@glipsnort It was suggested that I read a post of yours……
Based on your bio at the bottom, you may be one of the few people on earth able to address my actual point, particularly your studies of disequilibrium linkage and detecting positive natural selection. Though I have been unfortunately drawn into a side argument about what our random mutations might look like if we evolved from a common ancestor with pan, the issue of patterns in random mutations is only tangentially connected to my argument.
I would like to start with a statement of yours in the above link to briefly explain why such mutations are not directly connected to my objections before once again explaining what my central argument is….
“I cannot think of any reason why a designer should choose to make the differences look exactly like they were the result of lots of mutations.”
It is not that He chooses to go out of His way to do so. In the model I am proposing (which I believe is what the text of Genesis 1 is saying) it is not the intent of God to do this, it is simply an artifact of the process. A creation subjected to futility (resistance to God’s word being fulfilled) is trying to pull off something much like TE but is unable to completely do so. In the “land above” it is like TE- God speaks and the earth brings forth living creatures. Here, He has to intervene to get things moving before the earth takes it from there. This is exactly the kind of universe suitable for beings like us- we also are unable to pull off doing God’s will without intervention from God, as the Apostle Paul so movingly describes in Romans chapter six.
Now imagine that in the past there is an ape-like creature, perhaps the chimp ancestor. God wants a creature similar to that one, but modified for living on the ground with hands free with the idea that tool use will unfold. The code for that animal is taken and modified with changes/additional genes to produce a similar creature except that it walks upright and lives on the ground, possesses a locking knee and flat feet, mates from the front, and other such changes. Later some sub-group of descendants of this new creature shows promise in tool-making and so code from it is taken and modified with changes/additional genes to produce a version with more dexterity than strength, and the fine-motor and intellectual skills to become a true tool-maker. Some portion of this group shows promise, and a modified version of the DNA code from that species becomes the basis for the human race.
This scenario, which could be called “incomplete theistic evolution” or “assisted evolution”, would produce random point mutation signatures virtually indistinguishable from that which evolution would produce. The mutations acquired along the way for one species would be carried unto the next even though it was through Common Designer and not common natural descent. Thus we cannot test for which of these ideas is most likely to be correct by examining patterns of random mutations in shared genes, functional or otherwise. Rather, we have to look at the patterns of fixed functional genes which one group has and the other lacks and determine how likely it is that these changes are merely the result of known evolutionary processes acting at unremarkable rates.
I will leave aside for now the aspect of humanity which nature cannot produce. For the rest there is DNA which codes for parts, and also DNA which says how those parts are to be used. Today I am only asking questions about the former though the latter is more important. The same screw used in a barbeque pit can also be used in a sports car. The same circuit or capacitor can be used in a clock radio or a super-computer. The instructions about how to use the parts are more critical to determining what the device is than the fact that the instructions for the parts, and thus the parts themselves, are identical. That is why the changes in those genes are going to be even more telling than the questions which I have below about the “regular” genes, once we get to the point where we can ask them….
I return to my analogy of the inch worm found crawling along the top of your fence one morning, and your neighbor’s fence that afternoon. There is no need to suggest any mechanism of transport was involved other than the natural movement of the organism. Should the same inchworm be found that afternoon in another city five or ten miles away then those same processes must be considered “unlikely” and it is reasonable to suppose some other force is at work. It does not matter that given enough time an inchworm could crawl five miles. The question is how likely it covered that distance within the time it had to cover it?
In the case of our purported lineage from the chimp common ancestor, at least 700 genes of our 22,000 are gains which exist in no members of the pan genome. These are not just duplications, though under the evolutionary explanation they all started as such. These are new fixed genes. They function and do things that no previously existing genes did. Some perhaps have mixed results for us, but they are new genes.
Now I showed some math on a prior post calculating how long it would take a single new gene, under conditions in which luck was excluded and only improved adaptation mattered, to “earn” its way to fixity. You replied with math which showed that good fortune overwhelms improved function. That is, a neutral gene that was the “lucky” one of thirty thousand would on average move to fixity long before a gene destined to be beneficial could “earn” its way to fixity. Luck was so much more potent that even mildly deleterious genes could fix, though I think we agree that most new genes that do anything are deleterious enough so that they are weeded out over time.
What we are left with then is this: Substitution errors in existing alleles are very common. Gene duplication errors are much less common though not rare. Gene duplication errors which gain enough mutations that they become a functioning new gene are even less common. New genes that are not deleterious enough that they can enter the fixation lottery are even less common. Such genes actually achieving fixation are of course rarer still- they are the lottery winners. NOT the winners of a “new allele on existing genes lottery”, but the much less common “lottery of new functional gene locations”.
Does the number of functional new gene locations match would we would expect from known processes given the time allowed for them? That is one of the two main questions I think we need to answer to determine how reasonable it is to suppose that they alone produced these changes. The less reasonable it is to suppose they did so then the more reasonable it is to suppose that there is an unseen Hand at work after the initial creation of the universe (and therefore not just theistic evolution but TE + additional intervention). NOTE: I define “theistic evolution” as the belief that God did not have to intervene in the natural universe again to produce the living things in the world, including man. Rather He “set up the dominoes” of initial conditions so that we would be the inevitable result of ‘natural’ processes.
I would suspect that there are tens of thousands of substitution errors between us and pan fixed within the alleles of existing genes (I estimate 38,400). This is not surprising since there are hundreds to thousands of base pairs in each of the 22,000 genes and each base pair is a candidate for a substitution. In addition, several classes of easy substitutions exist which appear to be completely neutral.
Gene duplication does not have nearly so many chances since there are far fewer genes than base pairs within genes. But even once they occur they are simply copies of existing genes. To count as new genes they must undergo a mutation severe enough to produce something new- and unlike with the base-pairs that mutation is more often than not likely to be harmful. Only the exceptional genes can even enter this “lottery” to become fixed.
Thus the 4N * generation time you gave as a formula for average fixation time for the winners of the lottery has a severe hurdle to meet before it even becomes relevant to our calculations -it does not consider the problem of how long it takes to accumulate lottery “players” in numbers sufficient for a winner to be probable. The average “lottery winner” new gene may indeed be able to fix in only 60,000 generations, but how many generations pass before there are enough candidates accumulated so that equations about lottery winners are even applicable?
So based on observed rates, what is the expected ratio between fixed base pair substitutions and fixed new genes? 10,000 to 1? 100,000 to one? Higher? That is way beyond my actual calculation of 38,400/700 =54.
The comparison between us and pan is not the only place where we should look for God’s fingerprints……Language in this article seems to hint at that something out of the ordinary occurred in our genome, and that of pan…
where it says…
Eichler’s research team found an especially high rate of duplications in the ancestral species leading to chimps and humans, even though other mutational processes, such as changes in single DNA letters, were slowing down during this period. “There’s a big burst of activity that happens where genomes are suddenly rearranged and changed,” he says. Surprisingly, the rate of duplications slowed down again after the lineages leading to humans and to chimpanzees diverged.
So separate from the previous question, I ask you can we observe comparable “big bursts of activity” where genomes are “suddenly rearranged and changed” in the field today? If we cannot observe changes of similar magnitude anywhere today, how can we ascribe these changes to known genetic processes?
@Swamidass - I have put some of my thoughts together above…