacteria ‘evolved’ novel traits and that these were preceded by the evolution of ‘potentiated genotypes’, from which the traits could be ‘reevolved’ using preserved colonies from those generations. But how are we to know if these traits weren’t ‘potentiated’ by the Creator when He designed the bacteria thousands of years ago, such that they would eventually reveal themselves when the time was right? The only way this can be settled is if we have access to the genetic sequences of the bacteria colonies so that we can apply CSI techniques and determine if these ‘potentiated genotypes’ originated through blind chance or intelligence. But with the physical specimens in the hands of Darwinists, who claim they will get around to the sequencing at some unspecifed future time, how can we trust that this data will be forthcoming and forthright? Thus, Prof. Lenski et al. should supply Conservapedia, as stewards, with samples of the preserved ''E. coli'' colonies so that the data can be accessible to unbiased researchers outside of the hegemony of the Darwinian academia, even if it won’t be put to immediate examination by Mr. Schlafly. This is simply about keeping tax-payer-funded scientists honest.” 

So, '''will we share the bacteria?  Of course we will, with competent scientists'''.  Now, if I was really mean, I might only share the ancestral strain, and let the scientists undertake the 20 years of our experiment.  Or if I was only a little bit mean, maybe I’d also send the potentiated bacteria, and let the recipients then repeat the several years of incredibly pain-staking work that my superb doctoral student, Zachary Blount, performed to test some 40 trillion (40,000,000,000,000) cells, which generated 19 additional citrate-using mutants.  But I’m a nice guy, at least when treated with some common courtesy, so if a competent scientist asks for them, I would even send a sample of the evolved ''E. coli'' that now grows vigorously on citrate.  A competent microbiologist, perhaps requiring the assistance of a competent molecular geneticist, would readily confirm the following properties reported in our paper:  (i) The ancestral strain does not grow in DM0 (zero glucose, but containing citrate), the recipe for which can be found on my web site, except leaving the glucose out of the standard recipe as stated in our paper.  (ii) The evolved citrate-using strain, by contrast, grows well in that exact same medium.  (iii) To confirm that the evolved strain is not some contaminating species but is, in fact, derived from the ancestral strain in our study, one could check a number of traits and genes that identify the ancestor as ''E. coli'', and the evolved strains as a descendant thereof, as reported in our paper.  (iv) One could also sequence the ''pykF'' and ''nadR'' genes in the ancestor and evolved citrate-using strains.  One would find that the evolved bacteria have mutations in each of these genes.  These mutations precisely match those that we reported in our previous work, and they identify the evolved citrate-using mutants as having evolved in the population designated Ara-3 of the long-term evolution experiment, as opposed to any of the other 11 populations in that experiment.  And one could go on and on from there to confirm the findings in our paper, and perhaps obtain additional data of the sort that we are currently pursuing. 
 
Before I could send anyone any bacterial strains, in order '''to comply with good scientific practices''' I would require evidence of the requesting scientist’s credentials including: (i) affiliation with an appropriate unit in some university or research center with appropriate facilities for storing (-80ºC freezer), handling (incubators, etc.), and disposing of bacteria (autoclave); and (ii) some evidence, such as peer-reviewed publications, that indicate that the receiving scientist knows how to work with bacteria, so that I and my university can be sure we are sending biological materials to someone that knows how to handle them.  By the way, our strains are not derived from one of the pathogenic varieties of ''E. coli'' that are a frequent cause of food-borne illnesses.  However, even non-pathogenic strains may cause problems for those who are immune-compromised or otherwise more vulnerable to infection.  Also, my university requires that a Material Transfer Agreement be executed before we can ship any strains.  That agreement would not constrain a receiving scientist from publishing his or her results.  However, if an incompetent or fraudulent hack (note that I make no reference to any person, as this is strictly a hypothetical scenario, one that I doubt would occur) were to make false or misleading claims about our strains, then I’m confident that some highly qualified scientists would join the fray, examine the strains, and sort out who was right and who was wrong.  That’s the way science works. 
 
I would also generally ''ask'' what the requesting scientist intends to do with our strains.   Why?  It helps me to gauge the requester’s expertise.  I might be able to point out useful references, for example.  Moreover, as I’ve said, we are continuing our work with these strains, on multiple fronts, as explained in considerable detail in the Discussion section of our paper.  I would not be happy to see our work “scooped” by another team – especially for the sake of the outstanding students and postdocs in my group who are hard at work on these fronts.  However, that request to allow us to proceed, without risk of being scooped on work in which we have made a substantial investment of time and effort, would be just that: a request.  In other words, we would respect ''PNAS'' policy to share those strains with any competent scientist who complied with my university’s requirements for the MTA and any other relevant legal restrictions.  If any such request requires substantial time or resources (we have thousands of samples from this and many other experiments), then of course I would expect the recipient to bear those costs.
 
So there you have it.  I know that I’ve been a bit less polite in this response than in my previous one, but I’m still behaving far more politely than you deserve given your rude, willfully ignorant, and slanderous behavior.  And I’ve spent far more time responding than you deserve.  However, as I said at the outset, '''I take education seriously''', and I know some of your acolytes still have the ability and desire to think, as do many others who will read this exchange.
 
Sincerely,
:Richard Lenski
 
P.S.  Did you know that your own bowels harbor something like a billion (1,000,000,000) ''E. coli'' at this very moment?  So '''remember to wash your hands''' after going to the toilet, as I hope your mother taught you.  Simple calculations imply that there are something like 10^20 = 100,000,000,000,000,000,000 ''E. coli'' alive on our planet at any moment.  Even if they divide just once per day, and given a typical mutation rate of 10^-9 or 10^-10 per base-pair per generation, then pretty much every possible double mutation would occur every day or so.  That’s a lot of opportunity for evolution. 
 
P.P.S.  I hope that some readers might get a chuckle out of this story.  The same ''Sunday'' (15 June 2008) that you and some of your acolytes were posting and promoting scurrilous attacks on me and our research (wasn’t that a bit disrespectful of the Sabbath?), '''I was in a church attending a wedding'''.  And do you know what Old Testament lesson was read?  It was ''Genesis'' 1:27-28,<ref><bible book=Genesis chapter=1 verse1=27 verse2=28/></ref> in which God created Man and Woman.  It’s a very simple and lovely story, and I did not ask any questions, storm out, or demand the evidence that it happened as written at a time when science did not yet exist.  I was there in the realm of spirituality and mutual respect, not confusing a house of religion for a science class or laboratory.  And it was a beautiful wedding, too.
 
P.P.P.S. You may be unable to understand, or unwilling to accept, that evolution occurs.  '''And yet, life evolves!'''  [ http://en.wikipedia.org/wiki/E_pur_si_muove]  From the content on your website, it is clear that you, like many others, view God as the Creator of the Universe.  I respect that view.  I find it baffling, however, that someone can worship God as the all-mighty Creator while, at the same time, denying even the possibility (not to mention the overwhelming evidence) that God’s Creation involved evolution.  It is as though a person thinks that God must have the same limitations when it comes to creation as a person who is unable to understand, or even attempt to understand, the world in which we live.  Isn’t that view insulting to God?
 
P.P.P.P.S.  I noticed that you say that one of your favorite articles on your website is the one on “Deceit.”  That article begins as follows: “Deceit is the deliberate distortion or denial of the truth with an intent to trick or fool another. Christianity and Judaism teach that deceit is wrong. For example, the Old Testament says, '''‘Thou shalt not bear false witness against thy neighbor.’'''”  You really should ''think'' more carefully about what that commandment means before you go around bearing false witness against others.
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==References==
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Categories: Lenski affair, Reference pages