Re: Wistar Symposium "Mathematical Challenge to Neo-Darwinism".

On 2024-05-31 19:00:00 +0000, Ernest Major said:
 

On 31/05/2024 18:36, Ron Dean wrote:

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How the biologist responded to these "problems"? I've found nothing on the net. I found a book on Amazon for $300, but I'm not buying it. This symposium took place in 1966, so it's possible that the
challenges have been met in the intervening years since then.

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At 10% of that price there is https://www.amazon.co.uk/Failures-Mathematical-Anti-Evolutionism-Jason-Rosenhouse/dp/1108820441
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The summary for chapter 4 is "We discuss the famous Wistar conference from 1966, in which high-level mathematical challenges to evolutionary theory were presented. We refute these challenges and discuss the historical significance of the conference in shaping modern mathematical anti-evolutionism."
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However, I know of several challenges that so far as I know have not been answered.
The questions  are: There are over 500 amino acids found in nature, 50% left-handed, but if blind, aimless, unguided natural processes selected the 20 or 22 amino acids that used by all life what are
the chances of these particular particular 20 left-handed amino acids being selected?  I realize there are theories offered to explain why only left-handed amino acids were selected, but what about the 20? Or is it possible that any other set of amino acids would have worked just as well?

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The last time you made this claim I tracked down the source of the 500 number, and found that this was 500 different amino acids which occur in living organisms. I asked you to consider how many of these amino acids existed in meaningful quantities (if at all) on the pre-biotic earth. I presume that you haven't done so.
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I've also brought to you attention that 20/22 amino acids used by all life is an oversimplification. All variants of the genetic code encode 20 proteinogenic amino acids, so those are used by all life. Some prokaryotes have genetic codes that also encode a 21st amino acid, i.e. pyrolysine.

 Also selenocysteine.

 

 Wikipedia reports that the current consensus is that this originated in stem-archaeans, and has subsequently been horizontally transferred into some bacterial groups. A 22nd amino acid, selenocysteine, is also incorporated into proteins from the genetic code using a kludge. This is also not present in all organisms.
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However other amino acids are incorporated in proteins by post-translation modifications. I've previously brought to your attention that there's more hydroxyproline in human proteins than several canonical amino acids.
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Other amino acids play a role in biochemical metabolism.
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They you get into the weeds with amino acids such as canavanine (one of your 500). This is produced by some leguminous plants as an anti-herbivore toxin. It mimics arginine (a proteinogenic amino acid), from which it differs from by replacing a methylene bridge by an oxygen atom, resulting in it being incorporated into the herbivore's proteins to the detriment to their function. Specialist herbivores get round this either by having means of metabolising the canavanine before it gets near their protein synthesis machinery, or by improving the discrimination of their tRNA-arginine synthetases.
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There's a widespread belief that proteins are a relatively late addition to the biochemical repertoires, catalysis having been previous performed using RNAzymes. (RNAzymes are still essential for life.) If this is correct that would mean that amino acids and proteins can be added to the biochemical repertoires in gradual steps.
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People have studied the development of the genetic code, and inferred that the original code included fewer amino acids - perhaps as few as for. The addition of amino acids to the code would depend on availability and utility. The availability constraint biases the genetic code to simpler amino acids. The utility constraint biases the addition of amino acids to the code to amino acids which expand the functional range of proteins, i.e. which have properties (polar vs non-polar, basic vs acidic, hydrophobic via hydrophilic, etc.) not already found in the prior set.
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People have studied the robustness of the genetic code. The genetic code is not optimal for robustness against mutation, but is a lot better than a random one. Something similar may hold for the set of proteinogenic amino acids. Other sets might work perfectly well, but a set with, for example, only hydrophilic amino acids strikes me as likely to be relatively ineffective, or perhaps even not effective at all.