Nathan Lents at CFI: ID and Science Denial

[Art (Arthur Hunt)]

@NLENTS

I’ll drop a blog post later today or Monday and spread more credit around for the polar bear work.

This thread was also very interesting:

Repeating analysis of human APOB

While studying how Polyphen-2 works, I noticed that one of its features is to use a sequence comparison to help assess the effect of a mutation in a human protein. This made me wonder if the polar bear gene was included as a homolog in the analysis back before the 2014 Liu paper was published. Further I wondered if any new data has come out or any new updates would allow a new prediction by Polyphen for the exact same polar bear mutations. Basically, let’s repeat the Polyphen analysis for the following “damaging” mutations: Gene Position Ancestral Polar bear HDivPred APOB 716 N K possibly damaging APOB 749 D E possibly damaging APOB 2623 D N probably damaging APOB 3920 T P possibly damaging APOB 4418 L H probably damaging [PolyPhen2-716] [716-alignment] It is predicted exactly the same, which makes it seem like nothing has changed since it is giving the exact same probability to 3 decimal places. We can see the homologs used in the alignment, but I did not find…

Basically, none of the variants being discussed found their way into the finished polar bear genome.

This whole episode was/is a great example of teamwork - many participants here contributed.