Comments on Gpuccio: Functional Information Methodology

[Mercer (John Mercer)]

@BWhite

Prions do not reproduce. Prions make other like proteins conform to their misguided shape.

They produce more prions. That’s reproduction. That demonstration won a Nobel Prize, btw.

[Roy (30-year veteran)]

@BWhite

It is the claim of computer science that GAs are goal oriented.

No it isn’t.

And yes I have written and experimented with GAs.

I don’t believe you.

And the one you just wrote doesn’t produce FI.

Doesn’t matter. It’s still a GA. Put those goalposts back.

So you lose.

No.

[Giltil (Gilbert Thill)]

@Timothy_Horton

Nice bluff​

???

No bluff at all. See for yourself.

Google Scholar: eye evolution

Have you read any of them?

None of these publications address or even attempt to address the main point raised by @BWhite at 398, ie., whether
« vision systems could have evolved via blind, mindless and purposeless processes ». If you have read these papers, you know this and hence you are bluffing. If you haven’t read them, then you are also bluffing. In either case, you are bluffing.

[Mercer (John Mercer)]

@Giltil

None of these publications address or even attempt to address the main point raised by @BWhite at 398, ie., whether
« vision systems could have evolved via blind, mindless and purposeless processes ». If you have read these papers, you know this and hence you are bluffing.

Please explain how you made this judgment for the first review on the list:
https://www.sciencedirect.com/science/article/abs/pii/S016895259901776X

@Giltil

In either case, you are bluffing.

I think you’re projecting.

Speaking of bluffing, where’s your calculation of FIa for immunoglobulin V(D)J recombination?

[nwrickert (Neil Rickert)]

@BWhite

“Survival of the fittest” is not only wrong it isn’t telic by any means. With natural selection it is the “survival of whatever is good enough”. There isn’t any guidance.

But that is already guidance enough.

@BWhite

There isn’t any direction.

Sure there is. The direction is toward the enhancement of fitness.

If you see mutations as just accidents, then there’s nothing telic.

If you see mutations as part of the process, part of finding ways to enhance fitness, then I will count it as telic. And that’s how I look at mutations.

[Roy (30-year veteran)]

@BWhite

It is the claim of computer science that GAs are goal oriented.

P.S. Fields and disciplines don’t make claims, people working in them do. Anyone making any statement of the form "It is the claim of [some branch of science] that…" can safely be ignored - which is what I am going to do.

“One of the best ways to win arguments is to be so completely wrong that there’s no way anyone could feasibly correct you without teaching three entry level college courses in the process.” - MattyBeRad

[Giltil (Gilbert Thill)]

@swamidass

@moderators, we are far affield. I suggest closing and splitting.

It is not surprising that this thread initially aiming at discussing @gpuccio’s ideas is going far afield given that you have decided to close the main thread at the scholar corner. See my comment at 383.

[Mercer (John Mercer)]

@Giltil

It is not surprising that this thread initially aiming at discussing @gpuccio’s ideas is going far afield given that you have decided to close the main thread at the scholar corner.

Let’s get back to his ideas. You claimed:

@Giltil

@gpuccio has precisely shown that such complex proteins with very high FI (>500 bits) exist. Now the question is whether their evolution by the traditional RV+ NS mechanism is plausible. The answer is no.

Please show, with accurate data and calculations, that the answer is no for VDJ recombination. You’ve already failed to do so for the improvement of antibody affinity by somatic hypermutation.

[Rumraket (Mikkel R.)]

@BWhite

So please, go ahead and post the references.

So papers that show evolution doesn’t appear to be directed towards any particular goal, and is functionally blind to the future and instead contingent on historical outcomes that are difficult to reverse.

That’s easy. Read any paper on contingency and convergence in evolution. Such as:
Lenski RE. Convergence and Divergence in a Long-Term Experiment with Bacteria. Am Nat. 2017 Aug;190(S1):S57-S68. DOI:10.1086/691209

Blount ZD, Lenski RE, Losos JB. Contingency and determinism in evolution: Replaying life’s tape. Science. 2018 Nov 9;362(6415). pii: eaam5979. DOI:10.1126/science.aam5979

Harms MJ, Thornton JW. Historical contingency and its biophysical basis in glucocorticoid receptor evolution. Nature. 2014 Aug 14;512(7513):203-7. DOI:10.1038/nature13410

Starr TN, Picton LK, Thornton JW. Alternative evolutionary histories in the sequence space of an ancient protein. Nature. 2017 Sep 21;549(7672):409-413. DOI:10.1038/nature23902