swamidass
March 5, 2019, 10:10pm
8
John_Detwiler:
for one, I don’t see a reason that any of the results might not have positive phenotypic effect. I don’t think Behe is focusing on phenotype, he’s saying positive phenotypic effect is what cements the genotypic effects, which he claims are almost always negative from a stability perspective.
Yes, and the evidence he presents is from PolyPhen which does not demonstrate that there was a negative genotypic effect in any way:
Those Polar Bears
It is worth remembering that Behe’s response to the Polar Bear’s Fat created more problems. Behe: Responding to the Polar Bear’s Fat . This is his claim about ApoB:
Since few experiments can be done with grumpy polar bears, they analyzed the changes by computer. They determined that the mutations were very likely to be damaging
Two errors here:
They determined that the mutations were very likely to be damaging
The authors did not determine the mutations to be damaging. They ran a program that gave some results, and they (for a good reason) came to a different conclusion. On ApoB, one of the "damaged proteins, they write it is likely to be working more effectively. This make sense, because Polar Bears need a really effective ApoB because they eat so much fat.
We suggest that the shift to a diet consisting predominantly of fatty acids in polar bears induced adaptive changes in APOB, which enabled the species to cope with high fatty acid intake by contributing to the effective clearance of cholesterol from the blood .
damaging likely to degrade or destroy the function of the protein that the gene codes for.
In this context, the software program just outputs “damaging” if it is likely to be a function changing mutation. As a quirk of this program, it calls both increases and decreases in function “damaging.” It appears that Behe misunderstood how this program works. We expect many beneficial mutations to be called “damaging” by this software, but this does not mean that they are likely to degrade or destroy the function of the protein when applied to data like this.
Behe does think that mutations (essentially) always destabilize a protein, but this is not established with evidence. It is merely an assertion, countered by immense amounts of evidence.