Richard Lenski is a biologist who recently found evidence for the emergence of new traits among E.coli bacteria, in a fascinating experiment which he has described in a paper in PNAS (best lay coverage here). His results look a bit like evolution. You will note that his paper includes the original data. Andrew Schlafly is a startlingly predictable right wing christian activist who runs Conservapedia. I highly recommend a look around there if you’ve not already had the pleasure, because even the people who run Conservapedia find it hard to tell whether the edits are being made by god-fearing americans or naughty satirists.
Schlafly read Lenski. He got angry. He demanded the original data. It was pointed out to him that the original data was in the paper. He demanded the original data again. With menaces. The following exchange is mirrored humbly and verbatim in case of disappearance. It represents pwnage on a scale most of us can only dream of.
First letter
June 13, 2008 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-... 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
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
Second letter
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-... 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
Second reply
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 (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
...
> Richard Lenski is a biologist who recently found evidence for the > emergence of new traits among E.coli bacteria, in a fascinating > experiment which he has described in a paper in PNAS (best lay > coverage here). His results look a bit like evolution. You will note > that his paper includes the original data. > Andrew Schlafly is a startlingly predictable right wing christian > activist who runs Conservapedia. I highly recommend a look around > there if you’ve not already had the pleasure, because even the people > who run Conservapedia find it hard to tell whether the edits are being > made by god-fearing americans or naughty satirists.
> Schlafly read Lenski. He got angry. He demanded the original data. It > was pointed out to him that the original data was in the paper. He > demanded the original data again. With menaces. > The following exchange is mirrored humbly and verbatim in case of > disappearance. It represents pwnage on a scale most of us can only > dream of.
> First letter
> June 13, 2008 > 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-... > 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, onwww.conservapedia.com. > Thank you. > Andy Schlafly, B.S.E., J.D. Conservapedia
> First Reply
> 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
> Second letter
> 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.p...... > 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
> Second reply
> 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 > (Able806, who to his credit at least seems to have attempted to readour 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
On Fri, 25 Jul 2008 11:31:48 GMT, John Smith wrote: >> I will post your reply, or lack of reply, on www.conservapedia.com . >> Thank you. >> Andy Schlafly, B.S.E., J.D. Conservapedia
>> I will post your reply, or lack of reply, on www.conservapedia.com . >> Thank you. >> Andy Schlafly, B.S.E., J.D. Conservapedia
> Husband of the shrieking bitch Phyllis?
Son. Andy, and his brother Roger, posted here for a couple of months. Their postings were composed of the same stupidity that you see from Andy at Conservapedia. And it is hard to believe that someone with a college education is so stupid as to believe the drivel he states.
-- Dick #1349 "They that can give up essential liberty to obtain a little temporary safety deserve neither liberty nor safety." ~Benjamin Franklin
Home Page: dickcr.iwarp.com email: dic...@gmail.com
