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

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 . . .



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.

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.