Past EED rants


Live leaderboard

Poker leaderboard

Voice of EED

Wednesday 25 June 2008

Conservapedia vs The Scientific Method [DrDave]

In the last month or so, evolutionary biologist Richard Lenski published one of the most ground breaking scientific papers of recent years, though it may not appear that way at first glance. The paper describes the latest findings of a 20 year study into the evolution of E. coli bacteria.

The details of the experiment are simple, but extremely elegant. Lenski's team started with 12 populations of E. coli, and transferred them daily into environments of fresh nutrients. Samples were tested regularly for changes in mean fitness and interesting variations were noted. Cleverly, every 500 generations samples of each population were removed and preserved - creating a snapshot of the evolutionary history.

At around generation 33,000, Lenski's team began to notice an interesting change. Members of one of the populations had suddenly gained the ability to ingest citrate. Now, one of the defining characteristics of the E. coli family is its inability to use citrate, so the development of such a novel trait was extremely interesting.

Lenski's team then looked back through the 500-generation snapshots of this population and replicated the experiment with progressively older samples. The results showed that the citrate ingesting ability was re-evolved by samples preserved after about generation 20,000 with a high frequency, but that samples preserved before this generation didn't evolve the trait. The conclusion being that the citrate ability is contingent on an earlier, possibly neutral mutation.

The significance of this result may not be immediately obvious. It is really a confirmation of Steven Jay Gould's famous prediction concerning the reproducibility of evolution:

If the tape of life were rewound and played again a quite different set of organisms would probably succeed.

In other words evolution has no goals, no defined end-point. Since mutations are dependent on contingency, the probability of reproducing any particular trait is low.

However, though this is an interesting affirmation of a famous prediction, it may be seen as somewhat obvious. Of far more interest is the fact that Lenski's team observed not one, but two (and possibly more) subsequent ultimately beneficial mutations and the evolution of a complex, novel function. This is, naturally, quite a blow for intelligent design creationism, since this is precisely what they claim cannot happen (or happens with such low probability as to be ignorable). In fact, Michael Behe, the closest thing ID has to a real scientist responded to Lenski's findings with a quite perplexing turnaround. Behe's writes:

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. "If two mutations have to occur before there is a net beneficial effect -- if an intermediate state is harmful, or less fit than the starting state -- then there is already a big evolutionary problem." (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

What Behe is saying here amounts to "I predicted that getting two mutations is impossible, and now this paper has shown it happening, it has proved I was right all along". Erm, what?

But this blog isn't really about Behe, it's about conservapedia (the self styled "trustworthy encyclopedia"). Conservadepia, being the religious right's response to wikipedia, naturally has a vested interest in creation "science", so took it upon itself to challenge the filthy liberal Lenski, who had obviously falsified or misinterpreted data in order to shore up the collapsing edifice of materialism.

Andrew Schlafly, a lawyer and conservapedia founder took up the fight, sending a rather terse and unfriendly letter to Lenski. Schlafly's letter is rude, and contains a number of factual inaccuracies, and in it he demands that Lenski send him the experiment's data so that an independent party can verify the findings. Here's a sample, see if you think this is a reasonable tone to take:

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. ... 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.

Nice eh? Lenski responds, pointing out politely the error in Schlafly's claim of three new proteins, and urging Schlafly to actually read the paper - which already contains all of the data Schlafly requests.

Of course, Schlafly ignores this and once again reiterates his demands for the data (that he already has access to):

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.

At this point, even Schlafly's toadies and sycophants are cautioning him that he's acting like a complete tool. Have a read of the discussion page. Schlafly, naturally, responds by banning dissenting users.

Lenski's second reply is a thing of internet smackdown beauty. Have a read. Here's a good bit:

It is my impression that you seem to think we have only paper and electronic records of having seen some unusual E. coli. If we made serious errors or misrepresentations, you would surely like to find them in those records. If we did not, then – as some of your acolytes have suggested – you might assert that our records are themselves untrustworthy because, well, because you said so, I guess. But perhaps because you did not bother even to read our paper, or perhaps because you aren’t very bright, you seem not to understand that we have the actual, living bacteria that exhibit the properties reported in our paper, including both the ancestral strain used to start this long-term experiment and its evolved citrate-using descendants.

Brilliant. Lenski goes on to offer to send Schlafly samples of the living bacteria, provided all necessary protocols for exchanging biological material are followed. One suspects that Schlafly will not call his bluff.

You may think that this exchange is trivial, that it is representative of what can be found on most forums on most of the internet these days. That no reasonable minded person would place any credence in the ramblings of an obvious nutcase. But you'd be wrong. A recent Gallup poll of Americans showed that a staggering 60% of republicans and (alarmingly) 38% of democrats subscribe to a young earth creationist viewpoint. If there is any truth to this poll, it suggests that getting on for half of all Americans would side with a lawyer over a biologist in matters of good science, no matter how elegant or enlightening the experiment is, just as long as the lawyer took his cues from a 4000 year old manuscript.

Does this not strike anyone as extremely disturbing?


  1. Excellent post DrDave!

    It is extremely worrying that so many people seem to be less aware of what science actually is for various reasons. Kudos to Richard Lenski for standing up and replying.

    I also love to see a smackdown!


  2. Shocking, but not entirely surprising when a bunch of religious nutjobs get to found their own country.


  3. Amusingly, this continues without end. Schlafly and his minions prepared a complaint to the Proceeding of the National Academy of Sciences (PNAS, the journal that published the original paper). Here's the letter. It is of course mostly nonsense and manages, deftly, to include misunderstandings of statistics, microbiology and scientific method in only 250 words. The talk page features a number of commentators who patiently try to explain to Schlafly why he is wrong. To no avail of course, and the letter was finally submitted.

    Sure enough, PNAS rejected the letter for publication. Schlafly, of course, claims victory and no doubt sees this rejection as proof that he is right and the evil liberal scientists are attempting to surpress him.

    This will continue and continue, but one thing to take away from the whole affair is this rather amazing piece of smackdown that is seldom seen in the world of scientific publication:

    "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."

    Bravo sir!