Optimized amino acids

[lee_merrill]

What do you base that on? Again, you're making a probability statement without presenting any indication of what the probability is based on.

For one thing, it's based on the fact that the amino acid set we have is highly conserved.

Blessings,
Lee

[shunyadragon]

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


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

The set of twenty we have today survived and dominated because of natural selection, and the others did not survive, because they were not suited to compete and survive. This is true for hundreds of millions of years of evolution.

[shunyadragon]

For one thing, it's based on the fact that the amino acid set we have is highly conserved.

Blessings,
Lee

Simple, it was the most suited to survive, and reproduce, and the alternatives were not.

[shunyadragon]

If natural selection is involved in generating amino acid sets, this involves changing a basic part of the machinery of life, which would be difficult.

It is involved in forming the basic machinery of life, and actually you have not presented the chemistry of amino acids and proteins why this 'would be difficult' given the right environment, availability of amino acids, and basic organic chemistry. Also difficult is not impossible nor even unlikely.

Not as difficult as you describe. The possible geometry in chemistry for the different proteins and amino acids can form, and a limited number suited to survive in life forms is limited. The outcomes are limited by the Laws of Nature.

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

Well, I'm willing to learn, one reason to post here is to do just that. And I try and stay in the bounds of what is reasonable, in my statements.

Blessings,
Lee

There are a number of problems with your selective misuse of references you have been called on failed to respond.

[TheLurch]

For one thing, it's based on the fact that the amino acid set we have is highly conserved.

What makes you think "highly conserved" means "does not evolve much"?

[shunyadragon]

What makes you think "highly conserved" means "does not evolve much"?

What makes "highly conserved" mean anything?

[The Barbarian]

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...

[TheLurch]

What makes "highly conserved" mean anything?

Highly conserved just means that a system looks very similar over evolutionary time. But it's an extremely flexible term. You could use it to mean that a protein is present in different species (ie - "hemoglobin is highly conserved across mammals"), that their properties are the same ("the use of iron in hemoglobin is highly conserved"), or that their sequence is highly conserved ("an aspartic acid at position 182 is highly conserved"). So, you can call something highly conserved when its sequence is almost always present, but doesn't look much alike, or when its sequence is always nearly identical, but the protein isn't necessarily present.

To give a concrete example: the core TGF beta style signaling system consists of a minimum of five different proteins. Fruit flies have genes for one copy of each of them. Humans have over 30 different versions of the signaling molecule alone, 10 each of its 2 receptors, and (i think) 8 of one of the internal effectors. So, the system can be called highly conserved, even though many of its details are essentially unrelated.

So, if you're going to use it, you're going to have to be able to explain what it means in context, and what that implies about evolutionary history. Given past history here, i'm skeptical that the person shouting "highly conserved" even knows what the context is in this case.

[TheLurch]

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.

This is more of a chicken-egg situation. We don't know how many of the amino acids happened to be present on earth due to prebiotic chemistry (this is certainly the cases with glycine, which forms easily), and how many ended up byproducts of early metabolism, got incorporated into the standard genetic code, and are now found everywhere.

[The Barbarian]

This is more of a chicken-egg situation. We don't know how many of the amino acids happened to be present on earth due to prebiotic chemistry (this is certainly the cases with glycine, which forms easily), and how many ended up byproducts of early metabolism, got incorporated into the standard genetic code, and are now found everywhere.

We know a lot of amino acids, including those used by life on Earth, exist in the solar system apart from Earth. If I had to bet, I'd say that many other abiotic amino acids were present before life began here, and only some of them turned out to work in living things that survived.

[shunyadragon]

So, if you're going to use it, you're going to have to be able to explain what it means in context, and what that implies about evolutionary history. Given past history here, i'm skeptical that the person shouting "highly conserved" even knows what the context is in this case.

This confirms that in the context of this thread and how lee_merrill used term it is meaningless.

[lee_merrill]

Not as difficult as you describe. The possible geometry in chemistry for the different proteins and amino acids can form, and a limited number suited to survive in life forms is limited.

I don't understand what you are saying here.

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.

© Copyright Original Source

Source: ScienceDirect

Using both structural and sequence similarity among the Class II synthetases catalytic domains, Pro, Gly, Ser, Thr and Hist aaRSs appear to be rather similar. All of these are thus likely derived from a common catalytic domain related to a Pro/Gly aaRS catalytic domain. The Asp, Asn and Lys aaRS catalytic domains are all very similar and thus likely derived from a common one.

© Copyright Original Source

But this is speculation, based on structural and sequence similarities. And this does not demonstrate how the basic machinery of translation to amino acids could have evolved, as far as I understand it, they assume such machinery, and then speculate on how it might have changed.

Blessings,
Lee

[lee_merrill]

What makes you think "highly conserved" means "does not evolve much"?

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.

Blessings,
Lee

[shunyadragon]

I don't understand what you are saying here.

Source: ScienceDirect

Using both structural and sequence similarity among the Class II synthetases catalytic domains, Pro, Gly, Ser, Thr and Hist aaRSs appear to be rather similar. All of these are thus likely derived from a common catalytic domain related to a Pro/Gly aaRS catalytic domain. The Asp, Asn and Lys aaRS catalytic domains are all very similar and thus likely derived from a common one.

© Copyright Original Source

But this is speculation, based on structural and sequence similarities. And this does not demonstrate how the basic machinery of translation to amino acids could have evolved, as far as I understand it, they assume such machinery, and then speculate on how it might have changed.

Blessings,
Lee

What are your qualifications to critique this research?

[shunyadragon]

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.

Blessings,
Lee

Of course we do not 'see' amino acid sets evolving. The less adapted variations were eliminated by natural selection. Once the most optimal has been achieved there are no others evolving. The environment that the earliest forms of live began no longer exists. This has happened throughout the history if the evolution of life. Once the most dominate form continues the less suited forms do not.