Junk DNA, High R, Pinnipeds, and the Multiverse

[Paul_King]

@Rumraket

Among the worst part of it all is that Gpuccio’s argument directly depends on how much variation is sampled in the alignment. That’s a giant problem right there. If technically 10 out of the 20 different possible amino acid states are allowed at some position in the protein, but only 5 of these are among the variation known from species that have had the gene sequenced, that’s massively going to impact the FI you calculate as you go through each aligned site in the protein and there are strictly allowed variants for each position not actually present in existing variation

If I recall correctly it’s worse than that. He uses bitscores rather than sequences and only uses the best of those at each stage. That’s ignoring the variations in the sequences he does look at - even their existence.

[Rumraket (Mikkel R.)]

@Giltil! You there? Can you answer any of the dozens of criticisms you’ve been offered so far? Is Gpuccio just right because he is because he is because he just is damnit?

[Rumraket (Mikkel R.)]

@Paul_King

If I recall correctly it’s worse than that. He uses bitscores rather than sequences and only uses the best of those at each stage.

Well yes but the BLAST bitscores are calculated from alignments of protein sequences. So, in effect, the sequences were used at some stage. Still fatuous for all the aforementioned reasons.

[Paul_King]

Yes, but that is still throwing information away. The bitscores only tell us how the chosen proteins compare to the human version, not how they compare to each other. All Gpuccio’s method tells us is that more closely related species tend to have more similar proteins. He’s thrown away anything that would let him work out what is conserved, how much variation is allowed at each position and so on.

[Mercer (John Mercer)]

@Rumraket

If technically 10 out of the 20 different possible amino acid states are allowed at some position in the protein, but only 5 of these are among the variation known from species that have had the gene sequenced, that’s massively going to impact the FI you calculate as you go through each aligned site in the protein and there are strictly allowed variants for each position not actually present in existing variation.

Myosin is a fine case of that. Half of a conventional myosin heavy chain consists of an alpha-helical coiled-coil, which has a heptad repeat with hydrophobic residues in two of the positions and does not tolerate the kinks created by proline residues.

@Rumraket

This idea that we would expect all the allowed variation to actually be present in the form of sequences from each different species is just ridiculous. Particularly when we consider that some states might just have lower fitness and therefore be less likely to be present, yet would still strictly represent functional states, and therefore affect the probability of evolving the sequence.

Yup.

@Rumraket

The method is therefore extremely vulnerable to taxon sampling, and completely ignores the effect of fitness. It treats each site as black or white, with variants not seen in the taxon sampling assumed to be nonfunctional, which will inflate the FI. Besides the fact that it also assumes that the taxon sampling yields an exhaustive sampling of allowed variants.

Most of the fundamental assumptions are ludicrous. It just so happens that myosin, actin, and tropomyosin, some of the best-understood proteins we know, provide a simulacrum of everything that is blatantly wrong with this notion.

@Rumraket

Amazingly I’ve explained all this on this same website now four years ago . I got crickets back, like we get crickets now. In the latest FI thread I also linked an article co-authored by Swamidass where they prove with simulations that the sampled variations you can expect to be present in some taxon sampling used for your alignment, to “fantastically understimate” the real number of functional sequences.

It’s stupid. It’s just stupid. I cannot get over that there are people who buy it.

Just like Nigel Tufnel in Spinal Tap! Do you think that @Giltil understands why it’s funny?

[Rumraket (Mikkel R.)]

@Mercer

Do you think that @Giltil understands the point and why it’s funny?

I do suspect that he does. I just think he has taken it as axiomatic that we must be somehow wrong. How else am I to interpret this response of his?

@Giltil

Are you immune to all philosophical commitment?

[Mercer (John Mercer)]

I don’t know. Maybe he simply admires Nigel’s ideological commitment to knobs that go to eleven and sees nothing funny about the clip.

What seems clearer is that he can no longer see a way through his cognitive dissonance to defend the notion.

[colewd (Bill Cole)]

@Gisteron

You don’t have a clue. Because you have a commitment to reject any and all candidate explanations that do not involve literal magic, no matter how much experimental evidence there is to support them.

The use of the term “literal magic” simply says you are committed to methodological naturalism. This is the current method of science and the box the parsimony claim forces you into. The data does not however support this model as you cannot reconcile through population genetics the differences in genetics we are observing.

The scientific restriction is forcing you away from making real sense of the data which is indicating multiple points of origin vs a single point.

[Gisteron]

@colewd

The use of the term “literal magic” simply says you are committed to methodological naturalism.

That’s false.

@colewd

This is the current method of science and the box the parsimony claim forces you into.

This is incoherent. There is no “the parsimony claim” here.

@colewd

The data does not however support this model as you cannot reconcile through population genetics the differences in genetics we are observing.

Show us why not. With maths. If you cannot, then this is a lie on your part.

@colewd

The scientific restriction…

Being free to construct models with predictive power is not a restriction. Being committed to conclude some particular model irrespective of the data would be. But that’s a restriction you are under, not I.

@colewd

… is forcing you away from making real sense of the data…

By “making real sense of the data” of course you mean “concluding it’s magic”.

@colewd

… the data which is indicating multiple points of origin vs a single point.

Until you can point to any such data, this is best treated as just another lie.