Detwiler: Questions Behe, Polyphen, and Ratchets

[swamidass (S. Joshua Swamidass)]

@John_Detwiler

It does not predict stability. Period

It scores for progress toward known folds. Known folds have enough stability to fold. I think right now there are only just over 400 known folds. I don’t see how this wouldn’t be expected to correlate with stability even from just a sequence perspective.

Why not just use a predictor designed to predict stability? There is just no point it treating an apple like its an orange, when an orange is easily available. This is pointless thing to resist. There is publicly available software to do this. Take a look at this:

STRUM: Structure-based stability change prediction upon single-point mutation

@John_Detwiler

Negative selections weeds out mutations when they destabilizing too much. This prevents proteins from destabilizing entirely with time.

Obviously, but your problem is not broken proteins that kill an organism, it’s the build up of many many almost broken proteins that still function well enough to keep an organism alive and well enough to reproduce. I didn’t post those links just to show that snps often break proteins.

Usually SNPs don’t break proteins. You know that right?

So the math of population genetics, and simulations too, shows that this isn’t a problem. When you are ready to learn about it we are here to teach you.

@swamidass

If you must dispute mainstream science, it is not our aim to change your mind. Rather, we hope that you might understand what you reject, and that, perhaps, we might understand you too. We might also find ways to see how your most deeply held beliefs are not threatened.