The highly optimized genetic code

[shunyadragon]

But Koonin is an evolutionist, who does not believe in ID, and who does not have any religious agenda.

This does not change the fact that he uses bogus unethical probability methods.

By your argument it would seem all events have a probability of one!

Blessings,
Lee

No.

[shunyadragon]

But Koonin is an evolutionist, who does not believe in ID, and who does not have any religious agenda.

I will conclude that you are taking Koonin unethically out of context, and he is not happy based on the following published letter.

Source: https://www.pnas.org/content/117/33/19639

No waves of intelligent design

View ORCID ProfileEugene V. Koonin, Yuri I. Wolf, and View ORCID ProfileMikhail I. Katsnelson

See all authors and affiliations
PNAS August 18, 2020 117 (33) 19639-19640; https://doi.org/10.1073/pnas.2011220117
In PNAS, Phillips (1) attempts to explore the evolution of dynein, a major motor protein of the eukaryotic cytoskeleton, using different hydropathy scales, and comes to several dramatic conclusions. The results of this analysis are taken to indicate that self-organized criticality (SOC) is integral to evolutionary optimization, that evolution of all proteins occurs, primarily, via positive selection, that this pervasive positive selection is shaped by “water waves” traveling along proteins, and even that the optimization in protein evolution stems from intelligent design. However, the actual observations reported in the article do not appear to support or even to be compatible with any of these far-reaching conclusions.

What the paper effectively reports, is the existence of relatively long-range patterns of hydropathy in proteins, particularly, in dyneins. These patterns show periodicity, especially, in the heptad repeat regions that form coiled structures in the dynein stalks (2). The appearance of periodic hydropathy patterns in repetitive protein structures, certainly, is not surprising; furthermore, self-similarity, or fractal properties, are necessarily discernible in such structures. Such self-similarity brings the analogy to SOC (3), leading to the suggestions that SOC is the “magic wand” of protein physics and evolution (4). Generally, however, the presence of such patterns is a natural consequence of the structural organization of proteins, whereby certain proportions and quasi-periodic distributions of hydrophobic and hydrophilic amino acid residues are essential for the formation of individual structural elements, such as β-sheets and α-helices, and for globular domain folding (5). Ultimately, the patterns of amino acid residue distribution and, accordingly, hydropathy were shaped by selection. Does this, however, refute the neutral theory of molecular evolution and imply pervasive positive selection? Not at all. The simplest argument against this interpretation is the conservation of the structures and, accordingly, the hydropathy patterns of numerous proteins across hundreds of millions and even billions of years of evolution. Dynein, in particular, is conserved in all eukaryotes and retains the key structural elements and underlying sequence motifs throughout 1.5 billion years or so since the last common eukaryotic ancestor (6); hence the conservation of the hydropathy patterns that is apparent, in particular, in plots shown by Phillips (1). There is no reason to believe that the patterns of hydropathy in protein sequences are maintained by positive selection for functionally important “water waves” as opposed to the well-characterized purifying selection eliminating mutations that perturb the protein fold and hence are deleterious. Moreover, neutral evolutionary processes, in the form of constructive neutral evolution, can provide for the emergence of complex domain architectures, such as that of dynein, as well as multimeric protein complexes (7⇓–9). Positive selection leading to functional innovations is rare in the evolution of most proteins, especially, highly conserved ones, such as dynein.

In summary, it is unfortunate when observations on simple patterns in biological sequences are overinterpreted to overthrow the fundamental tenets of evolutionary biology. Invoking intelligent design in an attempt to buttress unjustified generalizations on evolution is non sequitur writ large.

© Copyright Original Source

[lee_merrill]

They are not saying that evolution probably could not have produced the SGC. Just that we haven't yet explained the robustness of the SGC.

Well, yes, current evolutionary explanations have been found insufficient.

From the same source:

"In the literature and also in our study many properties have very high reported optimalities, meaning that the probability of finding the standard genetic code by chance is very low. Selection is not an omnipotent force, so this raises the question of whether a selection process could have found the SGC in the case of extreme code optimalities. For some evolutionary hypotheses this has already been tried (Massey, 2010), but this question is strongly related to how many codes could have been tested by natural selection during code evolution, which is not yet answered. By studying these questions we might be able to rule out some evolutionary hypotheses and thereby further our understanding of the evolution of the SGC. Conducting a similar study to this with many different evolutionary hypotheses, but using GAs to determine how many codes must be tested in order to find genetic codes similar to the SGC, would greatly extend our knowledge on this topic." (emphasis mine)

So further studies would be needed, to rule out some hypotheses, this sounds inconsistent with what they said elsewhere. But it does seem no good hypothesis is in view.

The rate of expansion has nothing to do with whether the universe is infinite.

Well, it certainly does, if the rate of expansion is finite, and the universe has a beginning, then it must be fiinite.

The problem with both approaches is that the "ultimate explanation" doesn't really explain anything, but removes the incentive to keep looking for an explanation, which is what scientific advance relies upon.

I agree that Koonin's reliance on infinite universes is incorrect. But I believe there is a positive case to be made for God, unlike the lack of evidence for infinite universes.

Blessings,
Lee

[lee_merrill]

No.

So what events have a probability of < 1, and why?

I will conclude that you are taking Koonin unethically out of context, and he is not happy based on the following published letter.

So how am I taking him out of context, based on this letter? What is he really saying, according to you, if not 1 in 10¹⁰¹⁸?

Blessings,
Lee

[shunyadragon]

So what events have a probability of < 1, and why?


So how am I taking him out of context, based on this letter? What is he really saying, according to you, if not 1 in 10¹⁰¹⁸?

Blessings,
Lee

What is he saying. Your full of Bull Hocky!!!!!

[shunyadragon]

What is he saying. Your full of Bull Hocky!!!!!

You unethically misrepresent Koonin and he rejected the your religious based ID agenda can be justified by his research.

[Stoic]

Well, yes, current evolutionary explanations have been found insufficient.

So further studies would be needed, to rule out some hypotheses, this sounds inconsistent with what they said elsewhere. But it does seem no good hypothesis is in view.

No, it's not inconsistent with what they said elsewhere. There are a lot of things that science hasn't explained yet. It would be boring otherwise. But the fact that it hasn't been explained yet does not mean that it will never be explained.

Well, it certainly does, if the rate of expansion is finite, and the universe has a beginning, then it must be fiinite.

That would mean that it has a finite age. But not that it has a finite size.

I agree that Koonin's reliance on infinite universes is incorrect.

It's not incorrect, so much as premature. If we somehow determine that there is no reasonably probable pathway, we can always go that route. But until then, we should keep looking.

But I believe there is a positive case to be made for God, unlike the lack of evidence for infinite universes.

Even if you could prove that there is a God, saying "God did it" is not an explanation. It's just a way of giving up on looking for an explanation.

[TheLurch]

Ok, i'm apparently going to have to look at Koonin's speculation in more detail. Can you tell me where in that tome the probability calculations are?

[lee_merrill]

No, it's not inconsistent with what they said elsewhere.

Well, it is indeed inconsistent with what I quoted.

That would mean that it has a finite age. But not that it has a finite size.

Both a finite age and a finite size. Think of a point mass that you blow up at a finite rate--it's never going to be infinite.

Even if you could prove that there is a God, saying "God did it" is not an explanation. It's just a way of giving up on looking for an explanation.

But people give up all the time, when an archeologist concludes that a flint is an arrowhead, for instance.

Blessings,
Lee

[lee_merrill]

Ok, i'm apparently going to have to look at Koonin's speculation in more detail. Can you tell me where in that tome the probability calculations are?

Thanks! and it starts on page 434 at this link.

Blessings,
Lee

[Stoic]

Well, it is indeed inconsistent with what I quoted.

It's inconsistent with your interpretation of what you quoted.

Both a finite age and a finite size. Think of a point mass that you blow up at a finite rate--it's never going to be infinite.

If it's infinite in size, it would not have been a point mass. It would have been infinite in size all along. Only the currently observable portion of the universe would have been a point.

But people give up all the time, when an archeologist concludes that a flint is an arrowhead, for instance.

No. If he says "God created it" then he's given up.

[Stoic]

Ok, i'm apparently going to have to look at Koonin's speculation in more detail. Can you tell me where in that tome the probability calculations are?

If you want to see what he's calculating the probability of, see Anthropic Chemical Evolution, starting on page 386.

[Seeker]

No. If he says "God created it" then he's given up.

Yes, because miracles don't explain anyrhing. They are a useless hypothesis. I can elaborate more about that.

[lee_merrill]

If it's infinite in size, it would not have been a point mass. It would have been infinite in size all along. Only the currently observable portion of the universe would have been a point.

Well, by "the universe" most people seem to mean "the mass that constitutes the universe." Are you counting empty space outside this mass as part of the universe?

No. If he says "God created it" then he's given up.

I meant that the archeologist gives up on an explanation by natural processes. Science is about natural processes, it only allows deducing the actions of intelligent agents when the effects of natural processes have been ruled out.

Blessings,
Lee

[Stoic]

Well, by "the universe" most people seem to mean "the mass that constitutes the universe." Are you counting empty space outside this mass as part of the universe?

Sometimes "the universe" just means everything we know about. Sometimes it means everything.

If "everything we know about" is all there is, then it would be fair to say that the universe is finite. But we can't know that.

I meant that the archeologist gives up on an explanation by natural processes. Science is about natural processes, it only allows deducing the actions of intelligent agents when the effects of natural processes have been ruled out.

Concluding that something was made by humans, does not mean that it was not the result of natural processes.