Why are We Disagreeing with ID?

[CrisprCAS9]

@lee_merrill

This paper about constructing the MOTB ancestor cites 90% sequence similarity.

You didn’t actually read that paper, did you?

@lee_merrill

Well, I don’t see a function for just a hook, without flagellin, for instance.

Your incredulity is not an argument.

[Rumraket (Mikkel R.)]

@lee_merrill

This paper about constructing the MOTB ancestor cites 90% sequence similarity. With about 300 residues, that would be 30 changes, to get to the ancestor, so say about 30 changes to get to a homolog.

No. To get a homolog just means two genes are on separate lineages. They can be completely identical and yet still be homologous because they’re found in different species.

What is it you’re trying to calculate again? If you mean to say extant MotB proteins couldn’t have evolved from an ancestral MotB protein because they’re different from it by about 30 amino acids, I just have to say that you should acquaint yourself with the SARS-Cov2 Omicron spike protein, which was different from the original Wuhan variant by 32 mutations already when it was first detected:

I must repeat what I wrote in this thread:

@Rumraket

@Daniel_Arant

My first question is an overarching one: why is it simply assumed that one homologous protein can evolve into its homologue?

I’d flip this question around on it’s head and ask, if we can see that two proteins that share something like only 15% sequence similarity are still capable of performing essentially the same function (bind the same molecule or catalyze the same biochemical reaction), then why should we not think this?

If they can be THAT different yet still remain functional in the same way, then why should we think somewhere in the range of similarities between 100% and 15% there is some gap of nonfunctionality?

Presumably two proteins which are totally identical would not merit any doubt at all. So if we make them 99% identical, that’d still plausibly make them able to remain functional. Even if they have some degree of constraint on how much they can change before they stop being able to function, 99% seems to be similar enough that it shouldn’t be a problem. And the same at 98%.

We can imagine we keep going and at some point, maybe we start to think they’re beginning to be so dissimilar it might impact the function? Say we think maybe at 50% similarity we have some intuition that a lot of the protein sequence has changed, so how can it still retain the same structure or function?
But then we discover a variant of that protein that is 15% similar to the other one and yet it still functions. But then doesn’t that immediately imply the entire range spanning 100 to 15% must contain functional sequences? Shouldn’t that cause us to think there really is a pathway all the way from 100% to 15% similarity? We thought maybe 50% was some lower limit of similarity we couldn’t go beyond without breaking the function or structure, and yet now we find one that only has 15% similarity and it remains able to perform the function.

If we can find two proteins that adopt a similar structure which are 90% similar, and others that are 80% similar that still adopt the same structure and function, and then others that are 15%, how is this not exactly what we would expect to have if these proteins really did evolve from a common ancestor over very long periods of time?

And if these proteins are part of some larger structure, and other proteins in that structure exhibit the same pattern, and they show the same sort of gradual decrease in similarity with the distance of relationships between the species that carry them, then what could really justify the idea that they can’t have diverged gradually over that enormous period of time?

[Rumraket (Mikkel R.)]

@lee_merrill

Because a useless partial flagellum would be a burden to the bacterium, and would actually be selected against.

Yes a useless thing would be selected against. It’s just that partial flagella aren’t useless. Papers have been cited already that show this.

Does evidence actually matter to you? Are you one of those “if reality and Biblical doctrine differ, reality is wrong and Biblical doctrine is right” type of guys?

[Faizal_Ali]

@lee_merrill

Because a useless partial flagellum would be a burden to the bacterium

Another of your patented non-answers.

Could you please explain why you hold to the belief that a structure that is useful and which uses some of the components of the flagellum would be selected against? Thanks.

[Roy (34-year veteran)]

Last month:

@Roy

@lee_merrill

@Faizal_Ali

So he might begrudgingly admit that neutral processes can produce some changes…

But a random walk to a new protein-protein binding site is not going to get very far, very fast.

Since you can’t calculate poker probabilities, I doubt you know the mathematics of random walks either.

Feel free to demonstrate some expertise by, say, showing us how to calculate the expected distance from the starting point after a random walk of N steps on a flat plane.

If/when you realise you can’t, perhaps you could stop making baseless assertions.

This month:

@lee_merrill

@Mercer

@lee_merrill

Well, it seems transport is needed (as you said) for constructing a flagellum, but we need selectable functionality along the way.

What’s the evidence against neutral evolution?

But random walks don’t get very far, very fast.

Since you can’t calculate poker probabilities, I doubt you know the mathematics of random walks either.

Feel free to demonstrate some expertise by, say, showing us how to calculate the expected distance from the starting point after a random walk of N steps on a flat plane.

If/when you realise you can’t, perhaps you could stop making baseless assertions.

You might also want to try harder to remember previous responses, or at least which forum and thread you previously posted in. Repeating a point unchanged in a thread in which it had already been addressed is what earnt you the nickname Dory.

[lee_merrill]

@Mercer

@lee_merrill

@Mercer

What’s the evidence against neutral evolution?

But random walks don’t get very far, very fast.

You didn’t answer the question, which was about evidence. You’re not working from evidence.

But it’s true, a random walk doesn’t get very far, very fast, it’s not a good way to get somewhere.

@Mercer

@lee_merrill

Behe said he hadn’t read that particular stack of books and articles.

His claim in the book was that none of them even exist. He claimed that he meant something completely different when challenged under oath.

Well, I’m sure he meant the content doesn’t exist, not the title.

@Mercer

@lee_merrill

That would support what?

Your claim that antibody binding sites aren’t new.

I agree that they are new.

@Mercer

@lee_merrill

This paper about constructing the MOTB ancestor cites 90% sequence similarity. With about 300 residues, that would be 30 changes, to get to the ancestor, so say about 30 changes to get to a homolog.

Your point being?

That homologs to MOTB are fairly far away.

@Mercer

@lee_merrill

Well, I don’t see a function for just a hook, without flagellin, for instance.

What you don’t see isn’t really evidence, particularly since you have no idea how structures are built or function in real time.

So, would you claim that a hook without flagellin is functional?

@Rumraket

But then we discover a variant of that protein that is 15% similar to the other one and yet it still functions. But then doesn’t that immediately imply the entire range spanning 100 to 15% must contain functional sequences? Shouldn’t that cause us to think there really is a pathway all the way from 100% to 15% similarity?

That may be, though certainly parts of the protein would need to be conserved. And this may not be typical of all proteins.

Also, homologs to MOTB would seem to need to have other functions than MOTB, this would not be one function all the way to a homolog. No need for a stator if you don’t have a motor!

@Rumraket

@lee_merrill

Because a useless partial flagellum would be a burden to the bacterium, and would actually be selected against.

Yes a useless thing would be selected against. It’s just that partial flagella aren’t useless. Papers have been cited already that show this.

I’ve discussed Matzke’s paper in other forums, glad to discuss it again here if need be.

@Faizal_Ali

@lee_merrill

Because a useless partial flagellum would be a burden to the bacterium

Could you please explain why you hold to the belief that a structure that is useful and which uses some of the components of the flagellum would be selected against? Thanks.

A hook without flagellin would seem to be useless, for instance. If I’m understanding your question correctly…

[Rumraket (Mikkel R.)]

@lee_merrill

@Rumraket

But then we discover a variant of that protein that is 15% similar to the other one and yet it still functions. But then doesn’t that immediately imply the entire range spanning 100 to 15% must contain functional sequences? Shouldn’t that cause us to think there really is a pathway all the way from 100% to 15% similarity?

That may be, though certainly parts of the protein would need to be conserved.

If there is such a pathway then what is the problem again? Protein sequences will unavoidably drift apart as nearly neutral or beneficial mutations accumulate in them.

Again, look at the omicron variant spike protein compared to the delta variant:

That’s 32 mutations right there. In the span of about a years worth of viral evolution.

@lee_merrill

And this may not be typical of all proteins.

Divergence is typical of all proteins. Literally without a single known exception. There is no known protein family that has remained 100% conserved since it’s inferred origin unless it’s known from only one, or two species that share very recent ancestry. Once geological timescales get involved we see them having diverged from their common ancestors. They’re still doing it now for proteins inferred to have been present in the last universal common ancestor over 3.5 billion years ago.

Sequence space and the ongoing expansion of the protein universe - PubMed

Abstract

The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.

@lee_merrill

Also, homologs to MOTB would seem to need to have other functions than MOTB, this would not be one function all the way to a homolog. No need for a stator if you don’t have a motor!

In so far as they do not function as stators in other protein protein complexes, they’d need to have other functions besides that in order to be useful there. Yes. Obviously. That’s exactly what enables the possibility of evolving larger structures with irreducibly complex functions because the partial/simpler structures can have other functions than the larger one.

@lee_merrill

@Rumraket

Yes a useless thing would be selected against. It’s just that partial flagella aren’t useless. Papers have been cited already that show this.

I’ve discussed Matzke’s paper in other forums, glad to discuss it again here if need be.

No, the other papers that show other functions for parts of the flagella structure particularly for endosymbionts where they function as protein transport systems. Do you even read the papers that get cited? Does evidence matter to you? It should be a concern to you that you’re constantly leaving the impression that it doesn’t.

[Faizal_Ali]

@lee_merrill

@Faizal_Ali

Could you please explain why you hold to the belief that a structure that is useful and which uses some of the components of the flagellum would be selected against? Thanks.

A hook without flagellin would seem to be useless, for instance. If I’m understanding your question correctly…

I asked you about something useful.

You replied by talking about something useless.

Does that sound to you like an answer from someone who understood the question?