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Tuesday, July 1, 2008

Bacteria evolve; Conservapedia demands recount

Noises off

This is a story that starts in triumph, takes a detour through farce, and inadvertently ends raising some profound questions. The triumph is one of scientific progress in the study of evolution; the farce comes courtesy of those who run Conservapedia, who apparently can't believe that any scientific evidence can possibly support evolution. The questions, however, focus on what access the US public should have to the research that their tax dollars support.


E. coli have evolved the ability to
metabolize citrate in the lab.

Ars covered the research earlier this month, when a paper reporting it was first published in the Proceedings of the National Academies of Science. Richard Lenski and his colleagues have been conducting a long-term experiment in bacterial evolution, one that has encompassed over 30,000 generations of bacteria going back over 20 years. Many of the bacteria have evolved the ability to better utilize the sugar available in their cultures, but one strain underwent at least three distinct changes (at generation 27,000, 31,000 and 33,000) that enabled them to access citrate present in the medium—something their parents were incapable of. Lenski saved samples of every culture at intervals of 500 generations, and his paper suggested his lab was going back and sequencing the genomes of the intermediaries to try to find out the genetic basis for the evolution of this new trait.

Conservapedia meets cognitive dissonance

The denizens of Conservapedia were not amused. They apparently subscribe to the belief that acceptance of some scientific data goes against conservative values. The site tends to present the views of mainstream science and "creation science" as equally valid scientific perspectives, as evidenced by their discussion of kangaroo origins (which is actually much improved since we first checked). The site's relevant sympathies with creationism can be seen in its discussion of information, which uncritically repeats William Dembski's claim that "information cannot be created by natural (nonintelligent) causes." Despite never defining how to measure biological information, Dembski has used this claim to rule out evolutionary origins for new biological capacities.

Clearly, Lenski's bacteria appear to have evolved a significant new capacity. Fortunately, the residents of Conservapedia found a way out of this logical conundrum: Lenski was either misinterpreting his data, or he faked it. In an open letter to Lenski, Conservapedia's Andy Schlafly (an attorney with an engineering background) wrote, "skepticism has been expressed on Conservapedia about your claims, and the significance of your claims, that E. Coli [sic] bacteria had an evolutionary beneficial mutation in your study." Their solution? Show them the data: "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."

Lenski replied, noting that the whole purpose of scientific paper is to discuss and display data and to use them to justify conclusions; the data were in the paper itself. He also pointed out he'd placed a copy of the paper on his website for those without subscriptions to PNAS. Lenski also spent some time reexplaining some of his conclusions, and pointing out errors and misconceptions in the letter he had received. This response prompted a second letter from Schlafly, suggesting he wanted to review the data underlying the data presented in the paper, and noting that the work is taxpayer funded, giving him a right to it as a taxpayer.

Backstage drama

From here on out, standard Internet drama ensued. By the time of his next reply, Lenski had apparently read the discussion pages attached to the letters, and discovered that Schlafly hadn't actually bothered to read the paper he was demanding the data for. He has also discovered that some Conservapedia members were simply calling the whole thing a hoax, and accusing him of having engaged in research fraud. As a result, Lenski was apparently very annoyed, and his second letter is far more assertive.

Lenski again notes that the paper actually contained the relevant data, and that Schlafly's complaints suggested he wouldn't know what to do with any further data were Lenski to provide it to him. In this, he was backed up by a number of Conservapedia members, who said more or less the same thing in the attached discussion. Several of those individuals are apparently now ex-Conservapedia members, having had their accounts blocked for insubordination. In fact, anyone who questioned Schlafly's demands seem to have been branded an opponent of public access to scientific data; the statement, "I'll add your name to the list above of people who oppose the public release of data" peppers Schlafly's responses throughout the discussion.

Problems with group think and incendiary discussions are common complaints about what happens behind the scenes at Wikipedia. The irony here is that Conservapedia was ostensibly founded as a response to precisely that behavior. It appears that the victims may now be trying the role of oppressors on for size.

What should scientists share?


Lenski has offered to share the bacteria used in his work.

Lenski's primary argument is that the data needed to evaluate his conclusions are in the paper. Having read the paper, it appears that Lenski is completely correct; some of the data is depicted in graphical form instead of the raw, underlying numbers, but this appears to be largely a matter of making the data easier to interpret. In his response to Conservapedia, Lenski states (accurately) that the underlying data are in the form of the bacteria themselves, which he has stored in freezers at Michigan State. If Schlafly wants those, he can go through the standard channels. He needs to demonstrate that he can store and use them properly and that his use would serve some scientific purpose. If those conditions are met, Schlafly can go through Michigan State's standard Material Transfer Agreement procedures.

The exchange actually touches on some of the issues relevant to the free exchange of scientific data and materials, although that surely wasn't Schlafly's intent. In general, most scientists would agree that the open exchange of ideas and reagents benefits the scientific community, and that the public has a right to the know about the research they've funded. For this reason, the NIH has requested that all papers that describe research it has funded be made open access within six months of their publication; Lenski's beaten that deadline by over five months.

NIH

But his second letter raises some significant limits to how far he'll go in handing out the raw materials of his research. In addition to the issues described above, Lenski also intends to make sure he fulfills his ethical obligations as a research mentor by ensuring that his grad students and post-docs who performed the hard work of maintaining the experiment are the ones who benefit by publishing a description of it. He also made no mention of sharing the preliminary data for what his paper explicitly stated was the next step: sequencing the genomes of the new bacteria and their ancestors.

In terms of the argument over public access to taxpayer-funded data, the situation is fairly straightforward. Organizing raw data for public exchange takes time and money, which taxpayers would also foot the bill for. It's generally most efficient for the data to be organized once the gathering stage is complete; taxpayers get a better value for their money this way. In the same manner, it makes no sense for taxpayers to foot the bill for the preparation and shipping of samples to someone like Schlafly, who lacks the facilities or knowledge to do scientific work with the material.

But there's often a large gap between organization and analysis of data and its publication. Here, the ethical concerns—ensuring that the people who did the work receive credit for it via publication—often conflicts with the principles of openness and rapid progress. It's possible some other lab would be able to analyze the sequence data Lenski is gathering more rapidly and thoroughly; by fulfilling his ethical obligations, Lenski may actually be slowing the progress of science. This has been a source of tension within the scientific community for decades, one that has only been exacerbated by the fact that more data is now in electronic form and easy to exchange. It's not something I expect to see resolved any time soon.

Whither Conservapedia?


Lenski is keeping the genome data private
until his students can publish it.

Although he's brought up some interesting issues regarding the conduct of publicly funded scientific research, Schlafly appears to remain blissfully unaware of it. Schlafly only named specific data that he felt were missing on Friday, two weeks after the exchange of letters started; his comments in the discussion attached the letter exchange suggests he primarily questions Lenski's ability to recognize when bacterial contamination crops up in the experiment. Throughout the discussion, however, Schlafly has demonstrated a scientific illiteracy that undercuts his own arguments by demonstrating that any time Lenski or his coworkers spend accommodating Schlafly would truly represent a waste of taxpayer money.

Of course, that lack of understanding might be expected from someone who seems to believe that there are distinct conservative and liberal forms of science. Still, you can sense the beginnings of a response to the fact that the situation may be spiraling out of Conservapedia's control. When a contributor suggested the exchange was making the site look bad, the response indicated that the any problems could be dismissed as a case of biased perception: "What sort of Liberal defeatism are you bound up in, and why do you assume, without examining the facts of the matter, that this has not gone well?"

As to the longer-term prospect, that Lenski's genome sequencing will actually reveal the creative power of evolution in greater detail, that's apparently nothing that can't be handled by a post-hoc rationalization. "But how are we to know," one contributor asks, "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?"

How indeed? It's precisely the inability to test such a contention that led the scientific community to give up on supernatural explanations in the first place.

Original here

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