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Friday, June 13, 2008

Science: 1, Intelligent Design: 0

Folks who follow the ongoing slapfight between science and intelligent design are probably aware that evolutionary theory is sometimes criticized on the grounds of being non-falsifiable. Since we can't observe evolution occurring, the story goes, evolution is little more than a tautology. Perhaps worse, characters like Wild Bill Dembski even argue that random mutation and selection is incapable of producing new and useful features and will, instead, simply degrade an organism over time. Well, today science has an exciting new response.* And that response is: blow me.

Over at Michigan State University** fashion model/biologist Richard Lenski and his lab have made a very exciting discovery. See, they've been running an experiment over there for about twenty years. In this experiment, he and his team took a single sample of E. Coli and derived twelve different study populations. They then watched them reproduce- over and over and over. Now, this wasn't some kind of unicellular pornography,*** but a study in evolution. See, given time it was thought that random mutations from a variety of sources might build up in these bacteria and produce some noticeable changes. And, as it happens, they have:

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.

But wait, that's not all! As it turns out, Lenski's team has been storing samples of the different populations every few generations which allows them to, in effect, rewind biological time. And the outcome was, indeed, cool:

Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

The significance here is real: it is experimental evidence not only of evolution, but that mutations can accumulate over time- perhaps innocuous and useless in and of themselves- suddenly becoming helpful when a given set of them have appeared. It is, in effect, a direct challenge to Behe's craptacular "irreducible complexity" idea. And, given the amount of time during which the only life on Earth was microbial, there was a lot of time for mutations and variations to accumulate, bequeathing a wealth of variation to macroscopic species like our own. Many of our adaptations may have been made possible by the bounty of mutations built up in the genomes of our bacterial progenitors.

It goes without saying that science-haters are already hard at work either ignoring or castigating this research. Nevertheless, this is an important finding and one that will no doubt teach us a great deal both about evolution and about the lengths one must go to in order to pretend it doesn't work.

UPDATE: Andy Schlafly over at Conservapedia tries to call Richard Lenski out:

Or, more accurately, sends him an impolite e-mail demanding that Lenski defend his work against the top scientific mind of "Andy Schlafly, B.S.E, J.D.":

Or, in textual form:

June 13, 2008

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:

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 . Thank you.

Andy Schlafly, B.S.E., J.D. Conservapedia

To be totally honest I hope Lenski does provide the data just so we can see Schlafly try to interpret it. Actually, scratch that: his ignorance will simply cause him to exclaim that the dreaded "evolutionists" are presenting the data in a confusing way to obfuscate their failure. Yeah. Right. Because science is that fucking easy.

Stay tuned.

UPDATE TO THE UPDATE: Richard Lenski replies and, as it turns out, is quite the gentleman:

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.


Richard Lenski

Gotta love it. Now to see how Schlafly handles the matter...

UPDATE TO THE UPDATE TO THE UPDATE: The stupidity continues! Check out the latest news!

* Actually, this has been the response for some time. It's just that we've recently added some new evidence to the already mammoth pile of it.

** Rock on, Trojans!

*** "Oh, wow! Check out the flagellum on that! Raarrr!"

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Anonymous Anonymous said...

Actually, this might be a positive development. If Conservapedia begins emailing every scientist whose work they're skeptical of, I see two side effects. First, they'll have significantly less time to devote to producing the crazy, as they'll all be busy emailing biologists and physicists. And second, they might actually become something useful--a repository of scientific data that proves everything they believe wrong.

Best possible results? I think so.

Friday, June 13, 2008 12:20:00 PM  
Blogger Mister Troll said...

*sputter* *sputter*


Friday, June 13, 2008 7:11:00 PM  
Anonymous a very public sociologist said...

Ah, but surely an ID'er can say it was the influence of the Intelligent Designer working in mysterious ways that caused the E Coli to mutate!

Anyway, well done to Leski and his colleagues. The ID'ers don't like it up 'em!

Saturday, June 14, 2008 3:34:00 PM  
Anonymous Anonymous said...

You might be able to see a fair bit of traffic on the talk page ( after you last left comment.

Ironically, I was googling "B.S.E., J.D." when I found your blog. Apparently Schlafly is that infamous.

Saturday, June 14, 2008 10:20:00 PM  
Anonymous Anonymous said...


Did you see that Schlafly responded to Lenski? You should really check it out, if you haven't already...

Monday, June 16, 2008 12:32:00 PM  
Blogger Drek said...

Anonymous: The debate continues, indeed, but so far as I can tell Schlafly is recruiting additional signatures for his next e-mail to Dr. Lenski, he has not actually sent it yet. Evidently Andy Schlafly doesn't get enough reassurance from his "B.S.E., J.D." security blanket and he needs a whole crowd of supporters to hold his hand.

If I'm missing something, though, please let me know.

Monday, June 16, 2008 12:44:00 PM  
Anonymous Anonymous said...


Should've been clearer there. I was referring to Andy's claim that Lenski hadn't provided the data, followed by his audience explaining to him how science worked.

Now that I know he's writing another letter I may have to stop back by. Schlafly's ability to embarass himself is really second to none.

Monday, June 16, 2008 1:59:00 PM  

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