Thursday, October 22, 2009

Evolution in Action and Michael Behe's Reaction

Of the many scientists who are trying to understand evolution, Richard Lenski stands out for his experimental approach. He has maintained stocks of E. coli growing under stressful conditions for over 40,000 generations.

During that time, the cells have been forced to adapt to conditions of low carbon source (glucose) and Lenski's group has been tracking the mutations that arise. In the past, they have done a heroic job of identifying new mutations but that job has become much easier with new technology. Now that rapid genome sequencing is possible it becomes feasible to sequence the genomes of bacteria that were preserved from earlier generations and determine every single mutation that arose.

Barrick et al. (2009) have published the result from just such an experiment. They sequenced the genomes of the original, ancestral, strain and samples of a single lineage from 2,000, 5,000, 10,000, 15,000 20,000 and 40,000 generations.

This information can address a number if issues as they explain in the introduction to their paper.
Genomic changes underlie evolutionary adaptation, but mutations—even those substituted (fixed) in evolving populations—are not necessarily beneficial.Variation in the rate of genomic evolution is also subject to many influences and complications.On the one hand, theory predicts that neutral mutations should accumulate by drift at a uniform rate, albeit stochastically, provided the mutation rate is constant. On the other hand, rates of substitution of beneficial and deleterious mutations depend on selection, and hence the environment, as well as on population size and structure. Moreover, the relative proportions of substitutions that are neutral, deleterious and beneficial are usually difficult to infer given imperfect knowledge of any organism’s genetics and ecology, in the past as well as in the present.

Experiments with tractable model organisms evolving in controlled laboratory environments minimize many of these complications and uncertainties15,16. Moreover, new methods have made it feasible to sequence complete genomes from evolution experiments with bacteria. To date, such analyses have focused on finding the mutations responsible for particular adaptations. However, the application of comparative genome sequencing to experimental evolution studies also offers the opportunity to address major conceptual issues, including whether the dynamics of genomic and adaptive evolution are coupled very tightly or only loosely.
At 20K generations, there were 29 single nucleotide polymorphisms (SNP) and 16 deletions, insertions, and chromosomal rearrangements (DIP) for a total of 45 different events (see figure). Not all of these contributed to adaptation and the rapid growth phenotype but many of them did. Some were mutations that inactivated a gene and some were amino acid substitutions that change activity of an enzyme.

The authors do not report the distribution of beneficial vs neutral mutations but the data suggests that most of the 45 mutations were beneficial. The authors do not tell us how many of these beneficial mutations destroyed the activity of a gene and how many just changed the activity of a gene product but it looks like there were about equal numbers of both kinds of mutations.

Much of the paper is about adaptive vs. non-adaptive mutations. At 40,000 generations there were 627 SNP and 26 DIP mutations. The increase was due, in part, to an increase in mutation rate because of a mutation in the mutT gene. One might expect that the initial adaptation would result in selection for beneficial alleles and that neutral alleles would accumulate by random genetic drift in subsequent generations (i.e. from 20K generations to 40K generations). This is probably what happened from 20K generations to 40K generations

In the first 20K generations the strain adapted rapidly to the low glucose concentration and from then on its rate of growth under these conditions increased more slowly. This could also be explained by the initial fixation of adaptive mutations followed by fixation of non-adaptive, neutral, alleles. The authors argue convincingly that this didn't happen. Instead, almost all of the first 45 mutations were probably adaptive. Presumably, the mutations that arose later on (between 10K and 20K generations) were much less beneficial (lower selection coefficient) than the ones that first appeared in the population. This is the interesting, and controversial, part of the paper.

This is a paper that the IDiots can't ignore because it's all about evidence for evolution. It doesn't come as a big surprise that Michael Behe already has a poting on the DISCO website: New Work by Richard Lenski.

There was a time a few years ago when you could predict that the IDiots would try to discredit such a paper. The new strategy seems to be the opposite. They agree with the conclusions and offer them as support for Intelligent Design Creationism.

Here's the latest example from Behe's posting.
Despite his understandable desire to spin the results his way, Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection. For his work in this area we should be very grateful. It gives us solid results to point to, rather than having to debate speculative scenarios.
I don't think I need to comment on such stupidity.


Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T,K., Schneider, D., Lenski, R.E., and Kim, J.F. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature Oct 18. [Epub ahead of print] [PubMed] [doi: 10.1038/nature08480]

13 comments :

  1. You don't need to comment, but it's always good as a lay person to read a good debunking of stupidity. Concepts that are obvious to you are more nebulous to others. So while we can point that something is fishy or give a half-arsed explanation of where it fails, experts can give a precise one.

    As far as I can tell, Behe is just moving the goal posts and defining changes as deleterous to try and salvage ID theory. How'd I do?

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  2. And they say ID isn't testable...

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  3. I agree with Brian. It would be helpful for us laymen.

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  4. It's funny, but predictable the ID bunch forgot to mention another recent Lenski's paper where one important feature that characterizes E. coli as a bacterial species (inability to grow on citrate) has simply vanished throughout evolution.

    E. coli does not grow on citrate as a carbon source under aerobic conditions. One of the mutants isolated by Zachary et al (Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS 105:7899-906, 2008) was a citrate-using variant who evolved in one population after 31,500 generations.

    For people that are not familiar with identification of enterobacteriae, one of the traits used to identify E. coli in a faeces sample is growth on citrate. Lenski's group showed that even this typical characteristic of E. coli could be changed by evolution.

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  5. I have to wonder why Behe and pals are so afraid(?) top actually test their own claims. They seem to prefer to wait until legitimate scientists publish something, then they throw pebbles from the sidelines.

    Pretty patheitc.

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  6. Brian said: How'd I do?

    Behe said: ...Lenski’s decades-long work lines up wonderfully with what an ID person would expect....

    There is no such thing as what you would expect, on the assumption the the Designer is doing it. The Designer can do anything.

    Behe's line is really standard creationism: creationists do not say there is no evolution, but that it only has trivial effects (as judged by creationists, not by the organisms). However, when they choose to make an example of something, saying "Isn't that clever" then they just say the Designer did it. It doesn't matter that the same processes are involved. So either way, it is just what an ID person would expect. "Heads I win, tails you lose".

    Pete Dunkelberg

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  7. How Behe became a famous creationist:


    "By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning."


    Darwin's Black Box p 39, emphasis in original

    And he insisted that evolution cannot produce IC as it soon became know. IC amounts to co-adapted parts, which evolution can hardly help producing.

    BS-er Behe has racked in hundreds of thousands of dollars from honoraria for his repetitious talks. Controversial authors can get $10,000 and he has given hundreds of talks. For years the reports of his talks indicated that he went through the same slides and made the same jokes. Nevertheless he may well be a true believer in himself.

    Pete Dunkelberg

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  8. "I don't think I need to comment on such stupidity."

    Why not? Surely that's the whole point of having a blog about evolution?

    Personally, I'd like to see an informed explanation of exactly how and why Behe is wrong. If you don't, then who will?

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  9. Behe wrote:

    ...Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems.

    Well no, an ID person would not expect that. They would if they could exclude that no intelligence was involved in the process. This is something that can NEVER be excluded (ID says nothing about the designer, remember). This is especially true in the Lenski experiments where we know that some intelligence was involved - the preparation of dishes, selection etc. ID people love to point out that such experiments are intelligently guided and not examples of "blind processes".

    Behe has made the fundamental error of claiming that ID actually predicts something.

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  10. Hawks: "Behe has made the fundamental error of claiming that ID actually predicts something."

    Close, but IMO ID theory does predict one thing, but only one thing: that we will find things that we can't fully explain with the theory of evolution. OTOH, that same prediction follows from the admission that we don’t know everything yet, so whenever we find something we can’t fully explain, it’s not a sign of the unique strengths of ID “theory”.

    As Pete Dunkelberg points out, any specific prediction similar to those made by evolutionary theory are ruled out because gods can do anything. (And since ID is compatible with anything, it explains nothing, and so is useless).

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  11. I have to wonder why Behe and pals are so afraid(?) to actually test their own claims.

    They know magic can't be tested, so they don't bother with it.

    They also know they're full of shit. I doubt that Behe believes anything he's ever said. He gets paid to be a compulsive liar, and he knows that lying is the only thing he's good at.

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  12. It's interesting that darwinists seem to rely on insults. Behe didn't need to close with an insult. Not so with Moran. Why do darwinists seem so frightened by other intelligent people. ID may not make predictions but still anyone can conclude that the results of a test were not surprising. I'd like to see a specie of bacteria growing a leg. That would in deed be a surprise.

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  13. Bob O says,

    It's interesting that darwinists seem to rely on insults. Behe didn't need to close with an insult. Not so with Moran.

    We don't RELY on insults to prove the stupidity of IDiots. That's been proven many times. It's just that we like to remind people every now and then.

    Why do darwinists seem so frightened by other intelligent people.

    I'm not a Darwinist so I wouldn't know. However, as a scientist I do find myself intimidated—even frightened—by very intelligent people. It makes me realize how inadequate I am.

    The good news is that I can usually learn something from those intelligent people.

    ID may not make predictions but still anyone can conclude that the results of a test were not surprising.

    There's hardly any scientific paper that some IDiot won't endorse as proof of intelligent design. It gets boring after a while.

    Where's the evidence for an intelligent designer?

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