Behe: Responding to the Polar Bear's Fat

To be honest, I’m a more concerned that he cut out all the variants predicted to be benign, merely focusing on the HDivPred results is at least defensible.

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Surely his argument is that the vast majority of helpful unguided mutations “harm” the genes, to the extent that evolution can’t be fuelled by unguided mutations because they would be incapable of “building” anything new.

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Could you clarify what you mean? Are you saying that he also cut out some of the rows, not just columns?

Yeah, you can see in my screenshot, or in Behe’s ENV post - he only includes rows that have the prediction “possibly damaging” or “probably damaging”.

WHAT?? I didn’t even look! When am I going to learn not to take anything at face value?!

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I know, I was pretty amazed when I noticed too. It’s rare that they’re so obvious with their dodgy tactics.

From the looks of it, he had to go out of his way to make his table in such a way that it preserved the alphabetical order of the gene names. The table wasn’t simply sorted in order of predictions and then only one half copied and pasted: Behe had to explicitly go through and only copy and paste the rows with the prediction “damaging”, leaving the rest behind.

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That’s what it looks like. WOW, this is incredibly dishonest. My figure is like all red now! lol

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LOL

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But this is all beside the point. He said the original authors concluded they were damaging. They did not. Full stop.

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I’m about to tweet this out. Feel free to retweet and add your comments.

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Where’s my Twitter support???

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Thanks @T.j_Runyon! lol

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Thanks for taking the time to read and respond to their work and explaining things in a clear and coherent way.

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Dirty job but someone has to do it! Ken Miller has earned a break!

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I guess I have to change my login to “some other guy”.

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Very interesting. Thanks guys.

I’m actually surprised that Behe has stooped to this level of trying to diminish and insult us. I heard from Ken Miller and others that he was a nice and respectable guy, jovial even. I never met him, but his writing always seemed much more professional and mature than most of the rest of the DI folks. But the last couple things we’ve heard from him don’t seem that way at all.

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Agreed, this is incredibly disappointing. I’d love to see @Agauger and @pnelson respond to this obvious “creative” use of data.

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Exactly. All the program can do is flag mutations as “altering things from ‘normal’ somehow”. It is just by accident it is labeled “damaging.” This is well known in the field. The software, for example, does not have a category for “beneficial.”

Looks like the authors used poly-phen2 for the functional effect predictions. I haven’t used this before, but I’ve done a fair amount with SnpEff, and I think the principle is similar. All it can do is find variants that are likely to have some sort of functionally relevant effect and then attempt to determine how “dramatic” that effect is likely to be. If we’re talking about nonsense mutations or frameshifts, it’s probably reasonable to conclude that the protein was damaged. I doubt that without experimentation it’s feasible to assess whether many other kinds of variants are “damaging” or “beneficial”.

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Ah, remember this thread? Good, good times. Yes, this was the most damaging thing of all. Misleading word smithing is one thing, but to slice and dice the chart the way he did… it’s really hard to see this as anything but intentionally dishonest. I should have spread more credit around for all of the contributions that you all made, both here in this thread and in the previous one (which I can’t find) in which we began our discussion of the polar bear work. I’ll put up a blog post soon where I give more credit, point to these threads, and correct some of the misstatements I made about the early history of the DI. Thanks so much everyone! Peaceful Science rocks!

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