Evidence?
He isn’t. He isn’t even claiming anywhere near the majority are. Just that neutral mutations exist, and that protein amino acid sequences can drift apart from their common ancestors by fixing neutral mutations. And he’s right. Here’s another article on that topic:
Hi Rum
Check out uniprot alignments. Very few AA substitutions over long time periods.
I now think the Lynch’s model maybe biased toward certain genes/proteins and not a universal model. The paper you cited discusses “slowly evolving proteins” due to sensitivity of mis folding due to substitutions.
You just admitted that @gpuccio’s notion, that sequence conservation is related to functional complexity, has no basis in reality.
How does that look for human MYH7?
That’s not evidence for your claim.
So you have no evidence, you’re just blathering again.
Translation: “I read a sentence in the abstract”.
@colewd honest question here, because I can’t stop wondering: are you even aware that you are blathering, or do you genuinely believe you’re making sense? Or is this just some sort of half-assed form of trolling?
What is your explanation for this preservation? Why do we not see more amino acid substitutions if Lynch’s model is correct?
I’d ask you to demonstrate exactly how conservation is inconsistent with that model. But we all know all we’ll get is more nonsensical bafflegab.
Lynch models what happens under the circumstances where protein sequences can diverge and accumulate mutations over time.
Innumerable proteins exhibit this behavior, they diverge over time and continue to accumulate mutations. Here’s one that recently has gotten rather famous:
Conservation comes in degrees and covers the entire logically possible range. From a rate that implies strong positive selection for change, to zero, and everything in between.
Some proteins evolve and mutate much more quickly than others. Some evolve extremely fast(look above), some more slowly, and some seem to have basically stopped and remain completely conserved for over a hundred million years. The article I linked previously explains what factors control this rate of sequence evolution and divergence. Read it. Try, try to comprehend it.
So we agree some gene/proteins do not fit Lynch’s model of many available neutral substitutions?
From Lynch’s paper.
Even for the highly conserved catalytic core regions of proteins, approximately one-third of amino acid sites can tolerate substitutions (Materon and Palzkill 2001; Guo et al. 2004). Many other studies (e.g., Kim et al. 1998; Akanuma et al. 2002), including all of those cited by Behe and Snoke, have obtained results of this nature. A deeper understanding of the fraction of amino-acid-altering mutations that have mild enough effects to permit persistence in a population comes from observations on within- and between-species variation in protein sequences (Li 1997; Keightley and Eyre-Walker 2000; Fay and Wu 2003), which generally indicate that 10% to 50% of replacement mutations are capable of being maintained within populations at moderate frequencies by selection-mutation balance and/or going to fixation.
This (in bold) assumes the same starting point for similar sequences between different species.
Why do we see so many substitutions in human MYH7 if Lynch’s assessment is NOT correct?
Why do think this argument is about a single protein?
No.
A deeper understanding of the fraction of amino-acid-altering mutations that have mild enough effects to permit persistence in a population comes from observations on within- and between-species variation…
So why is there so much within-species variation in human MYH7, given that myosins are some of the most functionally complex proteins known?
What do you mean they are the most functionally complex proteins known? How are you determining functional complexity?
Bill, stop it. I wrote:
Why did you remove “some”? Did you do it to deceive or because you didn’t read it carefully before replying?
By having multiple, complex functions, of course. That’s not correlated at all with sequence conservation.
The goal of the two papers was to model the process by which gene duplication can lead to the generation and fixation of novel genes.
It is just further evidence of your utter incomprehension that you somehow think the existence of sequence conservation is a problem for this process.
How would you compare this to a protein that is not as complex? What is causing loss of function in proteins that are “less complex”?
If a protein requires a high level of sequence specificity to perform its function why would that not be an indicator of functional complexity?
This is not my argument.
Sequence conservation is evidence that certain proteins resist mutation and therefor are not applicable to Lynch’s model that assumes many available substitutions. It is not a general purpose model. I am not even sure it is useful at this point.
Not if the gene has been duplicated. That’s the whole point.
This is a very basic aspect of the papers you are trying to bluff us into believing you understand.
BTW, are you suggesting that Behe’s model, in which there are no available mutations that are not selected against, is universally applicable?
Do you realize the requirement of duplication favors Behe? Lynch is arguing that since many mutations are neutral waiting so for a duplication event is not necessary required.