Optimized amino acids

[lee_merrill]

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.

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

[shunyadragon]

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

It is only optimized, because it works, and that is how evolution works. There are good sources in scientific literature that do not consider the present 'optimized?' set not necessarily the only set that would work.This source also goes over the current view of how and why this set of amino acids formed. In general this combination formed early and worked therefore it became the common ancestor of all life.

Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431706/

One is the standard 'alphabet' of 20 encoded amino acids, shared by organisms that diverged as early as Escherichia coli and human beings. But numerous lines of evidence, from abiotic chemistry to protein engineering, combine to indicate that this alphabet could potentially have consisted of fewer, more, or just plain different amino acids.

. . .

Could alternative alphabets have been encoded?

In seeking a justification for the 20 amino acids we have, we imply that other alphabets were possible. Is this really the case? Early explanations for the size and content of the standard alphabet worked from the very premise that what we see today was somehow an inevitable outcome (see [24] for a review). But as scientific progress undermined these flawed ideas, only one argument against alternative alphabets retained its plausibility. This was the general evolutionary observation that as organisms evolve an increasing complexity, emerging characters can easily become 'locked in' by subsequent evolutionary innovations that are adaptive only in relation to these early characters. Perhaps, then, the first amino acids to enter the code, for whatever reason, were frozen into evolutionary history by a proteome (and hence metabolism) built from them?

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[TheLurch]

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.

Ok, then he just made a statement that's contradicted by the experts who actually study this for a living.

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

What in the world is remarkable about that? It's exactly what you'd expect.

[lee_merrill]

It is only optimized, because it works, and that is how evolution works.

What in the world is remarkable about that? It's exactly what you'd expect.

Evolution should pick the first set that works, which would be unlikely to be this highly optimized set.

Blessings,
Lee

[rogue06]

Evolution should pick the first set that works, which would be unlikely to be this highly optimized set.

Blessings,
Lee

Unless it continued to evolve and become more efficient.

[TheLurch]

Unless it continued to evolve and become more efficient.

People seem to forget this. Evolution never stops. And it does many, many things in parallel.

[rogue06]

People seem to forget this. Evolution never stops. And it does many, many things in parallel.

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

[shunyadragon]

Evolution should pick the first set that works, which would be unlikely to be this highly optimized set.

Blessings,
Lee

Should?!?!? How odd? You are anthropomorphizing evolution as making decisions and 'picking' things. Does not work. First there simply may be many many failures, and some that partly worked. Like the nature of evolution the most optimal survives and dominates if it adopts best, and one of the factor is, which set is the most optimized for reproduction.

These issues and other possibilities are addressed in the cited article.

[lee_merrill]

Unless it continued to evolve and become more efficient.

What in the world is remarkable about that? It's exactly what you'd expect.

Like the nature of evolution the most optimal survives and dominates if it adopts best, and one of the factor is, which set is the most optimized for reproduction.

Yet the scientists have been touting junk DNA as a marker of evolution, evolution is not expected to select (via natural selection) the most optimal solution.

Blessings,
Lee

[HMS_Beagle]

Yet the scientists have been touting junk DNA as a marker of evolution, evolution is not expected to select (via natural selection) the most optimal solution.

Evolution still drives populations towards the top of local fitness peaks even if it doesn't always find the optimum fitness peak.

[TheLurch]

Yet the scientists have been touting junk DNA as a marker of evolution, evolution is not expected to select (via natural selection) the most optimal solution.

How can you possibly say this if you have no idea how evolution works, as demonstrated repeatedly in this thread?

Look into "effective population size" and what it means for optimizing away junk DNA.

[shunyadragon]

Yet the scientists have been touting junk DNA as a marker of evolution, evolution is not expected to select (via natural selection) the most optimal solution.

Blessings,
Lee

What is called 'junk' DNA is considered evidence of evolution. It appears you are not aware of what is called 'junk' DNA, and that it is not really 'junk.' Junk DNA is an old term that simply meant 'There are DNA that we do not know what it does or appears to not have a function.' Since much of the 'junk' DNA has been found to have a purpose. Also, what was called 'Junk DNA is an evolution resource for future change. Even if some 'junk' DNA is worthless or meaningless it is clear the goal of evolution is not 'optimally perfect,' and leftovers are a normal consequence. In the history of evolution many attributes of life are not the most optimal, but are functional in the survival of species.

Source: https://blogs.scientificamerican.com/the-curious-wavefunction/three-reasons-to-like-junk-dna/

The recent dust up over the ENCODE project and its confusing finding that "80% of DNA is functional" surprises me greatly. What surprises me especially is that people are surprised by junk DNA. Unfortunately this time the scientists are also culpable since, while the publicity surrounding ENCODE has been a media disaster, the 80% claim originated in the scientific papers themselves. There is no doubt that the project itself - which represents a triumph of teamwork, dogged pursuit, technological mastery and first-rate science - has produced enormously useful data, and there is no doubt it will continue to do so. What is in doubt is how long it will take for the public damage to be repaired.

There's a lot written about the various misleading statements about the project made by both scientists and journalists and I cannot add much to it. All I can do is to point to some excellent articles: Larry Moran has waged a longstanding effort to spread the true wisdom about junk DNA for years on his blog. Ed Yong exhaustively summarizes a long list of opinions, links and analysis. T. Ryan Gregory has some great posts dispelling the myth of the myth of junk DNA. And John Timmer has the best popular account of the matter. The biggest mistake on the part of the scientists was to define "functional" so loosely that it could mean pretty much all of DNA. The second big mistake was not in clarifying what functional means to the public.

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Read further for a better understanding of 'junk' DNA. It is a layman level read.

Source: https://www.npr.org/2011/08/19/139757702/dont-throw-it-out-junk-dna-essential-in-evolution

Lowe and geneticist David Haussler from the University of California, Santa Cruz, have a paper in Science this week describing how some of these regulatory elements have changed over hundreds of millions of years of evolution.

"There are many genes that have changed remarkably little between a mouse and a human, for example, and yet they behave differently within the cell, and that's largely due to the way they are regulated differently," says Haussler.

Like many revolutions, only a handful of people saw this one coming. David Stern, a geneticist with the Howard Hughes Medical Institute, says as recently as two decades ago, scientists had little interest in the DNA that wasn't part of a gene.

"We used to call this junk DNA, and it's perfectly obvious now what we used to call junk DNA is actually chock-filled with the information that builds out organisms," says Stern.

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[lee_merrill]

Evolution still drives populations towards the top of local fitness peaks even if it doesn't always find the optimum fitness peak.

Agreed, so the absolute optimum may not be expected to evolve.

Blessings,
Lee

[lee_merrill]

Look into "effective population size" and what it means for optimizing away junk DNA.

Are you saying scientists have not touted junk DNA as evidence for evolution? Assuredly they have.

Blessings,
Lee

[lee_merrill]

What is called 'junk' DNA is considered evidence of evolution. It appears you are not aware of what is called 'junk' DNA, and that it is not really 'junk.'

Well, I am aware of the ENCODE project, so I tried to make a careful statement, phrasing it in the past.

Blessings,
Lee