Comments on Gpuccio: Functional Information Methodology

But was he using the stars to find his heading?

1 Like

That’s why the function matters here. The function of antibodies is to resist infection. If we only produced antibodies from the DNA we inherited, they would not be functional.

1 Like

No, the exact same sequence again. Not the same function.

is about 10^40 for a 100 aa long protein (cytochrome c for instance). so it’s very unlikely to get the same function again.

Same sequence you mean, and randomly without selection, yes that is very unlikely.

Also, the probability of randomly generating the same 100 aa protein sequence twice is 1 in (20^100)^2 = ~1.6x10^260.

But protein sequences aren’t generated by random assembly of amino acids. When two protein sequences that share common descent evolve a few amino acids convergently, the entire sequence isn’t being randomly assembled twice. Rather, the DNA which encodes the exact same protein in both lineages, acquire a few mutations that code for the same amino acid.

So if some ancestral species has this DNA sequence: AAAAATTAAATA
Then if two of it’s descendants inherit it, and these two descendants go on to establish their own lines of descent, then eventually in one of those lineages, the gene mutates to(say):
AAAAATTAAATG
And the mutation is favored by natural selection, so it sticks around for subsequent generations to inherit. Many other mutations happened, but they were not favored by natural selection.

And in the other lineage, the same mutation also happens:
AAAAATTAAATG
Same thing, in this species the mutation was also favored by a similar selective pressure. Many other mutations happened in a very large population, but they also weren’t favored by natural selection.

That’s how you get convergence in sequence. Not the same thing as randomly generating the exact same sequence twice without feedback from selection.

1 Like

My comment was in response to @Roy and @Timothy_Horton claiming that variation in environment is what enables evolutionary process to innovate and that this is not reflected in evolutionary algorithms.
I would love to see some numbers too.
Or is that numbers only required from those who are skeptical of evolution and claims supporting evolution don’t need evidence?

They’ve said that. They haven’t shown it, mainly because it isn’t true - EAs can and have been used to find solutions to problems where the solution was not previously known, and so could not possibly have been smuggled it.

Dave Thomas’s Steiner tree challenge is one such case - the optimal solution to that problem was unknown to Dave Thomas until the GA was run.

P.S. Any objection that this case involves only a small amount of FI can be trivially fixed by modifying Dave Thomas’s GA to find a Steiner tree connecting a much larger number of points.

2 Likes

are you saying that any given protein can bind to any given molecule? it’s not what the experiments showing us. for instance only one in any 10^12 proteins can bind to ATP.

actually they are talking about the same function. they give the cytochrome c example. according to their source about one in every 10^93 sequences will perform the cyrochrome c function. thus the chance to get cyrochrome c again is one to 10^37.

indeed in the case you mentioned. but not in the case i refer to. for instance: electric organ supposedly evolved 6 times. so even if we assume that we need only about 100 aa to that change the chance for that suppose to be about 10^40 per case.

I give up.

2 Likes

Citation?

As noted in the other thread, this is only true for EAs which have unchanging fitness landscapes, which necessarily includes non-interacting ‘organisms’.

Neither condition applies to biological evolution.

Are you saying that biological evolution cannot be defined as an algorithm?
If so, how is it a theory?

Good Lord.

I think I’m with you, @Rumraket.

3 Likes

No. I’m saying that biological evolution cannot be modelled using an EA which has an unchanging fitness landscape, and non-interacting ‘organisms’.

Why haven’t you tried running the EA I provided yet?

2 Likes

Yes. Not just that they can, but that they are in fact doing that. Just very weakly most of the time. We know this because we understand the basics of intermolecular bonding. Read up on hydrogen bonds, London bonds, Van der Waals forces and so on. Basic organic and inorganic chemistry. You need to understand these concepts, they’re important.

it’s not what experiments showing us.

Yes it is. Why are so many substances soluble in water, why are so many other substances soluble in fats, and why are so many substances soluble in both? What’s happening at the molecular level when something dissolves in a solution? Weak binding.

for instance only one in any 10^12 proteins can bind to ATP.

You didn’t read that paper, did you? Read the methods section and you will see what I mean. They detect their ATP binding proteins by only selecting the proteins that bind strongly enough to not be washed out of an immobilized ATP column material with elution buffer. After they have washed out weakly binding proteins, they elute out the strongly binding proteins with a buffer containing ATP. This doesn’t mean there are no other ATP binding proteins in the original sample, just that they didn’t bind it strongly enough to avoid being flushed out with elution buffer. But you have to at least read the paper to understand how they detect and select their ATP binding proteins to get that. And you probably have to read about intermolecular forces to understand how this all works.

And you probably also need to read up on column chromatography.

Quote them please. Prove it.

No, wrong again, and this time also completely illogical. If only one in 10^93 proteins(meaning one out of every 10^93 proteins) can perform the function, how can the odds of generating such a protein by chance be 10^37? First of all that simply doens’t make sense.

But more importantly, you’ve misread the article you’re referring to. They say that there are 10^93 different possible cytochrome c sequences, not that only one in 10^93 can function as cytochrome c.

Let me quote it for you:

Importantly, Hubert Yockey has done a careful study in which he calculated that there are a minimum of 2.3 x 10^93 possible functional cytochrome c protein sequences, based on these genetic mutational analyses (Hampsey et al . 1986; Hampsey et al . 1988; Yockey 1992, Ch. 6, p. 254). For perspective, the number 10^93 is about one billion times larger than the number of atoms in the visible universe. Thus, functional cytochrome c sequences are virtually unlimited in number, and there is no a priori reason for two different species to have the same, or even mildly similar, cytochrome c protein sequences.

So not one in 10^93 are functional cytochrome c’s. Rather, there are 10^93 possible functional cytochrome c. That’s not a frequency, it’s an absolute number.

Are those electric organs identical?

so even if we assume that we need only about 100 aa to that change the chance for that suppose to be about 10^40 per case.

I really have absolutely no idea what you’re talking about here. May I perhaps request that you take some time to re-read the different articles you are drawing these numbers from, read them more carefully for comprehension, rethink what you want to argue, and then come back and write a different post?

3 Likes

It really is sad and shameful how so many of the members here dismiss and squander the valuable free education provided to them by other members.

5 Likes

The next step is to explain why chromosomal rearrangements would be impossible for evolution to produce. As a counter example, donkeys and domesticated horses are reproductively isolated, but given the viability of the sterile mules it is quite apparent they share a common ancestor. Przewalski’s horses also differ in chromosome count from donkeys, but hybrids with donkeys are viable and fertile. There are also cases of completely normal humans with different chromosome counts:

https://genetics.thetech.org/original_news/news124

That backs what I have been saying, that there are many different starting points for the same function.

You need to show that this is true for all proteins.

Yes, exactly. I want to see what ID theory makes of these differences and why, specifically.

Highly improbable events are common.

@swamidass in the main thread

I’m pretty sure he is using an in clade control to do this. The in clade minus the out clade gives him the change.

Of course, this wouldn’t be necessary if an actual phylogenetic comparative analysis was being performed.

2 Likes

How can there be ID theorists if there is no ID theory?

Would you kindly show me where one of these people has shown that active information has been smuggled into the system for catalytic antibodies?

1 Like