Lenski shuts down Conservapedia
June 20th, 2008Or so it would seem. Andy Schlafly posted the following to the Lenski paper talk page at Conservapedia this morning:
Lenski has essentially refused my request that he make his underlying data available for public scrutiny, despite his use of public funding. Given the remarkably short time between submission of his PNAS manuscript and its acceptance (only 14 days), I doubt his paper even had meaningful peer review.
It’s unscientific for others to repeat as true an unverified claim based on concealed data. I wonder if PNAS violated its own stated policies by publishing Lenski’s paper, and I’m going to email its Editor-in-Chief to request an explanation.
Schlafly hasn’t posted the text of any response from Lenski, so I don’t know for sure if he replied or if Andy is interpreting silence as a refusal. It’s also painfully clear that Schlafly still has no idea what he’s talking about. Peer reviewers are not given anything other than paper to be published. They might see raw data if they ask for it, but generally they only review the submitted manuscript and associated figures.
As for the time frame of the review process, it is dependent on the paper under review. For a very good paper, reviewers might not ask for any revisions and the paper will be approved for publication quickly. If reviewers feel that revisions need to made or that other experiments need to be performed, it may be several months before a paper is approved. In Lenski’s case, this was his “inaugural article” in PNAS. All newly elected members to the National Academy of Sciences are given an inaugural article, which can basically be on whatever they want. No doubt it was reviewed, but I don’t think it was treated as a normal submission. Furthermore, only the most talented of scientists become members of the NAS, so it isn’t hard to believe that Richard Lenski would submit a paper that passed peer review with no requested revisions.
And for the last damn time, the data aren’t concealed. They are in the paper. Everything Schlafly needs to analyze Lenski’s work is right there. But anyway, it looks like this affair may be winding down. Schlafly claims he’s contacting the Editor-in-Chief of PNAS, but I don’t think he’ll get anything out of that either.
Edit:
I just looked at the submission guidelines for PNAS. Below are the guidelines for NAS members:
An Academy member may submit up to four of his or her own manuscripts for publication per year. Members must secure the comments of at least two qualified referees. Referees should be asked to evaluate revised manuscripts to ensure that their concerns have been adequately addressed. Members’ submissions must be accompanied by the names and contact information, including e-mails, of knowledgeable colleagues who reviewed the paper, along with all of the reviews received, the authors’ response, and a brief statement endorsing publication in PNAS. Reviews must be on the PNAS review form and should not be from the authors’ own institution. Members should follow NSF guidelines to avoid conflict of interest between referees and authors (see Section iii). Members must verify that referees are free of conflicts of interest, or must disclose any conflicts and explain their choice of referees. The Academy member must be a corresponding author on the paper. These papers are published as ‘‘Contributed by’’ the responsible editor.
It appears that the review process for NAS members is different than for non-members, and it only requires two referees rather than the standard five. Yet again, Andy Schlafly proves he is a fanatical moron.
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June 20th, 2008 at 3:17 pm
I joined the discussion at conservapedia trying to figure out exactly what they wanted. (I am in the general comment thread almost at the bottom.)
I look at the first claim of the paper (that a stain of E. coli mutated so that it could utilize citrate) was supported by direct data (optical density figures). I assert (but say I do not know of my own knowledge) that such data is direct, not derived from other data. (An example of derived data: radiation exposure above background, which depends on the dosimeter readings of the individual and the background readings, both of which are subject to errors.) So (assuming wjat I said is true, there is no raw data to report for, say, figure 1.
I do point out that there is raw data behind the assertion that the Cit+ strain is not a contaminate — presumably there are DNA sequence charts etc. which back up the statements that it contains the markers expected and the mutations expected, and one could presumably ask for these data, but that would only be useful, absent an allegation of fraud, if the tests were sensitive and difficult and subject to misinterpretation and error. I am assuming they are not, but am not an expert.
I quote extensively from the paper in the hopes that the discussion will move to specifics.
June 20th, 2008 at 7:41 pm
David,
I have to give you props for wading into that talk page. The sheer inanity as well Andy Schlafly’s dictatorial control of the discussion make that an extremely unpleasant place to spend any time. I actually read your comments there earlier and I think you made some excellent points. In terms of documenting the emergence of Cit+, the data are simply direct observation of bacterial growth. Optical density is just a quantitative measure of turbidity. For OD measurements, an experimenter takes a small sample from the liquid growth medium (about 1 ml) and measures the absorbance at about 600 nm using a UV-vis spectrophotometer. The raw data in that case will most likely be handwritten notes in a lab notebook. For growth on agar plates, the data will just be a simple observation of the presence or absence of colonies. It would be a short entry in a lab notebook, something like, “Streaked cells on citrate plate, incubated at 37C. Have 12 colonies 8 days later.”
In terms of determining that the Cit+ was not a contaminant, you’re absolutely right. There would be sequencing data. This is absolutely routine and reliable. I believe they also looked at for the Ara- phenotype, which I believe means the cells could not metabolize the sugar arabinose, as well as sensitivity/resistance to T5/T6 bacteriophage. In the latter, they are again just making direct observations of cells growing on nutrient agar plates and writing down results.
So, your discussion is pretty spot on. Looking at the raw data, which are likely just observations written in a lab notebook (along with some sequencing results) isn’t going to help anyone analyze the paper. I think Schlafly is going to run with the whole, “The data were concealed! OMG, fraud!” angle, which is damn stupid. Peer review cannot catch outright fraud, and the purpose of peer review is not to prevent fraud. Any given paper could be fraudulent, and papers with fake results have been published before. These are eventually caught when the scientific community attempts to replicate or build on the published results and fails. Anyway, good luck with any further attempts at bringing rationality to the talk page.
June 21st, 2008 at 1:27 pm
I really hope they try to go for the fraud angle. I graduated from MSU’s department of zoology and have met Dr. Lenski and some of his lab members on a number of occasions (though it was years ago) and have to say that all indications point to clean and ethical scientific behavior. Of course I could be wrong, but it is extremely unlikely. However, fraud in the Lenski lab is about as likely as God creating creating the universe and everything in it, so I wouldn’t be surprised to find out that these people go after the Lenski lab. I say let ‘em try and lose face doing it.
June 26th, 2008 at 8:27 am
Steve,
The conservapedia folks probably aren’t concerned with whether Lenski et al ‘actually’ behaved in an academically honest fashion so much as whether they can use Lenski’s refusal to “provide data” as anecdotal evidence for their readers that such is not the case. These people thrive on rhetoric, if they can turn to their wider readership and say “See, see! We said he was a fraud and then he wouldn’t give us his data!” if they can put themselves in a position to do this they’ve accomplished their goal.