Can the standard "Young Earth Creationist" model be falsified by genetics alone?

Most YECs adhere to a model which has the origin of the biosphere at about 6,500 years ago, with a world wide flood at about 4,500 ya. Important to this topic is that, in this model, humans descend from an original pair at 6,500 ya, and go through a flood bottleneck with an effective size of 6 people (Noah's three sons and their wives) at 4,500 ya.I will show that modern humans have far too much genetic diversity for this model to be correct. We will look at Y-chromosome diversity and mitochondrial diversity amongst other things, and compare what is known about mutation rates to the proposed time scale.In addition, we can look at other animals which would have required the Ark to survive the flood, and therefore should also show the symptoms of recent tight bottlenecking in their genomes.Participants, please be prepared to read a few interesting contemporary research papers which I'll bring up in the first few posts.For a start, here's a thirteen generation pedigree study which gives us some idea of the human Y-chromosome base substitution rate. Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing And this should give you some idea of modern diversity on the Y-chromosome. A calibrated human Y-chromosomal phylogeny based on resequencingThe first paper gives us a point mutation rate of 4 in 13 generations, or approximately 1 for every three generations, on the 1/5 of the non-recombining area of the Y-chromosome (which is ~95% of the total chromosome). The Y-chromosome is inherited from father to son, so, in the young earth scenario, we all have the Y-chromosome of Noah, with the only difference being the mutations that have occured since. The one in three substitution rate puts us all about 60 mutations away from Noah on this 1/5, as 4,500 years equals about 180 generations. That would be about 300 for the entire chromosome.The second paper searches areas of the Y-chromosome that comprise about one fifth of its total in 36 individuals, and comes out with far too many variations to fit the "Noah" scenario (and far too many to fit the 6,500 year Adam scenario). In fact, we can infer about 5,600 mutations between modern individuals and the common Y ancestor, making him around 20 times older than the Noah of YEC myth. Mods: Biological Evolution please.
Edited by bluegenes, : took out extra wordEdited by bluegenes, : Added explanation of links at Admin's request.Edited by bluegenes, : corrected miscalculations due to misreading a paper.

O.P. edited to explain relevance of links, and YEC model effectively falsified.

Me too. Although it's true that the two papers in the O.P. do actually combine to make a reasonable falsification of the standard YEC model, I hardly expect the YECs to agree with that conclusion.Speaking of evidence, here's a very interesting new discovery concerning the Y-chromosome that makes things even worse for the YECs. AbstractArticle based on paperThis is the discovery that the Y-chromosome thought to have gone to fixation in our ancestral lineage is not the only one existing today. It means that the flood couldn't have happened more recently than about 330,000* years ago, and, interestingly, Noah wasn't even a modern human.He would have had a simple stone tool kit, and he did damned well to build the Ark, IMO! *Actually, 237-581 kya is the 95% confidence interval according to the abstract.Edited by bluegenes, : Added the confidence interval

To simplify the point I was making about the Y-chromosome in the O.P., here's a chart from the paper. It shows a human Y-chromosomal phylogeny made from non-repeated areas of the Y-chromosome which comprise about one fifth of its total non-recombining region (the region that stays the same from father to son excepting when there's a mutation in the generation transfer), and has the numbers of mutations down each lineage marked. That makes it easy to clarify my point.At the mutation rate I was using as an estimate (based on a pedigree analysis), point mutations should average about one in fifteen generations on this area. If you look at the bottom right of the chart, you can see that there are 8 individuals from the same family - grandfather, father and six sons. That equals 7 generational transfers, and there are no mutations on these seven, which is in keeping with my rate. However, to make the point, let's assume a high average rate of 1 mutation in 7 generational transfers for this area of the chromosome. A high mutation rate is to the advantage of the YECs.We can see that mutation rates vary down different lineages, which can be to do both with varying tendency to mutate and varying generation times.Straight away we can see that the individual at the top is 285 mutations away from the common "Y" ancestor which, at our rate, would be 1995 generations and about 49,875 years. At a more likely lower rate, the paper itself comes up with ~101,000 to 115,000 years!An important point for the YECs is that the researchers' estimated rate is in keeping with the pedigree study I linked to in the O.P. - they also cite it in the paper, and the pedigree paper states that their results are compatible with those derived from human chimp comparisons. Pedigree studies within humans take away the YEC argument that we're assuming common ancestry.Even being generous to the YEC model with a maximum likely mutation rate, we can see that Y-chromosome data easily falsifies the Noah at 4,500 ya and Adam at 6,500 ya model. Edited by bluegenes, : sin tax

The observations are repeatable. Well, if you want to question the experts, the best thing to do would be to "go through genetics" to at least some extent.

Hi mindspawn. This post is easy to understand, and gives you one of many good reasons to give up on your irrational belief in Jewish mythology. Message 8

Well, if you don't understand the research, and you don't think it's important enough to find the time to attempt to understand it, why on earth have you decided to find the time to post on this thread and waste other people's time?* [size=1]*Consider that rhetorical. Please don't reply.[/size=1]

The pedigree study covers thirteen generations (the two individuals are 6 and 7 generations from a common ancestor). The resulting 4 mutations over thirteen generations is in keeping with other studies, but we can certainly consider a wide possible margin of error when dealing with such low numbers, and that the true average for 13 generations could reasonably be anything from 1 to 8 if we only consider that one study. Your YEC model requires there to be more than 40 mutations over an average 13 generations. We would know if tropical groups have significantly higher germ line mutation rates than high latitude groups because of the higher number of genetic conditions that we could observe. Your required mutation rate of more than 10 times would mean so many detrimental mutations that the tropical populations would surely be extinct before they got to high latitude, anyway! It gives the number of SNPs, and the tree I put in post 8 (see below) is constructed on SNPs only. Apples with apples, except that the second paper only covers one fifth of the chromosome, so remember to multiply the figures on the tree by 5! It isn't variations on the earliest mammalian Y-chromosome we're talking about! Those are far greater if we look at all other mammals! What we're talking about is variations on the last Y-chromosome that went to fixation across our entire ancestral population group, probably about 300,000 years ago, according to this recent surprise find. Message 7

Your link is self-defeating, surely, as it assumes common descent in order to demonstrate the higher mutation rate in tropical plants. Have you converted to common descent?However, if you're interested in climate related changes in human metabolic rates, here's a paper on the subject. There's a mild but significant increase in the rate in Arctic climates. Climatic influences on basal metabolic rates among circumpolar populations.

When I tell you that the Y chromosome is relatively small, and is about 1.5% of the genome, you can make some calculations yourself. What was the low mutation rate you were promoting on another thread, when you claimed it was impossible for humans and chimps to have diverged over the last 7 million years? Do you now want it to be much higher? Not at all. Your required rate is based on your model, and its need to explain the observed modern diversity. I'll explain.In your model, we are all about 180 generations from Noah, whose Y-chromosome all men have inherited on a direct male line. The required rate for your model is x/180, with "x" being the average number of mutations that separate modern individuals from Noah. If "x" seemed to be about 1800, for example, then your rate would be about 10 mutations per. generation transfer (about like a rate of 600 or 700 across the whole genome). Your paper is about differences between related species of plants, not differences within a species of animal. However, I know very well that mutation rates vary, even within species. Look at the tree I've posted above. You can count up mutations and see that they vary with some lineages having accumulated up to 20% above or below the average. There doesn't seem to be any strong correlation to latitude, but as you've developed an interest in the subject, the individual with the slowest rate is from a tropical lineage. Second sentence. They say that they restrict themselves to just under 9 Mb, and I know that the total is about 54 Mb. I didn't say it had only been collecting SNPs since the last one went to fixation. The point is, once you've got a "Noah" situation, and everyone in the population has the same Y-chromosome, any differences between individuals must have accumulated since. So, do you now understand the problem for your model?There are far too many differences for 4,500 years.

To put it mildly.Mindspawn needs the mutation rate on the Y-chromosome to be about 20 times higher than it is in order for a 4,500 year old Noah to be the founder of the super-haplogroup that it was thought covered all humans until this year. The recent discovery that a tiny minority is not actually in that group, and the data on their Y-chromosomes, means that he needs a mutation rate about 60 times the current estimates in order for Noah to be our Y-chromosome "Adam".As I said in the O.P., modern genetics on its own falsifies the standard YEC model without any reference to any other field, and without the assumption of common descent.

The generation time for the Y-chromosome would be determined by the average age of all fatherhood in the population. 25 is reasonable. The age group from 15 to 25 could certainly account for half of the births in some cultures, but the 25 to 50 year olds would usually match them. For non-human apes as a whole, I'd accept 18, and for women in human cultures of the past few thousand years, it could certainly be younger than 25, but for men it can actually easily go up into the early thirties, as it has been in western cultures for the last few hundred years, so I think 25 (180 generations to Noah) is fair enough. But this is an interesting side issue, and not really important. The Noah story means we should all be in one haplogroup dating from 4,500 years. The 1600 mutations (actually nearer 2,000) have happened since then. It's been known for a long time that rates vary in families. In population groups, they are subject to control by natural selection. Of interest to you is the obvious point that if they get too high, too many detrimental mutations are produced, so that the high rate itself is indirectly selected against as the lineages with too many detrimentals are disadvantaged. Accumulated since when? Noah? And the Y-chromosome is about 1% of the male genome (2% of a haploid genome, but the other chromosomes are double). Apart from the fact that we have no reason to multiply the Y-chromosome rate by 5!! No. Only if we pretend 10% of the total mutations come from 1% of the father's genetic material, and therefore 0.5 % of the material of both parents. We don't want to give a super healthy population that managed to multiply rapidly and spread around the world in about a thousand years starting from just one family too many detrimental mutations to cope with, do we? 160 isn't the "required rate". It's a rate you get if you assume 5 million years of time and 25 year generation gaps in non-human apes. Remember, I'm not working from scriptures that tell me that humans and chimps have to diverge at a certain time. I'd be perfectly happy with 9 million years and 18 year generation gaps, for example.But remember, with the model we're testing, we don't descend from a common ancestor with the chimps anyway. We're testing the hypothesis that we all descend from one 4,500 year old man.So, let's look at our main problem here. You seem to have come up with the idea that the mutation rate on the Y-chromosome is 5 times that of elsewhere, and that 10% of all germline mutations would be on the Y-chromosome. Where did you get this idea?The only thing I can guess at is that you've mistaken the hypothesis that men are about 5 times more prone to picking up and passing on germline mutations than women for something it isn't. If that's the case, what you're getting wrong is that this applies to the all the male genome, not just the 1% of genetic material that is that Y-chromosome.Let's take your example of the child who received 49 germline mutations from its parents. All things being equal, this might be about 25 from each parent, but with the 5 to 1 hypothesis, an average scenario might be that 40 mutations came from the father, and 9 from the mother. This might mean that the father actually had about 80 mutations spread between his 44 non-sex chromosomes, his "x" and his "y". Because the child gets half of its genetic material from the mother, it inherits the 40 mutations only.All things being equal, the 1% of genetic material that is the "Y" has 0.8% of a mutation, on average, but let's say one. So if the child is a boy, then he will automatically receive this, as there is no maternal alternative. Therefore, we can see that the Y-chromosome would in fact seem to be set to receive more mutations for its size than the average chromosome if it's correct that males mutate significantly more than females, merely because none of its mutations would be lost, like the missing forty elsewhere, due to the maternal effect.But perhaps that wasn't where you got the idea of the Y-chromosome having 5 times the rate. If not, where did you get the idea from?

Since this thread was revived, I've realised something was wrong, but hadn't the time to sort it out until yesterday. I was using the data from this paper to come up with the approximate number of SNPs that separate us from the most recent common Y-chromosome ancestor. But I'd noticed that if I did a back of the envelope type calculation with my results, I was coming up with a time estimate of just over a third of the authors' 101,000 to 115,000 years for the age of the Y ancestorThe authors found 5,865 SNPs on 8.97Mb (about 1/6 of the total non-recombining Y) of the chromosome. Using the chart below, I was multiplying the average lineage (about 330 mutations) by 6 to get an approximation of the number of mutations on the entire chromosome (about 2,000). However, realising something was wrong, and looking at the chart, I finally noticed that most of the 5,000+ mutations were missing from it. Looking back at the paper, I found out why, and what I had missed.From the paper (section title:Constructing the Y-chromosomal haplogroup tree).

quote:

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Third, we removed all sites that were recurrent in this set of 36 males or lacked ancestral information, and restricted the region considered to the 3.2 Mb with high coverage in the haplogroup A individual, NA21313 (tree 3, Fig. 2).

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The tree is made from a smaller portion of the Y (3.2Mb) which is actually about 1/17 of the total. So, I should have been multiplying by 17, which gives an average of 5,600 SNPs across the entire Y. That means that the Young Earth Creationist standard model requires an average 31 mutations per. generation transfer on the Y-chromosome since the time of Noah (4,500 yrs.)So, my apologies to those following the thread for not reading the paper with enough care, and for not spotting the problem earlier.

No they don't. They aren't. But if you want to "throw down a gauntlet", by all means start a thread on why you think mutation rates are a problem for human chimp divergence. Here's an interesting up to date paper about generation times. They think our ancestral generations and those of the chimps are long, and they estimate divergence at at least 7 to 8 million years in the introduction, and further on in the paper at 7 to 13 million years. They are well aware of recent mutation rate estimates.And here's the paper you mentioned earlier in the thread where they searched two parent child trios and found 49 and 35 de novo mutations in the kids. They say:

quote:

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The sex averaged germline mutation rate estimates we derived agree very closely with three other recent studies focusing on sex-averaged mutation rates in the most recent generation.
Averaging across these four studies gave a more precise sex-averaged mutation rate of 1.18 10−8 (0.15
10−8 (s.d.)), which is less than half of the frequently cited sex-averaged mutation rate derived from the human-chimpanzee sequence divergence of 2.5 10−8. These apparently discordant estimates can be largely reconciled if the age of the human-chimpanzee divergence is pushed back to 7 million years, as suggested by some interpretations of recent fossil finds, and by considering more recent (and slightly lower) robust genome-wide estimates of sequence divergence. These considerations suggest a plausible range for the divergence-derived mutation rate of 1.12 10−8 to 2.05 10−8, which encompasses the averaged contemporary mutation rate above.

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And there's no actual reason why the two groups can't start diverging more than 7 million years ago.But start a thread. Throw down the gauntlet, my good knight crusader.

Bump.The number of Y-chromosome mutations (SNPs) separating the 36 individuals surveyed in this paper from their common Y-ancestor would be about 5,600 according to the data.The standard YEC model indicates that there should only be about 300 such mutations (from 100 to 500) according to research on Y chromosome mutation rates and general mutation rates.The YEC model is therefore effectively falsified, as any common Y ancestor would be far older than the mythological Noah, and also far older than "Adam".