The douchebags from Conservapedia are trying to refute the Lenski E. coli evolution paper, and they’re basically accusing the Lenski group of outright fraud.  Their email to Lenski reads:

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

I can’t believe they sent that to Lenski.  To begin, the letter reveals its author to be an ignorant gomer.  Lenski’s paper makes no claim about the formation of three new proteins.  Only someone with no grasp of biology or Lenski’s paper would make such a claim.  And what exactly are they asking for?  If they read the damn paper, they’ll see the data.  Do they want copies of lab notebooks or something?  Can you imagine the Conservapedia dumbasses poring over years worth of lab notebooks?  A high school AP biology class would have more scientific expertise than Andy Schlafly and his gang of mouthbreathing dullards.  But you’ve got to hand it to the fuckwits, they’ve got some balls.   You’ve got to a have a hefty pair if you’re going to accuse a member of the NAS of fraud without basis.  And this comment from the talk page had me rolling:

From the AiG article:

“AiG’s Dr. Georgia Purdom is studying the research for an upcoming semi-technical article in the journal Answers In Depth.”

Apparently, Lenski has released his data to Purdom. Presumably, Dr. Purdom wouldn’t settle for fragmentary data that wouldn’t allow her to fully evaluate the claims. Had Lenski refused to disclose, it seems certain that AiG would have made note of it.

Ahahahaha!  Seriously, how naive are these dolts?  I guarantee that the eminent Dr. Georgia Purdom has nothing at her disposal other than the published paper.  And again, I’m curious what they expect Lenski to release, because he sure as hell isn’t turning over any lab notebooks to creationist loonies.

Remarkably though, Lenski responded to the email, and it’s pretty devastating:

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

Shorter Lenski:  “EPIC FAIL!!”

Update:

OK, now the simpletons are drafting a second email to Lenski.  It seems to be a collaborative effort in progress, but this is the most recent draft:

Dear Prof. Lenski,

Your recent paper in PNAS, “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli,”[1] has has interested us greatly. Knowing PNAS policy of making data available, we were hoping you would accordingly oblige us with your recorded observations for a few key points.

We respectfully request the data relating to the period during which the bacterial colony developed cit+; while we see excerpts in the paper, we were hoping to examine them in context. Your website[2] already discloses some older data, and seems well-suited for public release of the data underlying your recent paper.

Thank you in advance for your cooperation in this.

This is becoming precious.  I can’t get over the ridiculousness of dipshit Conservapedia contributors “reviewing” the work of a NAS member.  That’s like Uwe Boll supervising Martin Scorsese.  I mean, they clearly have no idea what they’re talking about.  That’s obvious from their conflation of bacterial colonies and populations.  A single colony didn’t become Cit+, the majority of an entire population did.  So, any scientist receiving that email will know right off the bat he’s dealing with dilettantes.

But I still don’t know what they’re fishing for, the data are in the 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. Owing to the low concentration of glucose in DM25 medium, the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment. 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.) After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1). A number 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 were Ara- , T5-sensitive, and T6-resistant, as expected (2). DNA sequencing also showed 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 of the others (30). Therefore, the Cit variant arose within the LTEE and is not a contaminant.

The evolved Cit variant grows to high density in DM0 (a citrate-only medium), produces vigorous colonies on minimal citrate (MC) agar plates, and causes a positive color change on Simmon’s citrate agar, all of which indicate that it can use citrate as a sole carbon source.

That is the data that the Lenski group has about the development of Cit+ in the population.  The only other thing Lenski could provide them would be hand-written lab notebooks, which would just contain the same information present in the above paragraphs (along with a whole bunch of mundane details about daily bench work, like setting up PCR reactions and such).  And they aren’t getting lab notebooks.

If I were Richard Lenski, I’d respond to any further correspondence from the Conservapedia crowd with a close-up photo of my sweaty balls and call it quits.

This entry was posted on Monday, June 16th, 2008 at 4:15 pm and is filed under Creationism. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site.