Assumed Evidence

For the end of the week from Brian we have Lab Studies Show Evolutionary ‘Evidence’ Is Merely Assumed. It’s about a (freely available) Nature feature on Joe Thornton, called Prehistoric proteins: Raising the dead.

Brian has written articles on Dr Thornton before. Back in 2009, some years before I started here, he wrote Irreversible Complexity–Evolution Loses Another Round. This was on a paper, An epistatic ratchet constrains the direction of glucocorticoid receptor evolution, described by the Nature feature like so:

In a final chapter to the story, Thornton tried to run that evolutionary sequence backwards. But when the researchers reversed the seven mutations in the ancient cortisol-specific form, they could not transform it back into a protein that worked like the common ancestor of the GR and MR. They instead engineered a dud, unable to respond to any hormone. That was because a handful of other mutations had also cropped up on the way to making a cortisol-specific receptor. They played little part in the receptor’s new function, but acted as an evolutionary ratchet, preventing it from regaining its old one.

Thornton showed that it was necessary to undo those mutations too, to reverse the change. To him, the work was a powerful demonstration that the path of evolution can be contingent on random events.

Brian tried to spin this as showing irreducible complexity, even though it in fact showed the opposite.

Later, early this year, was Study Finds Molecules Evolving in Wrong Direction. As this was much more recent I have already been over it, briefly in Molecules; Paddlefish; Whale Brains; and Dog Paws – the week of Jan 23. The paper that was about can be found here, and there was also a news release, though neither are free to read.

As for this one, Brian’s latest covers little new. He accuses Thornton of “only [being] willing to entertain evolutionary origins, even if the data suggested non-evolutionary causes.”

This is analogous to accusing a person attempting to determine the true cause of lightning, and who is fairly sure at this point that it’s not supernatural, of not being prepared to accept that Goddidit. At any rate, it doesn’t look like Thornton’s data actually does ‘suggest’ that it was God here. Nevertheless, Brian goes over his previous articles to try to show that it does:

Thornton’s lab efforts have actually highlighted exactly why living systems like protein receptors had to have been created. For example, his 2009 experiments demonstrated how one particular protein could not evolve into another by incremental changes, inadvertently refuting evolution.

As you can see from the Nature quote I gave above, that’s not a correct conclusion to draw from what he did. Brian also says:

And earlier in 2012, Thornton’s lab reverse-engineered mutations in a degraded protein. The lab replaced the putative original single protein with a less efficient conglomeration of broken-down proteins. The resulting cellular machine could do the job, but not nearly as well—like two men running a sack race against one man running normally. And both the cells and the scientists started with fully formed proteins—the very items whose origin was supposed to be under investigation.

Again, not a valid conclusion. I’m fairly certain that saying that “The resulting cellular machine could do the job, but not nearly as well” is completely incorrect. The creationists are just annoyed that he demonstrated an increase in complexity via devolution.

Thornton’s work shows that some of the best “evidence” for evolution merely assumes it.

Something like that… I’ve emailed Thornton to tell him about this article, as he apparently enjoys annoying creationists. “Thornton says that he didn’t set out to refute intelligent design, but the prospect of a fight hardly put him off. “Been there, enjoyed that,” he says.” But Brian’s arguments here are so without substance that I don’t even really need him to confirm that.


Hopefully the watermark under quotes from Thomas should be a little more visible here. If not I’ll try a background colour next week.

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8 thoughts on “Assumed Evidence

  1. I can see these “ICR” symbols behind the text without tilting my scree, what sorcery is this!

    Also, I’m having more difficulty following the creationist reasoning than usual here. They couldn’t devolve certain receptors because additional mutations had cropped up elsewhere that mucked up this process. But by removing these additional mutations the receptor could be successfully devolved.

    How the hell does that demonstrate irreducible complexity? It was ultimately very much reduced, it says so in the original article. You don’t even have to read further than the abstract.

    Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein.

    How does anything in any of the articles justify the statement

    “one particular protein could not evolve into another by incremental changes, inadvertently refuting evolution.”

    Hmmm? It could have evolved by incremental changes, there were just more incremental changes involved than first thought, changes which ultimately make it difficult to go backwards.

    At no point is it mentioned that they did successfully devolved the original protein in any of the ICR articles, which is odd given that it’s one of the main conclusions of the paper (which also happily refutes what the ICR is trying to say).

    Either Brian is a buffoon who missed the main point of this paper, demonstrating his inability comprehend science or he’s being deliberately dishonest.

    • I changed the image to one that was a little darker and had transparency. I really need the custom css thing for this kind of thing, but so far I haven’t made my system too complex.

      The way that Brian makes it sound like irreducible complexity is by completely ignoring* that these neutral ratcheting mutations could also be removed. Creationists are famed for their selective reading skills – and I do mean that, I’m fairly certain that it can’t all be explained away by simple dishonesty. Whether this qualifies him as a ‘buffoon’ – he certainly hasn’t won the Sensuous Curmudgeon’s Buffoon award yet, though I’m not sure what he has to do to qualify – or whether it just makes him a sufferer of a more extreme version of the biases we all have, is up to you to decide.

      *Not quite totally ignoring, actually. He does give in his earlier article the quote “Effectively, the five mutations burn the bridge evolution had just crossed.” But this is completely out of context, and he never explains that they can be removed (or anything else about them, for that matter).

    • Yeah, I count that as totally ignoring. The crux of his article is completely destroyed by the notion that if you remove the 5 mutations then it works fine and demonstrates evolution in action. The fact he doesn’t mention that is disingenuous/moronic and merely mentioning that “the 5 mutations burn the bridge evolution just crossed” doesn’t solve that problem.

    • No, they are still predominantly neutral. There is a creationist argument that claims that we each have ~60 mutations and that this is a sign of genetic denegration and everything is going to dust etc. But, of course, we’re all still here, aren’t we? At any rate, mutations would be extremely rarely fatal – as I’m sure you’re aware there are plenty of people with genetic disorders who survive regardless.

      Also notable is that whether a mutation is ‘harmful’ or ‘helpful’ is a little subjective. For example, you might think that an alteration that made an enzyme more efficient would be defiantly a good thing, but in fact it may make the system that the enzyme is part of as a whole less efficient. As an analogy to mechanical systems that we are more familiar with, you can think of it as throwing off the timing. Though in reality the problem would be more like the enzyme depleting the concentration of a substance it worked with and meant that other enzymes didn’t get enough.

      But in other places there may be room for legitimate improvement. In some cases, like here and with the famous Lenski experiment, that cannot be normally achieved without the earlier appearance of neutral mutations. But it’s all possible, just a little messy.

    • For the longest time it was thought that mutations which resulted in a loss of function were either fatal or caused quite severe genetic disease. However, a recent paper discovered that we all have ~100 gene variants that result in a loss of function.

      The reason we’re still healthy is that 28% of these variants have redundant copies that take over functionality and a further 82% of them are heterozygous. In other words we would also have a healthy copy of that gene to ensure we aren’t crippled by a loss of function.

      However, despite those fail safes there is still on average a 16% reduction in quantity of the proteins affected by these gene variants. This is sufficient for natural selection to select against these variants and so they do not increase in frequency throughout the population, instead remaining stable or decreasing.

      The curious exception is that some LoF variants are being selected for, suggesting that in some situations producing lots of proteins isn’t the best idea.

      The take home message is that the body has fail safes to allow it tolerate a surprisingly large amount of change and that sometimes that change can be good.

      http://www.sciencemag.org/content/335/6070/823.fullA

  2. As a non-biologist, I struggled a bit with the debate here.

    Some brief observations:
    (1) In Thomas’ blog of 2009 that he links to he says of the Nature paper referenced as footnote 1: “They found, “surprisingly,” that none of the transitional proteins functioned at all”. The Abstract at least makes no such comment.

    (2) To a layman Thomas APPEARS to be arguing that, assuming evolution is not reversible, it couldn’t have happened ‘forwards’ either. Why not?

    (3) The Abstract of the Nature paper cited (WITHOUT a live link) as footnote 1 of Thomas’ PREVIOUS 2012 blog states:
    “We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.”
    Whereas Thomas stated in his earlier 2012 blog that the study “showed how powerless natural processes are to generate complicated working machinery”. He then referred to so-called de-evolution, quoted Michael Behe, and concluded: “even though today’s version of V-ATPase might be more complex than the original version, it is not better, more efficient, or more effective”.

    • For the first, this was the ‘dud’ talked about in the review article I linked (there’s more in there about this than what I quoted, and it’s free and interesting to read). What they found was that, if they didn’t remove these five mutations, when they traced the lineage back they didn’t get a working protein. This is what Brian was harping on, of course. But if they did remove the mutations it was fine, and that Brian does not mention.

      The crux of his argument is that if the earlier stage was impossible then the whole thing couldn’t have happened. This is technically a straw man here as the dud step is not actually on the line, and everything works fine when you remove the five mutations as part of your changes. There’s also a bit of this “assuming evolution is not reversible, it couldn’t have happened ‘forwards’ either” thing, but that’s not true and seems to be there just to confuse you.

      He’s a bit erratic about the reference links, isn’t he? In that article as well he’s trying desperately to spin things the exact opposite of the way they actually are. I haven’t re-read the Nature articles, but I’m pretty sure that the

      “even though today’s version of V-ATPase might be more complex than the original version, it is not better, more efficient, or more effective”

      line is completely false. I think it was a 1-step-back(ish)-many-steps-foward situation, from what I remember.

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