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

Ernest Major wrote:

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.

 At 10% of that price there is https://www.amazon.co.uk/Failures-Mathematical-Anti-Evolutionism-Jason-Rosenhouse/dp/1108820441 

After I check the local library I'll look into this.

 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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Where there is mathematics involved, how is the math challenged? If not the math then what?
I don't think it's fair to call someone an anti-evolutionist. This is a disparagement meant to discredit an opposition without a hearing. It's like a court where the prosecutor presents his case, but  a defense is not allowed. But a fair decision is expected.
But you cannot challenge the mathematics. What is the chance of a single functional protein can form through unguided, random and aimless processes? For example, in the pre-biotic earth the first protein of say 150 (the average number amino acids in a protein is 500-400) amino acids in a specific order is needed. Even in an ocean of amino acids and 4.5 billion years. It's said  it would be less chance than the number atoms in the known universe. As you know in the pre-biotic universe there is no natural selection.
"......we can calculate the probability of building our very modest protein."
https://www.youtube.com/watch?v=W1_KEVaCyaAfunctional protein to be 1 in 10^164.
Remember, this is only one protein, and life requires hundreds of proteins".
https://www.str.org/w/building-a-protein-by-chance
I think this is where intelligence comes into play, there is no more simpler explanation!
Where is Ocham's razor?

 

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?

 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 question the source. Who can know how many amino acids were present at that time. Amino acids have been found in space rocks, meteors. The Urey-Miller experment, in conditions representing early earth atmosphere and electric discharges representing lightning produced several amino acids.
And later duplication of the Miller excrement produces even more than Millers did.
So, who knows how many amino acids existed on the pre-biotic earth.

 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. 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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I did not address anything except the common used 20 or 22 amino acids. Technically, you are right, I can accept that, but it does not undermine the concept I offered.

 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.
 Other amino acids play a role in biochemical metabolism.
 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.
 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.

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How far back would you have to go back for this? Certainly, at the time of the Cambrian explosion the genetic code as we know it today was present then. And as I mentioned at the time of the Cambrian explosion there had to be an explosion of specific genetic information (instructions).
The origin of which is inexplicable, except through intelligence. The truth is, information is degraded by errors, mistakes and copying.
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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This is supposition and hypothesis.

 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.
 

We've discussed this before. I think originally the genetic code was robust, but over time due to the 2/ND law and missed errors in copying, the robustness declined and continues to decline. This I
think was anticipated from the beginning of the genetic code and several proofreading and repair machines were implanted into the code. But even these proofreading and repair systems are subject to errors over time. However, they still catch overwhelming numbers of mutations and corrects them, but not all. The evidence I think supports this. Still, each generation inherits the mutations from previous generations and develops new mutations, all of which is passed on down. At some distant time the genetic code in each species becomes increasingly less robust until reproduction
ceases and we see this in many extinctions as recorded in the fossil record.
If one looks at the fossil record with _no_ biases, I think what we find is the abrupt appearance of most (if not all) species in the strata, then long periods of stasis followed by sudden disappearance.
I think Dr Stephen J. Gould was an honest scientist who voiced what was actually observed in the fossil record without bias or an overriding commitment to convention.