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

sweeping statement when I asked you to be precise. Another sweeping statement, my concerns are legitimate and listed. That's with your interpretation of the study. Just because there are variants between two genomes, does not require that the variants are actual SNPs. No-one knows which genome has the ancestral allele, and which genome has the mutated allele. This principle applies when comparing "A" to the rest, and also when comparing the 36 to the reference sequence. My point is obvious, its accurate, and yet its ignored.Every time I mention this, you revert back to your "600 variants" argument in individual "A", should I then forget about your original argument, and we base your entire argument on individual "A"? Because you seem to be ignoring that the other 35 individuals have variants, and NOT all those variants are mutations, some of them are original alleles. This is obvious. Oh really. And how many of those 600 differences are mutations, and how many are original alleles? What if they used multiple individuals in the reference sequence, surely that would emphasize the number of differences? Or are we just to assume all parts of the reference sequence have exactly the same perfect proportion of mutations? Surely that's a huge assumption. Kindly focus on this point please. Admit it, Face it. Something. Explain why they dropped the number of variants from 6662 to 6271 using the chimp's loci? If you can explain this clearly, you will then succeed in explaining why the chimp is irrelevant.Please understand I am just taking the wording at its face value, the wording does not say they "extracted the ancestral loci" , the wording is saying they "extracted the ancestral allele" for the 6271 positions. Doesnt this mean they found the ancestral allele in all these positions, where though? In the reference sequence?Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.

Faith I feel that the link in the opening post does have legitimate claims to mutations, and therefore the mutation rate can have some significance. Each human on earth has DNA that is divided into 23 chromosomes. 22 chromosomes are in males and females, only males have the Y-chromosome.The reason we can be sure of mutations even under flood assumptions, is because there was only one Y-chromosome on the ark, Noah's. All his son's would have inherited the same Y-chromosome, as does science confirm that all men today derive from one single male ancestor. And so any variation now found in genes in the Y-chromosome are caused by subsequent changes to genes since Noah.(mutations in genes)My problems with Bluegenes assertions are numerous, because its now obvious even to you that if they find 6271 variations when comparing the DNA of 36 people with someone else, not all the variants will be mutations in the 36 individuals, some differences will be mutations in the reference DNA.
This basic and obvious point has not yet been acknowledged by Bluegenes.Another problem with his analysis is that mutation rates are not yet fully established.Another problem is that lifestyle factors affect mutations, and it is common knowledge that large portions of early society were hunter-gatherers. ie a more difficult lifestyle.Another problem, that I am still investigating, is that mutations are caused by radiation, during periods of high radiation mutation rates will be higher.And so I feel there are far too many uncertainties for definite conclusions at this point in time about the number of generations since the already acknowledged common male ancestor of all humans.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.

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.

quote:

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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

You are specifically referring to the distribution between "A" and the 35, which is your fixation.
How do you distribute the 6271 mutations between the 36 and the reference individual? You keep ducking this question. Aah you are reverting back to the 615 again because you cannot explain how to distribute the mutations in the 6271 variant loci between the reference individual and the 36. This point would only stand if they really did compare two individuals. Unfortunately your reference sequence contains bits and pieces of DNA from more than one individual which throws out your logic. It could be 150 and 450, we just don't know. Haha, you are missing the point. Do you even understand the study? Haha all your calculations are irrelevant because they were left with 6271 variable loci when comparing with the reference sequence. Just because the loci VARY WITH THE REFERENCE SEQUENCE does not mean the variants are mutations.In addition if there was exposure to radiation, or lifestyle factors , this could greatly affect mutation rates, and my compressed timeframes view REQUIRES exposure to radiation due to my claim that radioactive isotopes actually decayed far faster than is currently measured.In addition the Y chromosome mutation rate is approximately 4.8 times higher than elsewhere, however this figure "4.8" I found in Wikipedia, and cannot verify it elsewhere. The mutation rate in the Y-chromosome is an unknown, and until you give more precise figures on specifically the Y-chromosome mutation rate this whole thread is irrelevant to actual reality.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.

Have you considered just how much extra radiation would have been produced under your ridiculous scheme? Well guess what? You don't have to rely on Bible hating scientists for your answer.Interestingly enough, there is a study examining exactly how much additional radiation and radiation energy would be produced by such accelerated decay rates. The eight year study called RATE was produced by the Institute for Creation Research. The RATE concluded that there was indeed evidence of billions of years worth of radioactive decay (assuming conventional decay rates). They also found that the amount of heat produced would have melted the earth if produced over the short time Genesis claims that the earth existed.Now being good Christians, they concluded that the accelerated decay happened anyway. But they could not make things work without some unknown intervention at work. Is this your argument too?

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.

OT, but Heat and radiation destroy claims of accelerated nuclear decay summarizes those results and adds the calculations of Noah's exposure to radiation from ⁴⁰K in his own body. Of course the calculation depends on what scenario one proposes for acceleration of decay, but I doubt there's on in which heat and radiation aren't an insuperable problem.Edited by JonF, : No reason given.

Heat was different before the flood. That is why fossils of rain drops are more common in the 4498 year old Triassic layers than the 4501 year old Permian layers.

Oh yeah? What about the scenario where you just don't give a crap about insurmoutable problems because you are just going to make up some more changed physics to resolve any issue.Here is my attempt.Back in the day, that extra radiation did have an effect. It shaved hundreds of years off the lifetimes of all of those humans. Noah and Methuselah might well have lived thousands of years were it not for that life, draining, body heating, radiation.

I need links, I need calculations. I don't care about the source of information, if the information makes sense then I respect it.Could you kindly give me your sources.

You are in fact incorrect.Not only are you incorrect, I already pointed this out in my post 76:"Thus, despite the small number of individuals, there was good geographical representation of global populations and of the haplogroup tree. After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)"SITES THAT DIFFER FROM THE Y-CHROMOSOME REFERENCE SEQUENCE. Not differences from each other, but differences from the reference sequence. These comments are based on your misunderstanding of the study. As pointed out above, they did not compare with eachother , they compared the 36 with the reference sequence. Now its up to you to explain where the mutations are in 6662 variant loci. The reference sequence , or the 36 individuals? How do we divide the mutations between them? Your conclusion of 5:3 is way too simplistic and does not acknowledge the full range of factors that increase mutations in the y-chromosome:
"The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a greater risk of mutation than the rest of the genome"
Also a lack of recombination in the Y-chromosome.The following study seems to indicate a much higher Y-chromosome mutation rate than either of us has quoted so far, but does not focus on SNP's. This study claims the field needs further study to establish y-chromosome mutation rates:
http://www.ncbi.nlm.nih.gov/...s/PMC1378017/pdf/10762544.pdfI don't find your simplistic ratio of 5:3 very convincing, seems like a thumbsuck to me. Wishful thinking on your part 1) Scientists themselves still claim Y-chromosome mutation rates are uncertain
2) You are still showing a misunderstanding of where those 6662 variants come from, this along with other factors directly affects your mutation count on which your argument is based.
3) You are ignoring the possibility of lifestyle factors , which have been proven to affect rates
4) My compressed timeframes view requires more radiation, which has a direct effect on mutations. Could you post a link. This is very interesting for me.Edited by mindspawn, : No reason given.

See the message immediately following the one you quoted. It doesn't exactly apply to your scenario, but it can form a basis for the calculations you are going to have to present when you get around to discussing radiometric dating.

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

Let me repeat my quote from the actual study:
"Thus, despite the small number of individuals, there was good geographical representation of global populations and of the haplogroup tree. After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)"Your response:
"the loci on which the reference differs from all 36 of the real people are its own mutations"You say that they "automatically exclude" the mutations in the reference sequence. Please quote from the study to prove your point, I have had the courtesy to back up my statements with actual quotes. You would be surprised how many time scientists miss some logic in making their conclusions and devising their studies. Applying what you think is logical to a document that explains things differently is just not good enough to make your point.And even if you were correct, your reference to another common ancestor further back in time ruins your mutation count, because its possible that all 36 individuals had the mutation, and the reference sequence has the original allele. The only method in which to tell the difference is to actually have the ancestral sequence, which they do not have, and they had to use the chimp to estimate the ancestral alleles.I believe the more unique variants found in small proportions of the population are more likely to be true mutations, and so referring to your graph, we can be pretty confident after the 52/41 , that these are all true mutations. But the 54, the 13 , the 41, the 185 and the 285 have a high chance of being ancestral alleles and not mutations which ruins your count. You are looking at one generation, however you need to factor in long term selection through variation via recombination. De-selection is limited regarding the Y-chromosome because it does not recombine.regarding my 4 points,
1) Ok the point is partially accepted, they are beginning to define an acceptable range that is currently applicable. This however does not reflect on past rates.
2) We are still in total disagreement.
3) You write: 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 chartsYou seem to miss my point here, its possible that ALL humans had a worse lifestyle during the first generations after the flood. They were also having children at older ages. The accumulation of mutations in the first few generations could have been dramatic compared to today, based on age and lifestyle factors.4) You say: 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.This was a weak reply, we are looking at the number of germline mutations already existing in populations and how rapidly they were formed. Even now with these mutations, populations can grow rapidly, so your point that populations would not have been healthy with many germline mutations does not apply, because we are healthy enough to expand rapidly. Did mankind rapidly gain its germline mutations during a period of high radioactivity? I believe its possible.

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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?