Optimized amino acids

[TheLurch]

How much do you know about it?

There is not a singular enzyme (aminoacyl trna synthetase) as you suggest. There are a set of them. One for each amino acid. The idea that they can readily change their specificity is not true.

I have a BA in biochemistry, a PhD in molecular and cellular biology, and have done over a dozen years of post-doctoral and faculty-level research in the biological sciences.

Don't equate casual phrasing with lack of knowledge.

EDIT: correcting my own error - apologies for the stupidity.

[TheLurch]

Well, if they evolved all the time, we wouldn't call them highly conserved!

You should go back and look up what "highly conserved" means.

[TheLurch]

The claim that some of the 20 amino acids were early and the others added later is based on the assumption of evolution.

Given that evolution has been demonstrated repeatedly, it's not something that has to be assumed, so i'm not sure what you're trying to say here.

But even if the claim is true, the additions occurred by the time of the so-called LUCA, and there are extremely few exceptions to the genetic code extant today.

You don't have any evidence that Lee's claim is incorrect.

I was pointing out that the thing Lee said he was unaware of happening was a central premise of one of the papers that he was indirectly presenting as evidence. And the evidence for that can be found by following links from the OP.

[DaveB]

According to the blog post, it's also the subject of the first reference:

Source: ibid

As it turns out, proteins are built from a specialty set of amino acids that have the just-right set of properties to make life possible, as recent work by researchers from Germany attests.[1]

© Copyright Original Source

The answer to "Did you not bother to read the blog post before citing it, or are you purposefully misrepresenting it?" appears to be "Both".

Actually, the first paper only says that the set has the right properties to make life possible. It doesn't claim that it is the best possible set among those that have the right properties..

Rana makes that point after referring to the first paper.

In other words, evolutionary mechanisms would have cobbled together an amino acid set that works “just good enough” for life to survive, but nothing more. No one would expect evolutionary processes to piece together a “just-right,” optimal set of amino acids.

Rana then goes on the says that the set is indeed optimized and cites the second paper for support.

[DaveB]

I'd just like to point out that this quote implies that blog author didn't read the paper he's citing. Far from a set of properties to "make life possible", the paper suggests that the current set was the result of the addition of over five new amino acid over evolutionary time, and therefore life was possible with significantly fewer.

The paper says that it is possible to make functional proteins with fewer amino acids, but that the "additional" ones provide protection from free radicals that could damage the proteins.

As Rana states:

As it turns out, these amino acids readily react with the peroxy free radical, a highly corrosive chemical species that forms when oxygen is present in the atmosphere. The German biochemists believe that when these 7 amino acids reside on the surface of proteins, they play a protective role, keeping the proteins from oxidative damage.

So I think the implication is that while you might have functional proteins, life wouldn't have been possible without the "additional" ones to keep the proteins from being damaged.

[TheLurch]

The paper says that it is possible to make functional proteins with fewer amino acids, but that the "additional" ones provide protection from free radicals that could damage the proteins.

As Rana states:

As it turns out, these amino acids readily react with the peroxy free radical, a highly corrosive chemical species that forms when oxygen is present in the atmosphere. The German biochemists believe that when these 7 amino acids reside on the surface of proteins, they play a protective role, keeping the proteins from oxidative damage.

So I think the implication is that while you might have functional proteins, life wouldn't have been possible without the "additional" ones to keep the proteins from being damaged.

Oxygen wasn't present in significant amounts until much later in life's history; oxidative damage wasn't unlikely to be a significant issue until over a billion years after life started. So the phrase "make life possible" is simply wrong, and implies he was either careless, or didn't read or think carefully about the implications of the papers he was citing.

[DaveB]

No, he read the paper: "Interestingly, some biochemists think that these 7 amino acids are not necessary to build proteins." My guess is he put down the wrong reference number.

But the fact remains that the set of amino acids we have is highly optimized, which is remarkable.

Blessings,
Lee

I do think that Rana had the right reference number. He is using the first paper only to say that the set has the right properties for life, not that it is the optimal set. There can be sets that have the right properties that are "good enough", but not optimal.

[DaveB]

Several times something evolves more than once. Eyes for instance.

Then why don't see see life with various sets of amino acids?

[Roy]

"As it turns out, proteins are built from a specialty set of amino acids that have the just-right set of properties to make life possible"

Actually, the first paper only says that the set has the right properties to make life possible.

You've changed "just-right" to "right". Perhaps "just-right" implies optimality, in which case the first paper could be claiming it's the best possible set.

No one would expect evolutionary processes to piece together a “just-right,” optimal set of amino acids.

[shunyadragon]

Then why don't see see life with various sets of amino acids?

. . because life has a common ancestor that evolved.

[lee_merrill]

. . because life has a common ancestor that evolved.

But the question is, why don't we see amino acids sets still evolving?

Blessings,
Lee

[shunyadragon]

But the question is, why don't we see amino acids sets still evolving?

Blessings,
Lee

Food chain . . . because they are food for quadrillions of existing micro organisms along with the other amino acids floating around.

[shunyadragon]

The authors state nothing of the kind. They are not attempting to explain how the set was chosen, they are simply showing that the set is optimized.

Here is the sentence in question.

Here, we demonstrate unambiguous support for a refined hypothesis: that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property.

Again, again and again . . . I need the full paper to assess what the authors propose as a refined hypothesis to explain ' . . . that an optimal set of amino acids would spread evenly across a broad range of values for each fundamental property.

What was referenced is at present meaningless.

[lee_merrill]

Food chain . . . because they are food for quadrillions of existing micro organisms along with the other amino acids floating around.

Being food would keep amino acid sets from evolving? But bacteria are food, and they evolve.

Blessings,
Lee

[shunyadragon]

Being food would keep amino acid sets from evolving? But bacteria are food, and they evolve.

Blessings,
Lee

They evolve, but not all do. Those that do not optimally evolve to survive became food for those that do, and do not successfully evolve. The same case is for the amino acid combinations in the earliest microbes that failed to compete and reproduce enough, therefore the set of twenty microbes we have was the most successful. This is the history of evolution. If you are not the optimum fit to compete you are the food for those that do.

'Optimal' in evolution is best suited to compete, reproduce and evolve. There of course likely other combination not as 'optimal.' and of course they did not survive. the 20 we have did likely evolve from a shorter set as noted in the research. Also cited was contemporary research has demonstrated other possible combinations, and again, they did not reproduce and compete with the microbes with 'optimal' set of amino acids.