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

Aah I see what's wrong here, we are just are not reading properly your document says:
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)"Variants, not from each other, but from the Y-chromosome REFERENCE sequence. This reference sequence is from the rare Haplogroup G. "Segment of the reference sequence derived from haplogroup G"Many of the variations would be mutations in Haplogroup G. Where we have wide representation of many other haplogroups (35 men) , they are more likely to represent the original Y-Adam than the rare Haplogroup G reference sequence, so to assume all variations are from the 35 individuals and none from Haplogroup G is just incorrect thinking.

I understand that we don't need an outgroup, but we have to be careful with our thinking if we do not have an outgroup. In this case they did have the Haplogroup G sequence. If 35 individuals from various Haplogroups all share 185 variants, and only one Haplogroup G sequence has all 185 variants, who do you think had the mutations that caused the differences?If you look at 36 individuals and 35 of them have black hair and only and has blue hair which one do you think has the mutation? That is funny. The essence of our discussion revolves around who has the mutation, and who the original, and yet you are using the chimpanzee to decide the difference. It is a bit silly even to admit this in a discussion with a non-evolutionist, the circular reasoning is hilarious. Unless we compare 36 individuals, and 35 are identical, and the 36th is showing 185 differences. To then conclude that all 185 variants are mutations from the 35 individuals is a bit of an assumption that is not self-evident by any means, giving the more representative nature of the 35 individuals, they are more likely to represent Y-Adam than Haplogroup G Actually the human Y reference is Haplogroup G, which is a rare Haplogroup, not a common one.I don't understand why you are referring to 615 SNP's when your argument comes from the ~2000 SNP's of Figure 2. Figure 2 has more relevance, because its not the total count that is relevant, humans will have thousands of variations at each locus if you sequence huge populations. Its the number that are found in each individual, and these can only be counted by mapping differences which was done with the ~2000 SNPs of figure 2. The further filtered 615 SNP's need a breakdown amongst those 36 individuals before becoming relevant. You assuming they are the final differences between two individuals, that is why you are dividing by 2, but the 615 SNP's are further filtered SNP's among 36 individuals.

It's a not particularly rare subgroup of F, which is common. But what I meant, if you look at the tree (below), is that it's on the branch in the common super haplogroup that all of the men are in except the basal "A". That's marked "DR" on the branch, opposite "A".You can see where it is, because there's another G in the 36.I've been telling you that there's a human reference since you asked. Here, from post 69: Message 66Now, when "A" is compared to the reference at high resolution on just the 3.2Mbp, there are 615 polymorphisms. It's in the paper."A" is NA21313.

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NA21313 High-coverage sequencing

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High-coverage sequence information was generated by amplifying 5- to 6-kb overlapping fragments by long PCR. Approximately equimolar amounts of PCR fragments were pooled and used for library preparation and paired-end sequencing (54 bp) on an Illumina GAII Genome Analyzer to obtain 475 median coverage (European Nucleotide Archive [ENA] sample accession no.: ERS006694; ENA Browser). MAQ (Li et al. 2008) was used for mapping and SNP calling in the high -coverage data. Read depth coverage (>1/2 mean depth) and mapping (consensus > 30, mapping > 63) filters reduced the raw variant calls from a total of 5684 to 2233. Subsequent filters included removal of heterozygous calls and sites that were within 4 bp of each other to create a high-confidence filtered list of 615 SNPs, none of which were discordant with the established Y phylogeny.

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And here's the description of tree 3 (fig. 2) which is below.

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...or SNPs with ancestral state information, no recurrent mutations, and high coverage in all individuals (tree 3) (Fig. 2). The branch leading to the haplogroup A individual was shorter than any other, most likely reflecting the low-coverage sequencing of parts of this chromosome and consequent under-calling of variants; this effect was largely eliminated in tree 3, where only high-coverage regions were used (Fig. 2).

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All you need is the information that you've got 2 humans who differ by 615 on 3.2Mbp, and you've got the falsification.Now I'll tell you something else about haplogroup G. It's very common amongst stone age Europeans. I'll leave you to figure out how it's so easy to find a modern haplogroup in the stone age, right after Noah.Of course, if the Y ancestor was more than 100,000 years old, then the stone age would be relatively modern, wouldn't it?

Here's another study, also on 8.97Mbp. This time, 1204 males from Sardinia have been studied. The first point to make here is that the number of point mutations to the common ancestor compares well with the other study. It's actually slightly higher (~1,000 on 8.97Mbp) and would work out to ~6,000 for the whole Y-chromosome. Paper looks interesting.And here's another one, also new. This time involving 69 menEdited by bluegenes, : typo

The more I look at figure 1 the more I see the human reference as only being a small yellow section, and the actual reference sequence being the chimp. I apologise for changing my mind on this, but it does appear that the actual reference sequence is the chimp.If you would like to insist that they used a human reference, then you need a clear quote from somewhere in the article because I only see the chimp being mentioned twice as the reference sequence, I need you to quote some evidence for your repeated stance that the reference sequence is not the chimp, and is in fact a human.1)Figure 1: Chimpanzee reference F2) "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 "

They used the chimp as the outgroup:
The informative SNPs were used to construct a parsimony-based phylogenetic tree. To root the tree, we used the chimpanzee genome reference as an outgroup and inferred the ancestral status at all SNP sites except for 26 that were discarded in further analysis The used the chimp as a reference sequence:
To account for missing genotypes, we assigned each SNV to the root of the smallest subtree containing all carriers of one allele or the other and inferred that the allele specific to the subtree was derived (fig. S8). We used the chimpanzee Y-chromosome sequence to polarize 398 variants assigned to the deepest splita task complicated by substantial structural divergenceUsing chimps as the references completely over-estimates the SNP's.
We need to reference humans against humans, and then divide the differences by two.

Wrong again. You really seem to be out of your depth. You cannot identify loci with human/human variations by comparing human Y-chromosomes to the chimps. All you get if you do that are human/chimp variations, which is a completely different set. So, of course they are comparing human to human to actually identify the SNPs. You've found one. Chimps are not in human haplogroup G, are they? Once again, they are not finding the human SNPs in that bit you quote. They are finding the ancestral alleles "for each position that was variable in humans". Read what you've quoted. They've already found the variables. The chimp is just used to root the trees, which, as I keep explaining, is irrelevant to our falsification of YEC.Once you know the number of variables (Single Neucliotide Polymorphisms) between two individuals, you can divide by two to get the aproximate number of mutations going back down each line to the common Y-ancestor. If the object of their research had been to falsify the standard Y.E.C. model, they wouldn't need to bother with their exacting phylogenetic trees. Their database would show that individual "A" differs by more than 600 SNPs from all the others on 3.2Mbp, and ~1700 SNPs on 8.97Mbp, and that means far to many mutations for the "Y" ancestor to have been within the last 10,000 years. They do not need to know the ancestral states of the alleles for that.We could do that if the chimps were all extinct.

Read. After they've found the SNPs, they use them to construct a phylogenetic tree, which is then rooted with the chimpanzee genome reference as an outgroup. They've massively falsified YEC before they get to this stage. I'll try to explain why they root the tree with the chimps.Almost all the tree can be made in all its detail by using the haplogroup "A" "Y" chromosome as the outgroup. What we're left with is 1334 mutations whose exact position we don't know. They belong on the brown haplogroup "A" line and the black root line of the other haplogroups. Where they've marked 868 and 466, we, without the chimps, would have to guess by assuming a figure for the "A" group that brings it into line with an average of the rest, so we might assume about 930 for the "A"s and 404 for the root line of the others. But whatever reasonable guess we made, it wouldn't affect our falsification.

Coyote , once again you are using your long timeframes to make your point, whereas this thread is about biology, not carbon-dating. That is why bluegenes has focussed on mutation rates and no. of mutations.If you are willing to work within the same frames of reference, thereby eliminating any possibility of unintended strawman arguments, can you repeat your point on the assumption that ALL fossil humans are post-flood. (I regard any human fossils less than alleged 250 million years old as post-flood)Edited by mindspawn, : No reason given.

I didn't ask for your theory on the matter. I asked you to SHOW ME FROM YOUR LINK where it refers to a human reference.
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)""we used all the 6662 sites in 36 individuals to construct a haplogroup tree, which was rooted using the chimpanzee Y sequence."You see once they had established the variants, they assumed ALL the variations were mutations in the 36 individuals, instead of mutations in the reference sequence. that is a HUGE assumption. Then they make another huge assumption, that only 391 of these 6662 are ancestral because these 391 match the chimp. Who knows, maybe 3000 of those variations in the 36 individuals could have been mutations in the y chromosome reference sequence, why only eliminate the ones matching the chimp, as if the chimp is Y-Adam? The mention of Haplogroup G is ONLY for the little yellow section in Figure 1.Its impossible for your human reference to be one of the 35, because how then can it have 185 differences with itself??? That's pretty laughable. Very funny. All 35 DR individuals share the same pattern of 185 nucleotides, this is no sign of a mutation, but could actually represent Y-Adam before mutations.The logic is still pointing to the chimp, whereas you have not yet quoted anything that proves your human reference.And they did not compare the individuals with eachother, they clearly compared them with the "reference sequence" so this whole discussion revolves around defining who exactly is this reference sequence."After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)" 600 differences between "A" and who?
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence)"Now the "A" was also compared with the reference sequence (not with the other 36 individuals). The 600 so-called SNPs found there are also all assumed to be from "A" and not from the reference, unless the "A" variant matched the chimp, see where the logic goes out. At this stage the chimp becomes the stand-in for Y-Adam. Edited by mindspawn, : No reason given.

No. That is your particular delusion. I'm certainly not going to share it.The consensus of religious scholars is that the flood that never happened occurred about 4,350-4,500 years ago. I have presented mtDNA evidence from my own archaeological research that shows continuity across that particular date. That one fact alone shows that the flood could not have happened as claimed.As for your delusions about dating, I started a thread to deal with that subject, and you have studiously ignored it.So no, I will not just assume your 250 million year old date for the flood and will not join in your delusions about altering the geological record by a factor of about 57,000 times.

That is the human Y chromosome reference sequence they are referring to. They don't need to specify that it's human, because you can only identify within human variants by comparing humans to humans. If you use the Y-reference for another animal, you'll just get the variants from humans to the other animal. To the authors of the paper, and to readers who understand it, this is obvious. Individual "A" is different on these. No loci where all 36 are identical are included. They would be the same as the common Y ancestor of all the group. Logic? They tell you what they use the chimp reference for. It is to determine the ancestral allele of the SNPs once they've found them Do you really think they've compared the 36 to a chimp reference on 8.97MBp of the Y-chromosome and found only 6662 variants? On SNPs alone, if the chimps differed from us by just 1%, you'd expect 89,700 on that section. A paltry 6662 total variants would mean that the chimps are the same species as us.Hey! You know what? It looks like the "Y chromosome reference sequence" is actually from the same species as us. Fancy that! Not at all. If you find 600 differences between "A" and the reference on that 3.2MBp, then you know that about 1/2 of the mutations that make the differences will have come from each lineage, so, we know that both individuals are ~300 mutations away from their common Y ancestor on 3.2MBp, and that blows out the 4,500 year old Noah on any plausible mutation rate.Forget the chimps. You can do this with the chimps and all other mammals being extinct, meaning we're the only ones with a "Y" chromosome.

Let's put this another way: there is no documented\recorded record\evidence of a world wide flood for the entire period covered by human, hominid and ancestral ape fossils.We can go back to one of the oldest known hominid fossils:
Ardipithecus ramidus | The Smithsonian Institution's Human Origins Program

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Ardipithecus ramidus was first reported in 1994; in 2009, scientists announced a partial skeleton, nicknamed ‘Ardi’. The foot bones in this skeleton indicate a divergent large toe combined with a rigid foot — it's still unclear what this means concerning bipedal behavior. The pelvis, reconstructed from a crushed specimen, is said to show adaptations that combine tree-climbing and bipedal activity. The discoverers argue that the ‘Ardi’ skeleton reflects a human-African ape common ancestor that was not chimpanzee-like. A good sample of canine teeth of this species indicates very little difference in size between males and females in this species.

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It would be hard -- imho -- to argue that this could be human remains, while it certainly is consilient with hominid evolution and early adaptation to bipedal ability.Or we can go back further to the oldest known primate fossil:
http://www.sciencedaily.com/...ases/2013/06/130605133550.htm

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The fossil was recovered from sedimentary rock strata that were deposited in an ancient lake roughly 55 million years ago, during the early part of the Eocene Epoch. This was an interval of global "greenhouse" conditions, when much of the world was shrouded in tropical rainforests and palm trees grew as far north as Alaska. Like most other fossils recovered from ancient lake strata, the skeleton of Archicebus was found by splitting apart the thin layers of rock containing the fossil. ....

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Note lake not ocean\sea, just for clarity, and that there were no marine fossils associated with these fossils.And we have not even gotten near to the K-Pg (formerly K-T) boundary.You can (try anyway to) ignore the age of rock formations in the pursuit of your pet delusional theory, but you cannot ignore the laws of geology that relate to the relative ages of layers, superposition being one: lower layers are older than upper layers.Law of superposition - Wikipedia

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The law of superposition (or the principle of superposition) is a key axiom based on observations of natural history that is a foundational principle of sedimentary stratigraphy

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Sedimentary layers are deposited in a time sequence, with the oldest on the bottom and the youngest on the top.

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The law was formulated in the 17th century by the Danish scientist Nicolas Steno.

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The K-Pg boundary is well marked around the world due to iridium rich dust in the layer.Cretaceous—Paleogene boundary - Wikipedia

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The Cretaceous—Paleogene (K—Pg) boundary (formerly known as the K—T boundary) is a geological signature, usually a thin band. It defines the end of the Mesozoic era, and is usually estimated at around 66 Ma (million years ago),[1] with more specific radio-isotope dates yielding an age of 65.5 0.3 Ma.[2] ...

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In 1980, a team of researchers consisting of Nobel prize-winning physicist Luis Alvarez, his son, geologist Walter Alvarez, and chemists Frank Asaro and Helen Michels discovered that sedimentary layers found all over the world at the K—Pg boundary contain a concentration of iridium many times greater than normal (30 times background in Italy and 160 times at Stevns).[5] Iridium is extremely rare in the earth's crust because it is a siderophile, and therefore most of it travelled with iron as it sank into the earth's core during planetary differentiation. As iridium remains abundant in most asteroids and comets, the Alvarez team suggested that an asteroid struck the earth at the time of the K—Pg boundary.[5] ...

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All human, hominid and ancestral ape fossils lie above the K-Pg boundary while the P-T boundary is below the K-Pg boundary.Of note Orthida brachiopods became extinct during the P-T extinction event. Fossils of these brachiopods are found on Mt Everest: ORDOVICIAN OF THE WORLD (downloads)

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The highest rocks on Earth, marking the summit of Mount Everest, are Ordovician limestones, deposited in a warm, shallow-water sea some 450 million years ago. More remarkably, these rocks still contain the fossils of marine animals such as brachiopods and crinoids that occupied tropical habitats during one of the most important intervals in Earth history, the Great Ordovician Biodiversification Event (GOBE). ... The shallow-water shelly faunas were dominated by suspension feeders including orthide and strophomenide brachiopods, and a robust pentameride crinoid, ‘Pentagonopentagonalis’ (col.) sp. Multivariate statistical analyses of the distributional patterns of the Brachiopoda, place the fauna within the Toquima-Table Head realm, a circum equatorial province contrasting against the higher latitude Celtic and Gondwanan faunas during the late Mid Ordovician.

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Just for amusement on another line of evidence that you need to wrap up in your "explanation" ... please note that brachiopods shells grow on a rather fragile stalk attached to the bottom of shallow seas.EnjoyEdited by RAZD, : ...

What should the rest of us make of statements like this? Because what this statement looks like to me is naked dismissal of evidence or argument provided by others without having to provide an evidence or logic based argument of your own.There is no reason to give your "regard" any credit at all.Edited by NoNukes, : No reason given.

If it is a human, then why can't you find the quote? Your whole argument hinges on that. And exactly which human is involved makes a big difference. If the "A" individual is the reference sequence this is impossible because then there would be no differences, but you are claiming >600 differences. If the reference sequence is one of the 35 then this makes a complete hash of the first 185 so-called differences, because they have to be deduced backwards from differences with the "A" individual.ie if the reference is human and one of the 35, he is more likely to represent Y-Adam because the 35 have a wider representation that the "A" individual. Therefore any differences of the 285 plus 185 between A and the rest are more likely to be mutations of A. It could be 400 with A, and 70 with the others, we do not know.Then we go further down the generations and get 54 differences between the next split. Who has Y-Adam nucleotides, and who has mutations, we don't know. It could be split 27 each group. But you count the next 54 differences twice even though most likely one of them has Y-Adam mucleotides.Already your simplistic adding of the numbers is out by 142 mutations across 35 individuals. (or arguably 34)As you get more recent , the same divide by 2 average would apply. The end result is that those 35 individuals only have about 200 mutations each if we take into account that we don't know who has the Y Adam original nucleotides and who has mutations.To compare this against the chimp is also a huge assumption considering you have already admitted that the chimp has big differences with a human. Why should the chimp represent the ancestral alleles unless you are an evolutionist, and to argue for evolution using evolutionist techniques is just circular reasoning. They should have eliminated all variations that matched Y-Adam to reduce the number of variants counted, and without Y Adam they were just guessing and underestimating the y-Adam matches with the non-reference sequences (eg individual A).1) So if you claiming the reference sequence is the chimp, then you have a huge problem.
2) If you are claiming the reference sequence is a human of the 35, then your figures are way out, and incorrectly calibrated against the chimp.
3) If you are claiming the reference sequence is the A individual, then how do they record 600+ variations between the A and himself?
4) Or maybe its another human, who knows because you wont tell me.ps just to explain the mutation problem, if two individuals vary from eachother, about half should have the ancestral allele, and half the mutation. When comparing the 6662 mutation sites they only found 391 with the chimp's so-called ancestral allele and assumed the rest to be mutations. They should have found over 3000 in the non reference sequences if they used the correct ancestral allele, which of course is not available (Y-adams DNA is needed). So using the chimp to eliminate non-mutations has a drastic effect on the study whoever the mystery original reference sequence is. This is true, he is different, but when differences are found how do they decide who has the ancestral sequence, and who has the mutation. By comparing them to a chimp.Whooohooo that's funny. So now we are distributing human differences according to a chimp. but nearly every locale where there are variants should be represented by the ancestral locale in one of those 36, because they have wide human representation. (or should I say 1 of the 35 because I'm still waiting for you to tell my who the reference sequence is) For non-evolutionists, there is no reason for the chimp to represent the ancestral allele. this would underestimate the number of ancestral alleles in the study group. Which i am sure it did, because they only picked up 391 ancestral alleles in 6662 variations, a highly unlikely underestimation.When you compare two humans in this sequence you have a perfect match of ancestral alleles and ancestral nucleotide sequences across 3,200,000 positions. Now in maybe a few hundred positions there isn't a match. What are the chances of both having a mutation at that spot? Close to nil. So every time you see a variation between two guys, you would expect one individual (the reference sequence) or the other individual to share mutations approximately 50% of the time.Of those 6662 variations, 6271 were found to be mutations. Only 391 were eliminated. May I suggest that using a chimp was as logical as using a chicken to eliminate ancestral alleles:Unbelievable Y chromosome differences between humans and chimpanzees - john hawks weblog
"Indeed, at 6 million years of separation, the difference in MSY gene content in chimpanzee and human is more comparable to the difference in autosomal gene content in chicken and human, at 310 million years of separation."
"I can't believe how sedated the reaction to this paper has been so far. The outcome of the sequencing is really, really weird. More than thirty percent of the chimpanzee Y chromosome has no homolog in humans, and likewise for the human Y in chimpanzees."They didn't eliminate enough ancestral alleles because they just do not have the DNA of Y-Adam, and instead used a chimp. they may as well have used a chicken. 600 differences? Calibrated against a chimp? In 6662 variations they eliminated only 391 "ancestral" variants. Taking into account the chimp Y-chromosome only represents 70% of the human y-chromosome, this figure just does not reflect the reality of true ancestral DNA. They should have eliminated a lot more variants as representing the ancestral nucleotide sequences. So you can cut down that 600, it just does not reflect reality.Then they didn't even split the differences , they allocated only 285 mutations to "A". what about allocating 385 to A, and the rest to the "reference sequence". Where is your claculation on that split? Your whole point is based on numerous assumptions including mutation rates, generation times, chimps being our ancestors etc etc Edited by mindspawn, : No reason given.