On average, it will take 4N generations. That’s the formula for a new genetic variant that is neither beneficial nor deleterious. It doesn’t matter whether the genetic variant is a change in a single base or the addition of an entire gene or the loss of a gene.
That’s the average time for new variants that do reach 100% of the population. Only a small fraction do, though. If you wait long enough, eventually 1/2N variants reaches 100% and the all of the others disappear again – lost to genetic drift. [quote=“Mark_Moore, post:1, topic:37511”]
As I understand things the norm would be for this new gene to only be on one “arm” of the chromosome. In such cases there is no being “homozygous” for new gene because it only shows up in one place.
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You’re getting your terminology confused here, but you conclusion is correct. The two arms of a chromosome are the two physical ends. The individual with the new gene will not be homozygous for it because it appears on only one copy of the chromosome, of the two copies that everyone carries. [quote=“Mark_Moore, post:1, topic:37511”]
Each couple has two children, who then also have two children and so forth, deaths subtracting out from births. In each generation one child gets the new gene and one does not. So far, the gene simply stays in the family. It does not grow as a proportion of the population.
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The problem is that what you’re describing is not real genetics. Even if on average couples have two children, in reality some have more and some have none – because sometimes people (and other creatures) are eaten by bears, or fall out of trees, or catch a fatal disease. If one of the unlucky ones carried the brand new gene, that gene dies with the individual. Alternatively, if the one with the new gene happens to have many offspring, the gene may well be passed to multiple children.
Similarly, we don’t actually pass on a copy of one of our chromosomes to exactly one offspring; that’s what we do on average. if I’m the one the new gene appeared in and i have two children, there’s a 50% chance that I pass on one copy of the gene, a 25% chance that I pass on two copies, and a 25% chance that I pass on no copies.
The upshot is that the actual number of copies of a variant fluctuates randomly from generation to generation. A new mutation can easily be lost through this process, or it can eventually drift toward 100% frequency.
@glipsnort knows what he is talking about, but your question is a good one. Now that you have his attention, ask him to just sketch out the math of how he would account for the differences here. There are a couple angels on this, but you will at least understand where he is coming from. Make sure you understand that before you spitball your own explanation.
One thing about @glipsnort too, he is honest about his work. If you have a valid critique, he will concede it.
Well I hope this would be a place where there is honesty in these things, though that is a rare thing these days.
I was not quite ready for this to become its own thread, but my initial take is that, yes glipsnort and I have been talking past one another. I am describing what would happen in the case of a single new gene earning its way to fixation and he is talking about from the entire group of genetic changes how long does it take the average “lottery winner” to reach fixation. I will have to look at the math and the data when I get a space of time. It may be that what he has said addresses my claims through another route but my initial take is that there is still an issue which I will try to express in the terms which he has laid out, looking at changes as a group rather than a single change.
Here is the thing @Mark_Moore to understand change in systems you have to know just a few variables (to a first approximation).
R: Rate of Change (per generation or year)
T: Time since separation or divergence (in generation or years)
D: Final distance or difference.
To first approximation:
2 R T = D
It’s not too complex. That formula pretty much holds where ever you look (though it is a simplification of a more complex formula). In the case of genes, there are some other factors too. Some of the genes specific to chimp and human were probably in the common ancestor, but deleted in one line (and not the other). So we have distinguish, in this case, between new genes forming and genes deleting (which your number does not).
@glipsnort was explaining that not all humans even have the same number of genes. That gets to another key quantity.
V: Rare Variation in a Species (std or variance)
It turns out that variation (especially the number of rare variants) is very closely linked to R (the rate of change). So we could also write out:
VT ~ D = 2RT
Here its not an equal sign, but a ~, which means loosely proportional, not equals. Remember also that all these quantities are measurable. D, V, T, and R. The fact that this proves such a solid relationship is strong evidence for common descent. There is going to be noise, but this formula basically holds. That is true for gene death/birth, but all sorts of other types of change.
@glipsnort did a phenomenal job explaining this in a recent article, the first one he did here. If you understand that, you’ll have the beginnings of how to make sense of this problem too.
Again, I must remind you that you are not making a presentation to Atheists. Your nominal audience believes God participated in the whole history of humanity.
So… if you are not shocked that humanity starts with just 2 people… and does not become extinct, I would think you could well handle a population of 10,000 or 15,000 … where (again) humanity does not go extinct.
God is at hand … God makes these things possible, if not inevitable.
@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…
Just to make sure I am not getting basic definitions here fundamentally wrong, here is how I would describe “theistic evolution”…
I define “theistic evolution” as the belief that God did not have to intervene in the natural universe again after the initial creation in order 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.
PS- my view of Genesis is most like that of Swamidass. In particular Gen. 2:1 says a “host” was created on the earth. Adam came later. But even if they started with two, they did not stay two, or 50,000, for six million years. That is a long time to stay on the ragged edge without going over it. Of course God could have repeatedly intervened over those ages of time to protect them from volcanoes, locusts, disease, intercene warfare or whatever else, but is that concept strictly TE? It seems more like what I am advocating, a very subtle version of it where God does not meddle with the genes or any special creation but does shape the environment to guide nature in a way so that some outcome will be produced. I think He did both, but if He did either do you consider it still TE?
You are describing deism - - the clock-maker method of creation.
God works in real time with his creation … answering prayers … zapping this and that genetic molecule, and adjusting the ecosystem of a whole planet.
It could be conceived of as not requiring any tinkering … but the I.D. folks are pretty convinced dominoes by themselves could never pull it off… it required a living master’s hand!
Glad to have the wrong idea then. But it seems the differences between this and Old Earth Creationism, especially if done the way I described in my post to glipsnort above, become very subtle and maybe vanishingly small…
And if He has ceased “making kinds” under this view of TE then processes which drove the genetic diversification of the past would not be happening today at the same rate as they happened in the past when God had His finger on the scale. I.E. my attempts to find the “fingerprints of God” in the kind of genetic analysis I am suggesting are applicable under both an OEC and a TE scenario.
Except you seem to reject the logic of speciation… insisting that chromosomes have some built-in meters that can say when there has been enough mutation… enough “micro-evolution” … and it brings everything to a halt.
Geology says that the Earth is very old.
Geology and Biology says that some species are very old.
You say that God had to make everything individually.
Okay… so why did God make things look like they were made by Evolution?
I laid out the pillars of my model of early Genesis on the previous thread… 1) The earth is old
2) Genesis 1 is describing creation occurring in two realms at once on days 3,4, and 6 - land above and land below. In the land above, God speaks “and it was so”. Very much like Theistic Evolution. The LAND brought forth living creatures. Down here, the LAND needs help from God to do God’s will in a halting and imperfect manner- just like us. Down here, God had to help the earth along by subsequent interventions making “kinds”. The earth took it from there. It looks like theistic evolution in the record of nature because that was what the land below was attempting to do. It did so poorly and if we look closely enough we should be able to detect that it needed help.
3) There was an army of people created in Genesis chapter one, not just one couple (see Hebrew for 'host" in Genesis 2:1). Genes from previously existing hominids may have been borrowed for the event but all mankind is a special creation. Here I would differ from the model of Swami, though like him I agree they were not in the image of God, but only the likeness. Indeed Adam after the fall did not say he was in the image of God but just the likeness (Gen 5:1-2) but God had a plan to MAKE (a process) man in His own image. Part of that process involved a TEMPLATE of a man in His image, in heaven (Christ) and on earth (Adam).
4) Around 13,345 years ago (I read the genealogies different from Ussher) it was time to take mankind from innocence to accountability. Adam was formed, and Eve. He was formed and made into an agriculturalist- moving mankind from hunter-gatherers to true civilization builders. The animals made in chapter two were only a small subset of the categories from chapter one related to domestication and agriculture. As far as moving man from hunter-gatherer to civilization builder, Adam got it done as this is the right time and place for those things to begin in human history.
5) The flood was local, around 6,500 years ago in an area near to the Turkey-Iran border. It wiped out the animals created in chapter 2, not 1, except for those on the ark., and the Adamic race - in particular the line of Seth. The flood did not kill all the descendants of those humans created in chapter one. The reason the text talks about the entire earth going to ruin is because the line of Messiah would be wiped out, not because everyone would drown. Some of the things in chapter 7 are from the perspective of Noah’s sons. To them it did seem like everything was wiped out.
But by your definition of TE, they shouldn’t. They should look like they were made by Him using the same processes as evolution but in an accelerated and directed manner. My answer is the same as it is on my first post of this thread- it was supposed to be evolution but the earth could not pull it off without God’s help. Which, now that I hear you define TE, sounds a lot like TE.
And I [quote=“gbrooks9, post:12, topic:37511”]
You say that God had to make everything individually.
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Well, if TE is what you say it is, then aren’t you also saying so to the same extent that I am? Maybe even moreso. I am saying that the intent was more like what you call Deism, but down here the earth could not pull it off. I never doubted speciation by naturalistic processes, just that species could only go so far from the type and that there were some gaps between families that could not be jumped by naturalistic processes- God had to intervene and “get the ball rolling” with a new general type that the earth diversified.
George you have me confused with someone else. Hugh Ross believes in speciation. OEC believe in it. I believe in it. It happens. All I said was that there was only so far a new species could go from its original type. New kinds are introduced due to Divine intervention. The “kind” may be a generalized new type that we would classify as a new family, or sub-order, or even order. Then speciation, using naturalistic processes, took it from there to fill out the lower ranks of the taxa.
Amiright when I say that the difference between us is that I think God intervened at discrete intervals in a way that produced a new type of organism which then diversified via naturalistic means while you think He had His finger on the scale the whole time and the same changes were introduced in a smoother way using natural methods in a supernatural way?
This is hardly Speciation the way it is intended to be discussed. How would we ever get mammals with flippers if your view of speciation was the true version?
Do we really need to craft yet another descriptor to distinguish between the fakers who say they believe in Speciation … but they just don’t believe in a lot of speciation???
This is where we start talking about God making it look like speciation. Why would there be primates who shared an identical broken gene to make Vitamin C, that all the other primates and non-primate mammals have that works perfectly fine? Why would God create sequences of animal forms like that?
I will repost what I said above to a similar statement…
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.
But would speciation even occur under your version of TE without the Divine hand? I am not sure if you are allowing “naturalistic” evolution more power or less power than I ascribe it.
@Mark_Moore, I think the problem you’re running into is that George doesn’t quite believe that Old-Earth Creationists are real. It’s a terribly sad state of affairs, but no amount of evidence seems able to sway him.
I don’t agree with your position, but I think the question you’re asking about the probability of novel gene fixation is at least a very good question to be asking. It’s not easy enough for me to answer, at any rate! I hope someone who knows their stuff has the time for it. I appreciate your courteous and thoughtful dialogue.
You make it sound so strange and odd and unlikely…
Put a mountain or a canyon in the middle of a population’s growth … and you get Ring Speciation almost automatically …
But of course, this is only the beginning. Once two populations are “unhooked” from each other … either one can go in a completely different direction, based on its own unique experiences with mutations, ecosystem and genetic drift.
I’m not quite sure why you keep stalking me. You clearly don’t understand what I reject and why I reject it. The problem with Old Earth Creationists is not that they don’t exist, the problem is how irrelevant they make themselves. Though I do agree with the proposition that some YEC’s try to do an impression of an Old Earth Creationist, when all they are doing is trying not to fit the standard YEC cliche.
How does a person who is convinced by the Science of Geology that the earth is 4.5 billion years old … then step to the next position and deny Evolution by Common Descent? Are Young Earth Creationists more logical because they consistently reject all science?
Or are Old Earth Creationists more logical because they accept Geology and Physics but reject Chemistry and Biology?
Sorry I have given the impression of stalking. I like reading a lot of threads and I comment when I have something to say. Thanks for expanding on your position here.