Optimized amino acids

[TheLurch]

That's what I mean when I say "highly conserved", we don't see amino acid sets evolving, which indicates that change in this area is fatal to the organism.

That statement is not just false, but nearly everything it's comprised of is false.

That's not what "highly conserved" means.
We do see amino acid systems changing since the last common ancestor, often through horizontal gene transfer.
Not seeing changes in a system does not mean that changes are fatal.

Why do you refuse to think before typing?

[lee_merrill]

We do see amino acid systems changing since the last common ancestor, often through horizontal gene transfer.

I would be interested to hear more.

Not seeing changes in a system does not mean that changes are fatal.

But it's a strong indication in that direction.

Blessings,
Lee

[lee_merrill]

Once the most optimal has been achieved there are no others evolving.

That is incorrect, see Behe's forthcoming book "Darwin Devolves", for instance.

Blessings,
Lee

[shunyadragon]

But I was asking what other sets exist today, which is what seemed to be being claimed.

Well yes . . . sets of amino acids may be 22, but if you read the second article carefully, high school English, it gives a basic outline why the twenty evolved and survived and other combos did not.

Source: https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445

An Evolutionary Perspective on Amino Acids
Summary

Scientists now recognize twenty-two amino acids as the building blocks of proteins: the twenty common ones and two more, selenocysteine and pyrrolysine. Amino acids have several functions. Their primary function is to act as the monomer unit in protein synthesis. They can also be used as substrates for biosynthetic reactions; the nucleotide bases and a number of hormones and neurotransmitters are derived from amino acids. Amino acids can be synthesized from glycolytic or Krebs cycle intermediates. The essential amino acids, those that are needed in the diet, require more steps to be synthesized. Some amino acids need to be synthesized when charged onto their corresponding tRNAs. We have discussed only two biosynthetic routes: the Trp pathway, which appears to have evolved only once, and the Lys pathway, which seems to have evolved independently in different lineages. Prevailing evidence suggests that metabolic pathways themselves seem to be evolving following the patchwork assembly model, which proposes that pathways originated through the recruitment of generalist enzymes that could react with a wide range of substrates. The study of the evolution of amino acid metabolism has helped us understand the evolution of metabolism in general."

© Copyright Original Source

Source: https://www.chemistryworld.com/features/why-are-there-20-amino-acids/3009378.article

Why stop at 20?
Adaptation to an oxygenated world may explain the expansion of the code to 20 amino acids, but why stop there? ‘I would say, look what 20 can do,’ says Freeland. ‘Apparently 20 is good enough for almost every living organism to have adapted to an unimaginable number of habitats over the entire history of life.’

In fact there are at least two additional amino acids used in organisms, although only one of these is found in human proteins – the selenium-containing selenocysteine. It is found in the active sites of 25 human proteins, but is incorporated by a more complex mechanism than normal protein synthesis. ‘This shows that the process had not stopped, it reached a point where incorporating new amino acids is extremely hard,’ says Lluis Ribas, a molecular biologist at the Institute for Research in Biomedicine, Barcelona, Spain. ‘If you want to do it then you need to find very original solutions.’

© Copyright Original Source

The best local optimum in the fitness landscape survives, not the best overall optimal solution.

The set of twenty is the optimum in the fitness landscape surviving. The future better optimal set may be 22.

[shunyadragon]

That is incorrect, see Behe's forthcoming book "Darwin Devolves", for instance.

Blessings,
Lee

Please cite carefully. because Behe is really bogus in his claims. As usual selective juggling of facts to serve the desired agenda.

From a intro review of his book . . .

Source: https://www.amazon.com/Darwin-Devolves-Science-Challenges-Evolution/dp/0062842617

A system of natural selection acting on random mutation, evolution can help make something look and act differently. But evolution never creates something organically. Behe contends that Darwinism actually works by a process of devolution—damaging cells in DNA in order to create something new at the lowest biological levels. This is important, he makes clear, because it shows the Darwinian process cannot explain the creation of life itself. “A process that so easily tears down sophisticated machinery is not one which will build complex, functional systems,” he writes.

In addition to disputing the methodology of Darwinism and how it conflicts with the concept of creation, Behe reveals that what makes Intelligent Design unique—and right—is that it acknowledges causation. Evolution proposes that organisms living today are descended with modification from organisms that lived in the distant past. But Intelligent Design goes a step further asking, what caused such astounding changes to take place? What is the reason or mechanism for evolution? For Behe, this is what makes Intelligent Design so important.

© Copyright Original Source

Problem 'Natural selection in Evolution DOES NOT act on random mutation. Evolution DOES NOT create things organically. Natural selection is in response to the Laws of Nature and the natural environment. There are more bogus problems here, and nothing you can cite to support your statement.

[Roy]

What are your qualifications to critique this research?

He has a D-K.

[Roy]

We do see amino acid systems changing since the last common ancestor, often through horizontal gene transfer.

I would be interested to hear more.

You already did, on page three of this thread. But you obviously weren't interested enough to follow up by doing your own research, and have clearly forgotten what you were told then.

Just keep swimming, Dory.

[TheLurch]

I would be interested to hear more.

Roy's handled this part.

But it's a strong indication in that direction.

I'll just point out that sterility creates just as strong an evolutionary selection as lethality, so you're clearly wrong. Again.

[shunyadragon]

He has a D-K.

What is a D-K?

[DaveB]

The abstract proposes a natural hypothesis to explain the set of twenty amino acids.

You are egregiously and dishonestly misrepresenting the article, and to add you have failed to produce the whole article.

While the authors surely believe in a naturalistic explanation for how the set of amino acids were "selected", the hypothesis of the paper is only that the set is optimal for the values that they are testing for.

[DaveB]

There is a great deal research presently working on this subject like the following.

Source: https://www.sciencedirect.com/science/article/pii/S0014579315008868

The evolution of Class II Aminoacyl-tRNA synthetases and the first code
Edited by Michael Ibba

A new evolutionary sequence for the catalytic domain of the Class II synthetases.

Two alternate catalytic domain extensions leads to a split of the Class II synthetases associated with the operational code.

The earliest Class II synthetase may form the link between a Thioester world and a Phosphoester world.

Abstract
Class II Aminoacyl-tRNA synthetases are a set of very ancient multi domain proteins. The evolution of the catalytic domain of Class II synthetases can be reconstructed from three peptidyl-hairpins. Further evolution from this primordial catalytic core leads to a split of the Class II synthetases into two divisions potentially associated with the operational code. The earliest form of this code likely coded predominantly Glycine (Gly), Proline (Pro), Alanine (Ala) and “Lysine”/Aspartic acid (Lys/Asp). There is a paradox in these synthetases beginning with a hairpin structure before the Genetic Code existed. A resolution is found in the suggestion that the primordial Aminoacyl synthetases formed in a transition from a Thioester world to a Phosphate ester world.

© Copyright Original Source

This paper is trying to explain the two different classes of synthetases that are used to process the current set of amino acids. It does nothing to show that life ever used any other amino acid sets.

[DaveB]

How remarkable that life on Earth would be optimized for the amino acids found on Earth. It's almost like life utilized what was available.

Oh, wait...

There are many amino acids found on the earth. Perhaps hundreds.

The question is why are the relatively few used optimal (in the properties that the researchers tested for)?

[DaveB]

That statement is not just false, but nearly everything it's comprised of is false.

That's not what "highly conserved" means.
We do see amino acid systems changing since the last common ancestor, often through horizontal gene transfer.
Not seeing changes in a system does not mean that changes are fatal.

Why do you refuse to think before typing?

Lee said "amino acid sets", not "amino acid systems".

[DaveB]

Problem 'Natural selection in Evolution DOES NOT act on random mutation. Evolution DOES NOT create things organically. Natural selection is in response to the Laws of Nature and the natural environment. There are more bogus problems here, and nothing you can cite to support your statement.

This is nonsense. The only thing that NS has to work on (in the ToE) are beneficial or deleterious traits that arise due to random mutation.

What are these Laws of Nature that you keep mentioning?

[DaveB]

You already did, on page three of this thread. But you obviously weren't interested enough to follow up by doing your own research, and have clearly forgotten what you were told then.

Just keep swimming, Dory.

You are conflating a few exceptions to the Genetic code with changes to the set of amino acids that life uses.