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.

Evolutionary Theory is the Emperor's New Clothes, but We're Good at Hallucinating Clothing.

Nothing new here, just reminded of the falsenesss of evolutionary theory and the certainty believers in it have,that will go with most of them to their graves. the reminder came from a former Christian, now atheist, saying science and history deconverted him -- oh hear the applause; and a talk show host's vacation in the Southwest USA among the dramatic buttes and arches and other such geological formations.

They let the science and history of the fallen mind take them away from God. History that is really prehistory that can't be accurately timed or properly interpreted either, from the present, unlike the history that works from known facts through multiple witnesses. The kind of science that is also about prehistory for which they have no witnesses and rely completely on mental constructs. They ignore of course the witness of the Bible. In fact they let the conjurings of the fallen mind discredit it.

Nothing new here, just reminded of the wonderful formations of the Southwest and how they scream "Flood" to my mind, but for some reason to others seem to be a certain debunking of anything biblical. To my mind the sedimentary strata themselves, so particularly visible all over the Southwest, are clear evidence of the worldwide Flood of Noah. How they manage to convince themselves they were laid down over long ages of time, one kind of sediment followed by a different kind of sedimenbt, in itself demonstrates the fallenness of the fallen mind. But the Southwest also exhibits sculpted formations that scream "water" again to my mind. My biblically informed mind. Why can't they see it? Mostly sandstone swirled into something that's even called a "wave." "Arches" that are carved out of once-wet sandstone, eroded by wind and weather over millennia into those shapes but clearly originally the work of a huge volume of moving water. The "hooddoos" that were originally a stack of stratified sediments that over time eroded into those spooky-looking humanlike forms. Made up of strata differentially eroded according to the hardness of the particular layer of sedimetary rock. The monuments of Monument Valley and all the other buttes scattered around the West. Like the Tepui of South America. Obviously, yes obviously, originally deposited by the Flood in enormous sheets of different sediments, segments of which were then left standing as the receding Flood waters carved away the surrounding deposition. Or possibly water draining from one of the gigantic lakes left after the Flood, which is one theory. The draining lakes do explaibn the badlands to the north so they may also explain the Grand Canyon and the Monuments and other buttes, but the draining Flood water itself is just as likely in some cases. Earthquakes caused by tectonic shifting as a result of the Flood lifting the land and breaking dams etc. etc. etc.

Anyway, just LOOK at the formations. WATER formed them. Just LOOK at Planet Earth wherever the geology is exposed to view: it's a wrecked planet. All geology demonstrates the wreckage. I've written about this for years and then I saw a creationist film by Del Tackett in which he said he sees the world as wrecked. Does he really or did he plagiarize it from me? (In the same film he used the phrase "the catness of cats" which I originated on the EvC forum. Did he come up with it independently or did he see it at EvC and like it and steal it?) I've never heard anyone else talk about the earth in such terms and most people want to affirm the beauties of Earth because it is God's creation and don't like the idea of its wrecked character, although that was due to human sin and not the original Creation. Once I saw the wreckage I saw only the wreckage. The beauty is in living things, in plant life and animal life, and in human creations, architecture, art. The geological foundation itself is nothing but wreckage to my eye. Proves nothing of course, but to my mind it should. You should be able to see it as I see it.

There's plenty of evidence in the geological facts too that can be argued one by one, but that overview works for me without the rest of it. Besides the strata the fossil contents of the separate sedimentary layers even more loudly screams "Flood." The Bible says the Flood was intended to kill all things living on the land and there it is, confirmed in the rocks. Some sea life survived the Flood although most of that died too, but the land life was wiped out, and there it all is in the rocks. How do you look at flat layers of different kinds of sediment with different kinds of fossils in them and manage to cconvince yourself they represent great ages of time in which those fossils were living things? How? It's absurd beyond absurd. If the mere fact of it isn't absurd enough, try thinking through how strata full of fossils that span huge swathes of the planet, even whole continents, could have formed at all. Think it through honestly. It's impossible on the idea of geological ages.

Oh well. They are going to go on believing the impossible. This fallen world is going to go lumbering on until God brings it all to justice in the end.

It was the formations of the Southwest that I wanted to write about but since we're talking about evolutionary theory the biological side of it should also be mentioned. Just mentioned. As with the geological evidence, there's tons of biological evidence as well, but I always like to find the bottom line if I can. In the biological arena I think it's in the fact that evolution itself leads to a condition in which further evolution becomes impossible. I use two examples, domestic breeding and endangered species. Endangered species are often endangered because they are no longer able to produce genetic variations. The cheetah is endangered for that reason. And what this means is that genetically it possesses too many "fixed loci" or homozygous traits. In the case of the cheetah this came about because of a genetic bottleneck, that is, the entire population of cheetahs is descended from a very few individuals.

Domestic breeding used to work toward "purebred" animals which are characterized by the same condition of fixed loci for the chosen traits. Homozygosity for the salient traits of a breed was practically the definition of a purebred. This is a stable condition that guarantees that those traits will remain constant in the populaton as it continues to grow and interbreed, that unwanted traits won't show up in the breed. In this fallen world this is an unhhealthy situation for the animal, often produces genetic diseases and weaknesses so when they finally realized that they stopped aiming for purebred status and now introlduce other animals into the breed to improve its health, sacrificing perfectioh of traits.
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My argument is that these examples demonstrate what evolution really is. In nature you get variations within a species because new populations form that are more or less isolated from the main population which permits new traits to become characteristic that distinguish it from the original population. Darwinism explains these variations as brought about by Natural Selection or the survival of the fittest. In actuality there is no survival problem in most cases, you just get a new population that happens to develop its own characteristics because it is reproductively isolated from the original population. Adaptations certainly occur but more by a natural gravitation to appropriate environmental supports than by any selective pressure. It's a form of selectioh in a sense but it's a random selection in the wild.

Each new population should demonstrate a tendency toward a reduction of genetic diversity, with those formed from the smallest number of individuals demonstrating the extreme reduction of genetic diversity in the number of fixed loci or homozygous traits.

Yeah I repeat myself about all this, over and over and over. I've argued it in great detail too, this is just an overview. The point is pretty obvious, though, it seems to me. Variation, which isn't evolution but gets called that, or "microevolution," always tends toward decrease in genetic diversity. This is the evidence that species are desigend to vary and that variation decreases genetic possiblities of further variation. Evolution is, quite simply, genetically impossible. No, mutation isn't the answer. If it were the cheetah would not be endangered and purebred aimals would not be stable but always morphing into something else which they never do.

Yeah it's been proved. But as in today's currupt politics if they don't want it to be true they won't let it be true.