Optimized amino acids

[shunyadragon]

What do you mean by this? Are you talking about the metabolism first hypothesis?

Not necessarily just simply facts, amino acids in and of themselves do not evolve. There are a number of viable hypothesis that involve the early evolution before LUCA.

[shunyadragon]

Not only was I aware of Pyrrolysine, I'm also aware of Selenocycteine.

The organisms that use Pyrrolysine have genes for a specific tRNA and aminoacyl-tRNA-synthetase for Pyrrolysine. And, it doesn't replace an existing amino acid/codon mapping, it codes to one of the stop codons.

You need to explain how either one (tRNA or aminoacyl-tRNA-synthetase) could have been selected for without the other one existing. They work together.

Is this a case of an additional amino acid being added to the set or a case of discovering an amino acid that was always being used in certain organisms?

The early sets amino acids were not necessarily 'always being used in certain organisms' until after the evolution of LUCA where the set of 20 was selected for over all other possible sets based on natural selection. I believe the evolution was progressive energy resource driven first dependent energy sources, than the progressive independent iron-sulfur to oxygen-phosphorus driven independent metabolism that naturally selected for the present 20 amino acid sets.

[Roy]

You simply don't have any evidence that there were life forms that used alternative sets of amino acids.

Not only was I aware of Pyrrolysine, I'm also aware of Selenocycteine.

The organisms that use Pyrrolysine have genes for a specific tRNA and aminoacyl-tRNA-synthetase for Pyrrolysine. And, it doesn't replace an existing amino acid/codon mapping, it codes to one of the stop codons.

Right. Those organisms use an additional amino acid that isn't in the usual set. They have an alternative set.

So you know shunyadragon does have evidence for life forms that used alternative sets of amino acids.
And you know my scenario about post-LUCA amino-acid set evolution is not merely hypothetical, and doesn't require new discoveries.
Those were lies on your part.

Alternatively, you could be lying now when you say you knew about pyrrolysine-using organisms all along. It doesn't really matter which.

You need to explain how either one (tRNA or aminoacyl-tRNA-synthetase) could have been selected for without the other one existing. They work together.

I don't need to explain anything to some-one who isn't interested in honest discussion. Anyway, if you already knew about pyrrolysine, then you might already know that there are lots of cases where organisms lack the aminoacyl-tRNA enzymes for one or more of their amino-acids.

Is this a case of an additional amino acid being added to the set or a case of discovering an amino acid that was always being used in certain organisms?

Probably the former, though it's obvious why a creationist bletherskite might prefer the latter.

[lee_merrill]

Ok, since i've been ignoring this while sick, it seems like a good chance to back up to some basic stuff. Lee, without resorting to internet searches, can you answer the following questions:
How many different sets of amino acids are currently in use? (Or, put differently, how many distinct genetic codes are there?)
What is the name of the class of enzyme responsible for matching amino acids to genetic codes?
Has that enzyme class shown signs of recent evolution?

These all seem relevant to your claim that the genetic code hasn't evolved. Do you actually know them?

No, I don't know these, you may of course bring them up and we can discuss them. I do seem to recall a mention of synthetase in my searches on this subject, though.

Blessings,
Lee

[TheLurch]

No, I don't know these, you may of course bring them up and we can discuss them. I do seem to recall a mention of synthetase in my searches on this subject, though.

So, after page after page of arguing about the evolution of the genetic code, you're admitting that you don't even know how much the genetic code evolves? Really?

[lee_merrill]

So, after page after page of arguing about the evolution of the genetic code, you're admitting that you don't even know how much the genetic code evolves?

Glad to learn if I'm wrong, that's part of the reason for such forums.

Blessings,
Lee

[TheLurch]

Glad to learn if I'm wrong, that's part of the reason for such forums.

I've asked this several times in response to your "happy to learn" posts, but you've never answered it. So i'll try again: if you haven't learned in the first place, why do you make such confident assertions about a topic? Wouldn't it be better to ask questions and learn first? Doesn't it bother you to say things that are untrue?

[lee_merrill]

I've asked this several times in response to your "happy to learn" posts, but you've never answered it. So i'll try again: if you haven't learned in the first place, why do you make such confident assertions about a topic? Wouldn't it be better to ask questions and learn first? Doesn't it bother you to say things that are untrue?

Well, I state my conclusions if I feel the evidence merits a conclusion, otherwise I will indeed ask questions. And you need to show me that amino acid sets are evolving, before I change my conclusion.

Blessings,
Lee

[shunyadragon]

Well, I state my conclusions if I feel the evidence merits a conclusion, otherwise I will indeed ask questions. And you need to show me that amino acid sets are evolving, before I change my conclusion.

Blessings,
Lee

Demands such as these reflect the fact that you are 'not willing to learn.'

You were shown in proteins and DNA is evolving to include new combinations that include up to 22 amino acids.

[TheLurch]

Well, I state my conclusions if I feel the evidence merits a conclusion.

You've just admitted that you don't know or understand much of the relevant evidence. So why have you stated a conclusion regardless?

[lee_merrill]

You've just admitted that you don't know or understand much of the relevant evidence. So why have you stated a conclusion regardless?

So enlighten me! I've stated my conclusion based on the knowledge that I have, having read that 20 amino acids are common to all life.

Blessings,
Lee

[lee_merrill]

You were shown in proteins and DNA is evolving to include new combinations that include up to 22 amino acids.

I don't recall this, can you give me a link?

Blessings,
Lee

[shunyadragon]

I don't recall this, can you give me a link?

Blessings,
Lee

Do your home work I cited the specific reference in response to the same question. More important you are obviously ignoring the excellent references by The Lurch, and making phony claims of 'willingness to learn.'

[shunyadragon]

So enlighten me! I've stated my conclusion based on the knowledge that I have, having read that 20 amino acids are common to all life.

Blessings,
Lee

I have repeated this many times with references, that yes the set of 20 dominates all life after the first LUCA for a very good reason. It was the most effective set of 20 amino acids to evolve for independent energy utilization, self-replication in the environment of the early earth. This has been the course of evolution throughout the history of life, and the older variations simply do not survive, nor do they have any reason nor ability to.

Yes, again the sets of amino acids do continue to evolve. Do your home work. So far in the course of this and other threads you have failed to do just that. The Lurch is right, and better educated than either of us.

[TheLurch]

So enlighten me! I've stated my conclusion based on the knowledge that I have, having read that 20 amino acids are common to all life.

I'm wondering at what point you'd recognize your ignorance is such that you aren't willing to draw a conclusion. And why you hadn't reached that in this discussion.