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

The link is about some studies that have given exceptionally low mtDNA mutation rates that mismatch other studies (and, in terms of time, Y-studies like the ones I'm using). Check out the "out of Africa" estimates in the paper we're discussing, and you can see that they support the dates given in the article, and start even younger.I don't know why you brought up those. The uncertainty is the wrong way round for your model. What you need are exceptionally fast Y mutation rates to support your model, and no-one has found those. You need superfast rates!

Well, yes. You'd assign all (germline mutations) to the grandson. The thing about the non-recombining area of the Y, and the beauty of it for this kind of thing, is that the grandson gets his grandfather's exact chromosome, plus whatever mutations have occurred in the two generation transfers. So, in the Noah hypothesis, we all have his chromosome altered by whatever mutations have happened on our paternal lines since. If we have a reasonable estimate of the mutation rate, we have a fairly good molecular clock. We can also make nested Y hierarchies like the one in the chart I've been using, and they tell us interesting things.For example, the "G" haplogroup with its specific defining marker mutation starts about 1/3 of the time back to Noah. A sub-haplogroup of this was common in Europe in the stone age, and is found frequently in sites that are undeniably neolithic by the artefacts found in them. So, the YECs cannot deny this. Dating or no dating they are definitely stone age.On the 4,500 year old Noah hypothesis, these would be 1500 years old or less, so we end up with stone age people in Europe after the decline of the Roman Empire, which makes me laugh. tzi, the famous iceman is in this haplogroup.

The papers are about the non-recombining area of the Y-chromosome, which is passed from father to son. Without mutations, the son's is identical to the father's. That means that all modern men have Noah's "Y" chromosome, and it differs only by the mutations that have happened since. If we can get a good idea of the average mutation rate, then we can get a good idea of about what time all men have a common "Y" ancestor.One of the papers gives us a good approximation of the mutation rate, which compares well to information from other research, and the other counts mutations on a large area of the genome.To cut a long story short, there are far too many differences on the Y for the common Y ancestor to have been just 4,500 years ago. So, those who understand the information in the papers will understand that they contain a reasonable falsification of the standard YEC model.The only thing that YECs can do, if they want to stick to that model, is claim that there was a very high (extraordinarily high) mutation rate after the flood for a sustained period of time. That isn't actually plausible, but it's the only thing left to do.I'll look at your blog post, but I wanted you to be clear on the uniqueness of the Y-chromosome first.I'm glad you've turned up to help mindspawn, and any other YECs are welcome, as YEC is what the thread's about.

From the common "Y" ancestor. It cannot be 4,500 years ago, which the standard YEC model claims. I think, apart from mutual moral support, you're correct in that assessment.

Your perception of "many problems" comes from your mistakes, or from willful misunderstanding, conscious or subconscious. If you understood the information in the paper, you would be at least 99% sure that your young biosphere model is false. Stop decieving yourself! It won't fool people who understand the two papers I'm using. Do you realise that you need the SNP mutation rate to be more than 10 times what was found in the 13 generation pedigree study? No amount of variables can give you anywhere near that. It had those loci which all the humans had. The rest were deleted in the chimps (or not designed into it, from your point of view). The loci that are non-existent in the chimp still contain mutations which have occurred in the human group since the common Y ancestor (there's more there's one allele present on those loci). Once again, you're showing that you don't understand what you're reading. The chimp doesn't have any alleles for the loci that it doesn't have, to state the obvious. You're also showing that you don't understand why the chimp is irrelevant to our falsification. Do you understand the following? If we want to find out approximately how far two humans are from a common Y ancestor, all we have to do is compare a sizeable section of their Y chromosomes. The chimps can be extinct. If you find two individuals with 600 differences on 3.2Mb, you've falsified the standard YEC model, because no plausible mutation rate can give you that effect. You will find your 600+ by comparing any haplogroup "A" individual with individuals from any other haplogroup. I'm focusing on the chimp because you keep bringing him up, and I keep having to explain why he's irrelevant to the falsification. You can identify all the SNPs and the quantity of different variable points between any two individuals without an outgroup.

That's with the interpretation of anyone who understands the study. Your point isn't accurate. As I've said before, the only mutations that can't be identified within humans and placed are the 470 on the root and "A"'s line. As I keep pointing out, you can distribute those anyway you want, and we've still got our falsification. What I mean by the 600 is that when "A" is matched against any single one of the others, there are always at least 600 loci that differ by a point mutation between the two. That means an average of 300 each. However you distribute it, that fact alone falsifies the standard YEC model with high confidence. All of the variants mean that a mutation has taken place since the common Y ancestor of the two individuals on one lineage or the other. So, it doesn't matter how you distribute them (250 and 350, for example), it's far too many for the common ancestor to be 4,500 years ago. The reference sequence is probably used to make sure that they've got the 36 actual people correctly aligned on their database. Once you've got them aligned, it's no longer needed. Picture a huge initial database in your mind. It's divided into 8.97million rows and 37 columns, with the 37th as the Y reference. Once you've got it aligned properly, you can search it for all the rows on which the 36 actual individuals are identical. You take those out, and you're left with a much smaller database with 6662 rows. Those are your variants. All of these have to involve some kind of mutation since the common ancestor, because he's identical to himself on all loci. They don't "drop them" as variants. They use them all in their first tree, all the SNPs in the second, then they leave the SNPs for which they don't have an ancestral allele (~5%) out of the third tree (the 3.2Mb one) presumably because they want the root to be more accurate. In their SNP time estimates for the common ancestor, they include all SNPs once again. No. In the chimp.

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Ancestral states
We extracted the ancestral allele for each position that was variable in humans (assumed to be the allele present in chimpanzee) using the Ensembl-Compara pipeline (Vilella et al. 2009), release 66, and obtained calls for 6271 of the total number of 6662 variable sites (Fig. 1; Supplemental Table S2).

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On the 3.2Mb tree, that's how they assign the 470 as 285 on "A"'s line and 185 on the other. As the chimp is known to have ~98.3% identical alleles as us on the sections that it shares, it should be pretty accurate. For the rest of the variables that differ within the other 35 individuals, "A" acts as an outgroup as well as the chimp.To give you an idea of how easily YEC is falsified, look at the common ancestor of the 35 non-A individuals on the 3.2Mb tree. They average over 150 mutations from this ancestor. If we take my suggested very highest plausible mutation rate of 10 10⁻⁸, that gives us 0.32 mutations per. generation on that area. Divide 150 by 0.32 and we get 468.75, which is the number of generations back to that ancestor which, multiplied by 25 gives us 11,719 years as the date of that individual. If we do the same thing on the more normal mutation rate found in the Chinese pedigree study (3 10⁻⁸), we get 39,062 years.That ancestor is not the ancestor of the "A" groups, and neither is the ancestor of all 36 the common ancestor with the rare group that was discovered this year, and which seems to be at least twice as far back again.Edited by bluegenes, : corrected mutation rate

No. I keep explaining to you that if you want to find the variations between 36 individuals, you compare them to each other. You wouldn't include the reference individual in your search for the variants, because there's no point. You would then have to take it back out again, which is easy enough, but why put it in in the first place?As for distributing the mutations, I explained the process in an earlier post. Look at the 3.2Mb tree (bottom of post) again (the process, and the results, are the same on the larger 8.97Mb charts, but they're in the supplemental material, and only show in Word programs, so I can't post them - you can look by clicking on the "Supplemental Materials" link on the left, then on the bottom link "Supplemental Figures.docx").For that tree, the database has been cut down to about 2,000 rows. Those are the loci on which the 36 columns (people) are non-identical, and on which the differences are SNPs rather than other mutations. They can then query the database, and sort out the relationships of the individual. For example, look at individual R1b_1. If you run a query like "all columns with less than 50 differences from" (his column), the database will show all of his closest relatives, the R1bs below him. Once they've grouped the people into their haplogroups by making those kind of queries, they can start to allocate mutations from the variables. For example, a query on the columns for R1b_1 and R1b_4 for differences will give you two short columns of 19 rows with the alleles marked. At this stage, you can use a number of distant relatives, for example A, D, and G as an outgroup. You query their columns for the 19 specific loci, and you've got the ancestral alleles for those 19, so they can be marked in as 10 and 9.In this way, you can account for the mutations all the way up. When you reach the point of the two "super" haplogroups, DE and FR, there are still 67 variants unaccounted for between those groups, and at this point there's only "A" left as an outgroup, although they can cross check with the chimp.That gives you the 54 and 13. Then for the remaing 470, they only have the chimp, but their allocation should be ~98% correct, because the chimp only differs by about 1.7% on SNPs, and it has all of the loci, because they've thrown out the 5% or so that it didn't have.All that is how it could be done if you're doing it semi-manually, to show you the general principles. In reality, they now have clever programs that can generate the trees from the database for them.So, if you understand all that, you'll know that I'm not ducking the question, and that YEC is false. It's easy to for them to compare any 2 individuals, and they have to compare them all to get the variants and make their trees. The Y reference is not included in the search for variants. It would be stupid to include it. It's the same as the idea that you were pushing post after post that they had identified the variants by comparing the 36 to the chimp.The variants in 36 individuals are easily established once they're aligned to each other on a database. They are the loci (rows in my description), on which they are not all identical. In other words, you remove all the rows on which all 36 match (over 99.9% of the 8.97 Mbs). I explained that to you. That 4.8:1 is not the ratio of the Y SNP mutation rate to that of the rest of the genome, but the estimated male to female mutational difference. As the rest of the material passes through the male half of the time, the mutation rate ratio should be 5:3. For example, if the general mutation rate is about 1.8 * 10^-8, the Y would be about 3.0 * 10^-8, which is exactly what we find on the Chinese 13 generation pedigree study. That's just wishful thinking on your part. We can be 99% confident on the data available that it is not over 10.0 * 10^-8. That's more than 3 times what's found in the Chinese study.I pointed out in the last post that the common ancestor of the 35 non-A individuals falsifies Noah at 4,500 years. In order to squeeze him down to that time, you would have to cut the generation gap to 20, and have a mutation rate of ~20*10^-8, and allocate all the 470 mutations to the "A" individual.He's certainly not the common Y ancestor of all humans, and neither is the common ancestor of all 36, because of the recent discovery of a new and ancient haplogroup that differs as much or more from "A" as "A" does to the others.

Yes, they align them with the Y reference, but the reference is not included in the 6662 variants, because they only want the variants between the others. The loci on which the reference differs from all 36 of the real people are its own mutations, and these are automatically excluded. It's the same if they wanted to exclude any one of the 36 from the tree. It's easily done by eliminating the loci on which that individual differs from all others. Do you understand that it's easy to know what variants are unique to the reference sequence, because it will differ from all 36 on those loci. Are you suggesting that they, like you, can't figure that out? They don't put it step by step in the paper, because it's obvious, and their normal readership will understand that, and therefore would not raise the objections you're raising. Then you ask: Which I've already gone to great lengths to explain. Are you seriously suggesting that the mutations cannot be assigned? Surely you can work out that in order to draw trees, they have to compare them to each other, and that they have all the information necessary in their database for allocation, except for the root of the tree, for which an outgroup is necessary. Exactly. And the other material passes through the sperm 50% of the time, giving it the same risk on half the transfers, but about 1/5 on the other half. That gives you a 5:3 overall ratio. That's about microsatellites. And of course further study is needed to find out exactly what SNP mutation rates are, as well as with microsatellites. All that can be said with certainty now is that they (the SNPs) are less than 10*10^-8, which is all you need to know to falsify YEC. Can't you work it out for yourself? Of course. No-one is saying that they know that the SNP rate is exactly 3.0*10^-8, are they? The uncertainty range from the Chinese paper is given (maximum: 7.0*10^-8). That's well below the rate I'm using for falsification. I'm certain where they come from, and so are the authors of the paper. It's only you who suggested earlier on that they would be stupid enough to include differences between humans and chimps, and it's only you who is continuing to suggest that they would be stupid enough to leave in mutations that are particular to the Y reference. Not at all. I've pointed out the reality of variant rates along lineages, and that you can see by how much lineages can vary for a prolonged period of time on the charts. And a direct effect on disease. Your model requires a very healthy population in order to spread rapidly around the world before the end of the stone age, whenever you think that was. New Y chromosome found that defines a new basal portion of the tree and pushes the ancestor back to over 300,000 years

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Rooted maximum parsimony phylogenetic tree of 36 Y chromosomes.

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All their trees are made from the 36 only. It's logically impossible for them to include the mutations that are unique to the Y reference, because there's nowhere to put them.The Y reference over the 8.97Mb is a composite of two individuals. A small portion (about 1/8) is from a haplogroup G individual. On this, there will be a handful of loci that differ from the other G individual and from all the rest. Those belong to the reference, and there's nowhere to put them in the tree. The rest of the area is from haplogroup R1b. That's a subhaplogroup well represented in the chart, and the reference will contain a handful of unique mutations right down on the twigs of the tree, just like the other R1b individuals. Again, for the loci concerned, there's no place on the chart, which should help you understand what I meant when I said removal is automatic.Apart from those individual mutations on the twigs, the reference sequence will be identical to the other R1b individuals on the 7/8, and identical to the G individual on the 1/8. Would I?If you're going to argue that there are mistakes in a peer reviewed paper, you'll have to show those mistakes. Then you should point them out to the authors and the journal. You're not making sense. Any variation on the Y within any group of men means that a mutation has taken place sometime since the common Y ancestor of that particular group. My reference to the newly discovered haplogroup just means that the most recent common ancestor of the 36 isn't the actual common Y of all humans, it is even further back. But as the mutational distance from the common ancestor of the 36 is already far too great for a 4,500 year old individual, that fact just adds to the solidity of a falsification that's already there.What do you mean by the the reference sequence "has the original allele"? Like anyone else in the R1b and G haplogroups, you can tell when it has the original on a variant within the 35 DR individuals when it shares the allele with "A" and the chimp. When you get to the last 470 variants, it will have the same allele as the chimp (but different from "A") for the 285 variants attributed to "A", and a different allele to the chimp and "A" for the 185 on the DR line. Again, you're not making sense. All those figures you mention are variant loci. That means for each one, there has been a mutation since the common ancestor. All the numbers you mentioned can be established using both "A" and the chimp as an outgroup, excepting the 185 and 285. For those, the chimp is the only outgroup, but as it's established that the chimp is ~98.3% identical to us on SNPs over the whole Y, the allocation of those 470 variants will be approximately correct (regardless of common descent or "common design"). For SNPs, that won't greatly effect the rate difference between the Y and the other chromosomes, because the majority of them are neutral. Remember that nearly all of the genome is not actually coding genes. The 5:3 should apply for point mutations, but for other types of mutation, that factor could effect the Y, and you may see it put forward as an explanation for the structural differences between ours and the chimps. Those are nothing to do with point mutations. Of course, if you want to argue that a high proportion of SNPs are negative, go ahead. But remember, if the proportion of SNPs that were negative was as high as 10%, we would have gone extinct at the high mutation rate of 10*10^-8 that I'm using for falsification, because negatives would occur on average slightly over once every two generation transfers on the whole Y.Also, it's presumably easier for detrimentals to persist in the population on the chromosomes with two copies than on the X and Y. Apart from that being an unsupported claim, you seem to miss my point. Look at the slowest mutating lineage of the 35 DR individuals (it's "D"). There are 140 mutations back to the common ancestor of the 35, and we can find some of the fastest mutators with slightly over 200, which is ~50% more. If we then assume that the 13 generations of Chinese to be mutating at that slowest rate (although all the Asians on the chart aren't particularly slow), and consider the fact that their rate is 3.0*10^-8, then we can see that the highest likely mutation rate over a prolonged period would be 4.5*10^-8.As for your dramatic accumulation of mutations in the first few generations, what mutation rate are you suggesting? If you put it at 10 times the Chinese rate for ten generations, you've got about 10 mutations on that 3.2Mb section, which is no help to you at all. It puts "A" at 275, and the DR line at 175. And you're going to have problems with detrimentals right across the genome at that very high rate. There's absolute zero evidence that the rate can be that high, and unsupported speculation doesn't weaken an evidence based falsification. It was a reply to a weak claim. Surely you see what's wrong with that? The lineages that get severe detrimentals or accumulations of mild detrimentals get selected out. If you increase the mutation rate across the genome, you increase the detrimentals. So, if you want the early population to have a mutation rate of about 10 times the present, for example, you've got a very unhealthy population. The higher the rate of negative mutations, the greater the death rate before adulthood, and the harder it is for the population to expand. Why?

Yes. That's the inevitable course of the thread. What I was talking about is the relative differences on different lineages back to the point of a common Y ancestor. The fastest can have about 50% more mutations than the slowest, meaning that the variance (which relates to all the variant factors we've been discussing) is about 25% either side of the average. I then pointed out that if we generously assume the Chinese 13 generations to be as slow as the slowest lineage, the highest mutating lineages are going at about 4.5*10^-8, to which I could add that the average rate would be ~3.75*10^-8. Bear in mind that, assuming 180 generations back to a 4,500 year old common Y ancestor, you need the average mutation rate over time to be ~52*10^-8 to account for 300 mutations from the ancestor on any lineage on that 3.2Mb section. Nice to see a Christian posting research that points out the possible benefits of female promiscuity. Yes, I know all this, and agree, but it doesn't support your claim. See below. You started off arguing for an average generation gap of 18! He means that people like Shem, Terah and Abraham are health hazards. I agree. Yes, that's all fine. Now, work it out with this model. Lineage "X" goes back to the common ancestor with an average generation gap of 36 years, and therefore twice the mutations per generation than lineage "Z", which has a generation gap of 20 years, and therefore 1.8 times as many generations back to the ancestor. Take both back to the time of their common ancestor, and the result is a ratio of 10 mutations (for X) to each 9 (for Z). You see greater differences than that on the phylogenetic tree chart! We survive because the detrimentals get weeded out by death.Would you like to increase the early mutation level to the extent that every single individual conceived has a lethal mutation?What happens is that population groups get rid of detrimental mutations by producing an average of more than 1 offspring per. adult. A population can then maintain stability, or increase in size, because the extras cover for chance accidental deaths and deaths due to detrimental mutations. But if the mutation rate increases, the percentage of conceptions with detrimental mutations increases, which means the number of births/conceptions per. adult needs to increase as well in order to maintain/increase the population size. There's a limit to how high mutation rates can go. For the moment, I'll leave your geophysics alone, apart from agreeing that higher radioactivity can increase mutation rates, and I'll discuss the genetic angle. What I think we should look into is estimates on the current (low radiation) detrimental mutation rate. By this I mean the rate per. individual born. I've seen this estimated as high as 1.3 per individual, with most of these causing only very mild decreases in fitness, but a minority, perhaps 10%, causing significant decreases. If that's about right, imagine increasing the whole genome mutation rate by 10 times. That would mean 13 new detrimentals per. head, at least one causing a significant decrease in fitness on its own. I think that would mean extinction.What I'm wondering is whether humans could have a rate even double what it is now, and still have a growing population (without the help of modern medicine). I think we should look into it, so I'll check out the recent research.What you're doing now is correct from a YEC point of view. You won't find significant inaccuracies in the research papers I've been using (remember the two recent similar studies I linked to that reflect the results of the first). So, as I suggested to Faith earlier, the only thing for YECs to do is to argue for a very high mutation rate since Noah, especially early on. I knew we would end up here, in the realm of implausibly high mutation rates, deformity and DEATH.

No, you've got it slightly wrong there. There are 470 loci on which the "A" individual differs from all the others, and none of the others differ. "A" is also involved in all the other variants in the sense that he differs from any mutation that has happened within the main group, because he has the original. If that worries you, I can reassure you by telling you that there were 7 "A" individuals in the paper on 1200 Sardinians (it's not unusual to find a splash of African haplogroups in southern Europe), and they matched up very well. Unfortunately, that paper was only up for free for a brief period, and is now under a pay wall. Like our own paper, it showed that the "A"s are the slowest mutating group back to the ancestor. Both papers recapture the phylogeny of a 2008 paper, which was drawn up from other areas of the "Y", and was the most detailed up to that point. That factor only affects negatives. With the "Y", those are removed by the ending of defective paternal lines by negative selection. It's important to distinguish between mutations that happen on genes, and mutations that happen on the whole genome. Around 98% of SNPs will not happen on areas that have any great significance to the phenotype (coding+regulatory genes etc), and therefore will be effectively neutral. So, the "getting rid of negatives through recombination factor" isn't important when we're looking at largely neutral mutations and mutation rates to estimate historical things, like the time of existence of our common Y ancestor. But negative mutations are important if you propose very high mutation rates (see below). Those factors exist in both past and present. If we looked at (A)lifestyle, we could ask whether people are more likely to have chemical mutagens involved in their lives now and in the recent past, or in the long distant past, couldn't we? As for (B), paternal age, we might find research that suggests that it is higher than ever before in industrial societies. And (C), radiation, we could ask whether or not our own activities have increased our exposure to it over the last 60 years or so. Not really. I just thought it was nice in the sense that it made me laugh. I wondered if you understood that the implications were that the wives of people like Shem and Abraham would be better off hedging their bets (sleeping around) if they wanted a high chance of healthy offspring. Laughing aside, that point is actually very relevant to what we're discussing, and you actually linked to articles that made my point: high mutation is a health hazard. No. A couple would make no measurable difference. For example, give them 10 times the Chinese mutation rate, and two 70 year olds would contribute 1 mutation each on our 3.Mb tree. If the 98 year olds were four times that, that would be 4 each. The chances of the 98 year olds producing sons with serious (but not necessarily disabling) detrimentals are definitely odds on. They would have mutations on a lot of actual genes. Which is why, as your paper suggested, their wives are better off playing around with toy boys. Actually, there's no evidence to suggest that any human society ever had a sustained average paternity age of over 36 anyway.
. I'll explain very broadly, with approximate figures, so that you might realise what you are claiming would mean. In the last post, I pointed out that you would require an average mutation rate over the "Y" of 52*10^-8. At the 5:3 ratio, that means you're effectively proposing a mutation rate of 30*10^-8 for the whole genome. That translates into about 900 SNPs per generation transfer. About 2% of the genome is composed of coding and regualtory areas that, for health reasons, you don't really want to bombard with radiation induced mutations. Normally, we might expect an average hit on these regions of about once per. generation transfer, but at your rate, we've got about 18 hits. These hits are thought to be almost always at least slightly detrimental, and can range through being more seriously disadvantageous, to fully disabling. To illustrate those loosely defined categories in relation to just one function, think of being slightly short sighted, very short sighted/visually impared, and genetically blind as examples.The problem with your mutation rate is that, whereas now we might have about 2.5% (your figure) in the disabled category, and about 10% with a wide range of more minor (in the cushy modern world) disadvantaged category, and the rest of us with very minor defects, everyone would be quickly in the middle category, and the fully disabled would be about 18 times higher than at present. At your extraordinary mutation rate, natural selection has no time to rid the population of these detrimentals. And before you think of proposing a very high birth rate to absorb the mutational load, consider how many kids you would expect the average genetically disadvantaged woman to have and to be able to raise.So, not only is there no positive evidence to actually support your high mutation period, your claim that it is possible is actually incorrect. It isn't possible. Edited by bluegenes, : spellin

To add to my other reply, you don't seem to have worked out what your early rate would have to be in order to account for the "Y" mutations. You are multiplying by 4 when it should be ~20.Here's a paper for you. At least 53/1000 people will have developed a genetic disorder before the age of 25. At your mutation rate, that would be the entire population.The rates required to squeeze the human population into the standard YEC model are impossible, so the standard YEC model is falsified.It's straightforward.

I would have thought that a "free for all" is to your advantage. It allows you to make unsupported claims, like suggesting an extremely high mutation rate for our species over a 2,000 year period.So far as moderation is concerned, this thread has been entirely free, and we've established that the standard YEC model is false beyond reasonable doubt on human genetic information alone.That's quite an achievement, don't you agree?So, who needs moderation?