Lenski affair

{{gold}}{{cpmothball}}{{conservapedia}}{{hatnote|Were you looking for the [[Bill Clinton|Lewinsky affair]]?}}
The '''Lenski affair''' was an attempt by politically-conservative activist lawyer [[Andrew Schlafly]] (creator of [[Conservapedia]] and endorser of [[creationism]]) to challenge the groundbreaking research of Michigan State University professor and National Academy of Science member [[Richard Lenski]]. Lenski and his student Zachary Blount had reported observation of [[evolution]] in bacteria. Schlafly wrote to Lenski [[Release the data|demanding raw data]], but Lenski refused, citing Schlafly's lack of credentials as a qualified bacteriologist. Schlafly's challenge resulted in publicity on the [[Internet]]. [[Richard Dawkins]] [[Conservapedia:In the media#September 2009|discusses]] Lenski's research and the affair in his book ''The Greatest Show on Earth'', referring to Schlafly's implied doubts about Lenski's results as 
an "impertinent suggestion".<ref>Dawkins, Richard (2009) "The Greatest Show on Earth" page 131 (Chapter 5 "Before Our Very Eyes"), Simon and Schuster, ISBN 1416594787</ref><ref>[https://web.archive.org/web/20100524123029/http://www.youngausskeptics.com/2009/09/review-the-greatest-show-on-earth/ Review: The Greatest Show on Earth], Young Australian Skeptics</ref>

==Background==
[[Image:Lenski's long-term lines of E. coli on 25 June 2008, close-up of citrate mutant.jpg|thumb|left|The population designated Ara-3 (center) has evolved to use the citrate present in the growth medium.]]
On June 9, 2008, the ''[[New Scientist]]'' published an article describing preliminary results of a long-running [[experiment]] started by Lenski.<ref>[http://www.newscientist.com/channel/life/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab.html Bacteria make major evolutionary shift in the lab], ''New Scientist''</ref> Lenski and his team had taken a single strain of the bacterium ''E. coli'', separated its descendants into twelve populations,<ref group=note>How Biblical!</ref> and proceeded to observe their [[mutation]]s over the course of two decades.<ref>[http://myxo.css.msu.edu/ecoli The process discussed] on Lenski's website.</ref> The ''E. coli'' were fed a measured amount of glucose every day. At one point, one of the populations exploded far beyond the parameters of the experiment. Lenski eventually discovered that this population had evolved the ability to metabolize citrate, an organic [[molecule]] which was part of the solution the ''E. coli'' lived in, but which ''E. coli'' cannot normally uptake. Thus, evolution had been visibly observed, with an exquisite amount of [[evidence]] establishing the timeline along the way. Not only that, but the experiment was [[reproducibility|repeatable]]; Lenski started new experiments with the frozen "archives" of the population which exploded and found that beyond a certain point, that particular population of ''E. coli'' were highly likely to evolve the ability to digest citrate. The paper also highlighted the role of [[historical contingency]] in evolution and the role of [[potentiating mutation]]s.

Naturally, this news item was posted to Conservapedia, bringing it to the attention of Schlafly.  As he is a creationist, this obviously [[Cognitive dissonance|flew in the face of his views]] and [[Lenski results challenge creationism|could not be tolerated]].  After a discussion in which he expressed skepticism, he proceeded to send Dr. Lenski an email requesting further data and set up a page on his blog/"[[Conservapedia|encyclopedia]]" titled "Lenski dialog."  The ensuing exchange of emails is below.

==Correspondence==
{{:Lenski affair/Correspondence}}
==Elements censored in the reply==
Keen readers at Conservapedia noticed that the phrase "''[Ed.: citation omitted due to spam filter]''" was contained in the second of the professor's replies at their site. Inquiries about this withholding of information were made by some readers at Conservapedia. After at least two users were blocked for pursuing the issue, it was revealed that the offending link was to none other than a certain RW. It was further established that the initials RW referred to a "[[RationalWiki|Wiki claimed to be Rational]]" — in other words, ''the very wiki you're reading right now''. This ironic desire to conceal data caused some concern at Conservapedia and mirth at RationalWiki. Our article above has the full information included in the professor's reply. For those who are interested, the link Conservapedia censored is ''[[Expelled: No Intelligence Allowed]]''.

As a final [[irony]], Conservapedia subsequently erased from the talk page all references to their failure to print the entire response.  

Also, a lesser point is that the emphasis (bolding) in the second reply is from the original, but was omitted in Conservapedia's transcription. This was almost certainly a simple oversight.<ref group=note>[[Hanlon's Razor]] applies. If Schlafly read and copied the email in a plaintext format, as opposed to viewing it as HTML, he wouldn't have seen it.</ref>
(UPDATE: As of August 21, 2015, the bolding appears to have been replaced. It is unknown when this happened.)

==Consequences==
Mr. Schlafly certainly intended that his letters to Prof. Lenski would have the effect of somehow discrediting his work or discomforting him in some way. In the event, the consequences couldn't have been more different.

*As a result of Mr. Schlafly's tomfoolery, [[Streisand effect|he raised the status of Prof. Lenski's evolution-demonstrating paper from the status of "highly significant" to "Internet science-blog phenomenon."]] It is difficult to think of any other action which would have so raised the profile of this research. 
*Many non-specialists no doubt took an interest in the exchange. For many, the take-home sound bites would have been "Scientist proves Evolution in Lab" and "Religious [[Fundamentalist]]s don't Understand [[Science]]." Others may have gone on to gain a deeper understanding as a consequence.
*Conservapedia once again became the laughingstock of the Internet. And this time, the blame couldn't be put on any alleged [[Conservapedia:Parodist|parodists]]. Mr. Schlafly ''personally'' started the ball rolling, continued with it against the publicly-expressed doubts of his associates, and went back a second time when he didn't like the first answer. 
*By refusing to include the link to RationalWiki in Prof. Lenski's second reply, Mr. Schlafly did ''more than any other individual'' to raise RationalWiki's profile on the net. Amazingly, Conservapedia then compounded the error by clumsily attempting to [[Streisand effect|hide its own open correspondence]] concerning the matter.
*Schlafly showed his take of the episode like [http://www.conservapedia.com/Professor_values#Immoral.2C_Unethical.2C_or_Bizarre_Behavior this]: "Richard Lenski of Michigan State University was rude and demeaning when replying to a member of the public who asked about his research."    

In conclusion, it is difficult to imagine a course of action more incredibly, enormously, staggeringly counter-productive to his cause than that undertaken by Mr Schlafly.

Schlafly currently spends his days editing (and censoring content of) [http://www.conservapedia.com/index.php?title=Richard_Lenski&oldid=486247 this tripe] that poses as an encyclopedia article.

==Beating a dead horse[[File:Deadhorse.gif|32px]], horse kicks back==
===Conservapedia letter to PNAS===
On August 4, 2008, Conservapedia then drafted and emailed, over Andrew Schlafly's signature, this letter to PNAS:<ref>[http://www.conservapedia.com/index.php?title=Letter_to_PNAS&curid=70036&diff=495430&oldid=495379 Emailed to PNAS "with minor improvements"]</ref>

{{QuoteBox|
''Title:'' 
:Identification of flaws in the following paper published in PNAS: Blount ZD, Borland CZ, and Lenski RE, "Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli," 105 PNAS 23, pp. 7899–7906 (June 10, 2008).  

''Author:'' 
:Andrew Schlafly, B.S.E., J.D. 

''Author Affiliations:'' 
:www.conservapedia.com, teacher of pre-college students  

''Text:''
:The following flaws in this PNAS paper negate its claim that ''E. Coli'' bacteria evolved through a beneficial mutation:<ref>Detail is at [http://www.conservapedia.com/Flaws_in_Richard_Lenski_Study "Flaws in Richard Lenski Study"] and its talk page.</ref>

::1. Figure 3 depicts an "historical contingency" hypothesis around the 31,000th generation, but the abstract states that mutations "arose by 20,000 generations."  The paper fails to admit that the Third Experiment disproved the contingency hypothesis depicted in Figure 3.
::2. Both hypotheses propose fixed mutation rates, but the failure of mutations to increase with sample size disproves this.  If the authors claim that it is inappropriate to compare for scale the Second and Third Experiments to each other and to the First Experiment, then it was also an error to treat them similarly statistically.
::3. The paper incorrectly applied a Monte Carlo resampling test to exclude the null hypothesis for rarely occurring events.  The Third Experiment results are consistent with the null hypothesis, contrary to the paper's claim. 
::4. It was error to include generations of the ''E. coli'' already known to contain trace Cit+ variants.  The highly improbable occurrence of four Cit+ variants from the 32,000th generation in the Second Experiment suggests an origin from undetected, pre-existing Cit+ variants.
::5. The Third Experiment was erroneously combined with the other two experiments based on outcome rather than sample size, thereby yielding a false claim of overall statistical significance.

:The underlying data for this publicly (NSF) funded research have not been publicly released, despite requests for such release and NSF policy that "data collected with public funds belong in the public domain."<ref>[http://www.nsf.gov/sbe/ses/common/archive.jsp Data Archiving Policy], National Science Foundation</ref>

cc: 
:Randy Schekman, Editor-in-Chief, PNAS, University of California at Berkeley (by email and postal mail)
:New Scientist (by fax - 0171 261 6464)
:Rep. Brian Baird, Chairman of the Subcommittee on Research and Science Education of the U.S. House Committee on Science and Technology (by postal mail)
:Judicial Watch (by email)
}}

As with the letter to Prof Lenski, the letter was a joint effort by editors from Conservapedia, with the initial draft being drawn up by DinsdaleP. User Stitch75 provided some constructive criticism, both on the content and style of the letter.

Schlafly disregarded any and all advice, silencing Stitch75 with: 

{{cquote|'Stitch75', you seem to think that the truth depends on whether PNAS accepts it. It doesn't. [[Dunning-Kruger effect|Lenski's paper is badly flawed regardless of whether he admits it, PNAS admits it, or you admit it. That's the beauty of the truth: it doesn't require admission by anyone]]. I'm fine with Lenski and PNAS refusing to admit the flaws in their paper. After all, if they really cared about quality then I doubt they would have published their flawed paper after merely 14 days or less of peer review.<ref>[[:File:Talk-Letter to PNAS - Conservapedia 1285938022559.png|Screenshot of talk page. The corresponding history for that page does not include links to the opening few comments]].</ref>}} 

It is possible — and the suggestion was raised — that Schlafly deliberately submitted a flawed letter, which would enable him to cry "[[censorship]]" when it was not published.
 
On August 24, 2008, Andrew Schlafly posted a news item on the front page of Conservapedia that notification had been given, by PNAS, to all the co-authors of Lenski's paper regarding the above letter. The editorial board would review the letter and consider one of the following: acceptance, rejection, or revision. They settled on "rejection," as the following reply shows.

===PNAS reply to Mr. Schlafly and his Conservapedia===
Dateline: September 11, 2008.<ref>[https://web.archive.org/web/20160310213143/http://www.conservapedia.com/index.php?title=Letter_to_PNAS&curid=70036&diff=495430&oldid=495379 Draft of PNAS Letters Response from Conservapedia] (archived from March 10, 2016).</ref>

{{quotebox|A member of the Editorial Board has evaluated the letter and concluded that PNAS cannot publish it for the following reasons:

:From what I take to be the underlying issue from the numbered points, Mr. Schlafly's main concern has to do with the fact that one experiment failed to yield a statistically significant result, and this happened to be the experiment with the largest sample size. Every experiment has limited power to detect a difference of any given magnitude, and so in a series of experiments some may yield non-significant results even when the null hypothesis is false. The non-significant experiment may even be the one with the largest sample size. There is nothing exceptional in this--it is a matter of chance. Nevertheless, from a statistical point of view, it is proper to combine the results of independent experiments, as Blount et al. did correctly in their original paper. If the overall result is significant, as it is in this case, then the whole series of tests is regarded as significant. Mr. Schlafly seems to suggest that experiments differing in sample size cannot be combined in an overall analysis, and if this is what he is suggesting, he is wrong. 

:I think Letters published in PNAS should raise points that in themselves, or in conjunction with the authors' response, should be of wide interest to the readership of PNAS or should illuminate some obscure or subtle point. The issues raised by Mr. Schlafly are neither obscure nor subtle, but are part of everyday statistical analysis at a level too elementary to need rehearsal in the pages of PNAS.

:Mr. Schlafly's final comment about release of data is uncalled for. My understanding is that the authors have made the relevant materials available on their web site. This seems to me to meet the requirement that "data collected with public funds belong in the public domain." If Mr. Schlafly believes that the disclosure is incomplete, that is an issue that needs to be argued with the original funding agency, not with the readers of PNAS.
}}

==Conclusion==
In a 2012 paper, Blount et al. identified and sequenced the mutations leading to the Cit(+) [[phenotype]]. By demonstrating the actual series of mutations that eventually give rise to the phenotype, the scientists eliminated any concerns of horizontal gene transfer or contamination.<ref>[https://archive.ph/51XCB Genomic analysis of a key innovation in an experimental Escherichia coli population], ''Nature''</ref>

==See also==
*[[Analysis of the Lenski Paper]]
*Conservapedia talk:Lenski dialog - RW's restored version of the talk pages: ([[Conservapedia:Lenski affair talk 1|1]])([[Conservapedia:Lenski affair talk 2|2]])([[Conservapedia:Lenski affair talk 3|3]])
*[[Conservapedia:Schlafly's alleged Flaws in Lenski's Study]]
*[[Lenski results challenge creationism]]
*[[Pwned]]
*[[Release the data]]

==External links==
*[http://www.conservapedia.com/Conservapedia:Lenski_dialog The same data on Conservapedia]
*[[PZ Myers]]'s [http://scienceblogs.com/pharyngula/2008/06/24/lenski-gives-conservapdia-a-le/ take] on ''Pharyngula''
*[http://web.archive.org/web/20140601094702/http://www.badscience.net/2008/06/all-time-classic-creationist-pwnage/ All-time classic creationist pwnage], from [[Ben Goldacre]]'s ''Bad Science'' column
*[http://www.newscientist.com/blog/shortsharpscience/2008/06/creationist-critics-get-their.html?DCMP=ILC-hmts&nsref=specrt10_head_Lenski%201%20Schlafly%200 Creationist critics get their comeuppance], ''New Scientist''
*[http://arstechnica.com/articles/culture/conservapedias-evolutionary-foibles.ars Bacteria evolve; Conservapedia demands recount], Ars Technica
*[[talk.origins]] [http://groups.google.com/group/talk.origins/browse_thread/thread/ca3cb3c93db6bd45/420dfabba7af9a3a?q=schlafly&lnk=ol& thread]
*[http://acandidworld.com/2008/07/06/conservapedia-distrust-of-science-when-you-neednt-win-the-war-to-make-the-point/ Conservapedia & Distrust of Science: When You Needn’t Win the War to Make the Point], by [[User:Caius|AmesG]]

==Notes==
{{reflist|group=note}}
==References==
{{reflist|2}}

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Categories: Science, biology, evolution, internet, Lenski affair