Not Germane to my Main Argument but a Side issue, on Proteins and Gene loci and Douglas Axe.

Douglas Axe is a member of the Discovery Institute, a proponent of Intelligent Design, and from the following video snippet and an interview I heard recently I gather that his main scientific focus has been on trying to find out how likely it is that evolution could come up with a new function, which apparently means a new protein. He doesn't use the term mutation but he must mean that such a transformatiion would come about through mutations. So he's testing the idea of random mutations as a main driver of evolution.

https://www.youtube.com/watch?v=8ZiLsXO-dYo

How many changes, i.e. mutations I assume, to a given protein, would have to occur to bring about a completely new protein with a completely new function? He says he and his colleague concluded that it's outside the realm of possibility.

It seems like a good question but it raises further questions in my mind. isn't the locus, the stretch of DNA that defines a gene, determine the function? Doeesn't it govern the production of only two proteins if it's heterozygous, only one if homozygous> Mutations usually don't change the function of the protein at all despite changing the chemical sequence. These are "neutral" mutations. "Deleterious" mutations do something that interferes with the normal functioning protein which I don't understand on the genetic level, and the occasional "beneficial" mutation apparently changes the expression of the protein, but again I don't know what this means on the genetic level. It would be nice to be able to ask Douglas Axe to explain these things to me.

Is it the protein or the locus that determines the phenotypic expression? I've thought of it as primarily the locus, the space occupied by the gene on the DNA strand, that determines what it produces phenotypically. Perhaps I'm not appreciating the role of the protein, this is another question. Clearly the protein directly produces the phenotypic expression but I think of this as occurring within the determining space occupied by the gene. The very same protein if produced at a differeint locus would result in a different phenotypic expression determined by that different location. That's how I've been thinking about it. So Axe's focus on the structure of the protein as the determiner of function apparently apart from the locus or the gene itself, is a puzzle to me.

Thinking of it this way I think of the gene itself, the locus, the space occupied on the DNA strand, as the determiner of a very specific phenotype and this seems to fit everything I've read about this. We have a gene that determines, say, fur color. The protein gives the formula for WHICH fur color but it's the gene that says it has to be a fur color that is produced, it isn't going to be anyh other trait. It isn't going to produce a new fur texture if that gene is for color for instance.

So what is Axe thinking of when he investigates the likelihood of producing a new protein with a new function. Wouldn't any changes still be only an expression of whatever the gene locus governs? That is, changing the function of the protein isn't going to change anything that would further evolution. You'd get a novel fur color perhaps but you couln't really get anything deserving of the idea of new function.

But of course maybe I have this wrong in some important way.

But then my model is God's perfect Creation that has been corrupted by the Fall. In the original Creation DNA would function perfectly and not be subject to mistakes in replication, i.e. mutations. Mutations are part of the disease processes brought about by the Fall. If they sometimes produce something "beneficial" this is purely a fluke due to the fact that the whole system involves sequences of chemicals so that occasionally a beneficial sequence, which I suppose is most likely to be the recovery of an earlier function that had been lost in the mutational assault, but in general mutations are a disease process. Mercifully they usually have a neutral effect, not changing the function of the protein even if they change part of its sequence.

But overall mutations are destructive. I hypothesize that junk DNA is the result of the assault, as it were, of many mutations on a particular gene locus, ultimately rendering it completely unable to function. Mercifully, again, although this must have resulted over time in the loss of many valuable functions in the body, usually a given trait or function is the expression of many genes, not just one, so if one dies and enters the junk DNA cemetery as it were, the phenotypic function itself is not lost.

This is a different level of argument than I got into in my previous post which I'd normally avoid here but Axe's comments were intriguing.