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

Nice thread Bluegenes. Due to my lack of knowledge about genetics, I would like to ask you some questions:
1) Correct me if I'm wrong, but the first study focussed on only two Chinese individuals, surely this is not enough to be representative of standard mutation rates across world populations?
2) Isn't it true that sun exposure has an effect on mutations? If so the "Middle East" biblical theory would necessitate a higher mutation rate for all ancestry, and yet slowing down in recent times for northern hemisphere populations of high latitudes (including the Chinese).
3) Does the second study focus only on base substitutions as per the first study? ie are we comparing apples with apples between the two studies?
4) If the y-chromosome evolved, is it possible that the base substitutions found therein are representative of millions of years of mutations since the y-chromosome's alleged introduction over 200 million years ago? ie doesn't the small number of mutations found put doubt on evolution, rather than the large number of mutations disproving creation?Edited by mindspawn, : No reason given.

Coyote if you think about the logic of this argument of yours, the whole point is based on dating methods. Which is a separate argument to Bluegenes genetic argument.I would say that man is post-flood, and due to incorrect dating methods was erroneously dated to 10300ya and instead was less than 4500ya. If you let me know how the fossil was dated we can delve into that aspect of it to see if I could be right. But you would have to open another thread for that because its irrelevant to this thread. Let me know if you do so.

Increases in germline mutations are related to higher temperatures and also UV damage. both are more prevalent in lower latitudes.Temperature affects on germline mutations:
Hotspots for evolution - Understanding Evolution
Just a moment...UV exposure causes increases in mutation rates, I'm still looking into the inherited effects though :
Ask a Geneticist | The Tech Interactive
Mutation - Wikipedia
Ultraviolet radiation (nonionizing radiation). Two nucleotide bases in DNA — cytosine and thymine — are most vulnerable to radiation that can change their properties. UV light can induce adjacent pyrimidine bases in a DNA strand to become covalently joined as a pyrimidine dimer. UV radiation, particularly longer-wave UVA, can also cause oxidative damage to DNA.[27]

Could you kindly discuss the temperature effects on germline mutations. I did say that I'm still looking into inherited UV mutations, but I did provide links that show temperature affects mutation rates to a significant extent. Which in itself puts doubt on the claims of the opening post because these two Chinese are not based in a warm area, and as such are not representative of average mutation rates for mankind. But even the sample size of just two individuals is insufficient for any generalized claims.

You are confirming that the mutation rate you are using was established from the comparison between just two Chinese individuals. Your sample is not large enough to make a convincing scientific conclusion. I feel you need to post your other studies to get more support for your mutation rate. You have based my so-called "required rate" on your rates that are based on two Chinese guys. For the moment you haven't got enough evidence to support your claimed mutation rates. And I have posted evidence that in fact the tropics do have higher mutation rates. Reading through that study, I couldn't find where only one fifth of the y-chromosome was mentioned? Kindly point this out, I got the impression they deliberately used "high coverage" individuals when analyzing those 36 y-chromosomes. I don't see why the y-chromosome would have only been collecting SNPs for 300 000 years, when its been allegedly "evolving" for 200 million years and collecting SNPs in the process.

1) If you do believe in common descent you should acknowledge that mutation rates are higher in lower latitudes. How then can you claim that high latitude rates are normal if you do not believe that yourself?Just a moment...2) I'm not sure that the studies were based on the assumption of long term common descent, they seemed to be studying species with only recent variation from definite nested hierarchies. (not assumed long-term hierarchies as per evolutionary theory)3) The theory behind it makes perfect sense whether you believe in long-term common descent or not, there is no reason to doubt that mutation rates would increase in the tropics:
"This is a reasonable hypothesis since warm-weather organisms likely have higher metabolic rates, and some substances involved in metabolic reactions can cause DNA damage, potentially leading to a mutation. Mutations, in turn, increase genetic variation, the raw material of evolution"Conclusion: this all puts doubt on your usage of two high latitude Chinese guys to establish a universal mutation rate across all areas of the globe.

I don't really understand your point here. It just seems we are both agreeing I need to research the UV angle more.Regarding temperature effects on Mutation rates , I believe once Bluegenes and I have reached better consensus on SNP mutation rates, the factor of 2 will become more significant.

Fair enough, although I would put the number of generations at about 250. Since the flood many societies had early teenage marriages, and hence teenage pregnancies. To establish whether the "Noah" model is correct we need to establish a normal mutation rate for these 250 generations and see if it fits in with 1600 mutations over 6500 years. No problem, I will put my emphasis on increased mutations in low latitudes on hold for now until further evidence. However I also note your agreement that mutation rates do vary. There are obviously reasons for this. Thanks, I was looking for it lower down in that article, that's why I missed this. Ok I understand where you are coming from here. So now that we have general consensus on other matters, let's get into the nitty gritty of actual mutation rates.Your first link gave an estimate of 3.0 10−8 mutations/nucleotide/generation. The following is another estimate of mutation rates, remember the y-chromosome is only 2% of the genome and there are ~5 times as many accumulated mutations in the Y-chromosome than elsewhere.Not Found | Journals | Oxford Academic
"The two most direct methods yielded estimates of 10 10−9 (from electrophoretic variants of polypeptides) (88) and 8.6 10−9 (from a meta-analysis of 40 cases worldwide of de novo mutations producing unstable hemoglobin or hemoglobin M) (89)"We now have the following rates of mutation for the y-chromosome:
Study 1: 1.8 mutations per generation (from the two Chinese guys)
Above link: 3 mutations per generation (10 per billion bp, x5 for the y-chromosome)Ignoring the study based on a small sample, and assuming the rate of 50 mutations per billion bp in the y-chromosome, over 250 generations we would expect 750 mutations since Noah. Instead we have 1600 or so. That is more than double what we would expect, but we are getting closer.But there seems to be general consensus that a clear mutation rate has not yet been established. For example in the following article we get 35 and 49 germline mutations in one generation. Approximately 10% of all mutations are in the y-chromosome and so this would indicate an approximate rate of 3.5 to 4.9 y-chromosome mutations per generation. At 4.9 and assuming a 18 year generation over most of the period since Noah we would be so close to the observed mutations in study 2 of the OP post as to put doubt on the claimed timeframes of the second link in the OP.Variation in genome-wide mutation rates within and between human families | Nature GeneticsDue to the fact that we do not know exactly what caused the differences in the mutation rates between the 36 individuals in the study and we do not know the full environmental factors in the last 4500 years, its entirely possible that rates per generation were faster in earlier generations.Despite what you said in your opening post, it appears that all rates actually measured between actual modern generations, including rates quoted in this thread are far too slow to match the required rate of 160 per generation to explain human diversion from the common ape ancestor: Sandwalk: Estimating the Human Mutation Rate: Phylogenetic Method
"Nachman and Crowell (2000) looked at silent mutations in eighteen pseudogenes common to chimps and humans. They found a total of 199 substitutions in 16,086 nucleotides. Converting this to a mutation rate requires several assumptions. If we assume that equal numbers of mutations occurred in each lineage (~100) then the mutation rate works out to ~2.5 10-8 mutations per nucleotide. This calculation depends on the time since divergence (~5 million years), the generation time (they assumed about 25 years), and to some extent the population size (about 10,000).That mutation rate corresponds to 160 mutations per diploid genome per generation"It seems to be that the proof of evolution turns out to be evidence against evolution. A rate of between 18 to 45 germline mutations is actually measured in humans, and yet a rate of 160 mutations is required to explain divergence from apes. Edited by mindspawn, : No reason given.

The truth is I only need a factor of 2 in order to explain the differences since Noah 4500 years ago.Evolutionists need a factor of 4 to explain the differences since apes split with their common ancestor Sandwalk: Estimating the Human Mutation Rate: Phylogenetic Method
"The differences (substitutions and small deletions only) amount to 1.4% of the genomes or 44.8 million mutations."
If you follow the reasoning in that blog, you see that between 112 and 160 mutations are needed per generation to explain the observed divergence between the human/ape genomes.Edited by mindspawn, : No reason given.

I faced the challenge, and have already shown that the opening post vastly underestimates the true rate of mutation, so I'm getting closer. As explained to bluegenes there is little consensus on core rates, and various studies contradict eachother. In addition there are many factors that effect the rate of mutation (ie our temperature discussion) and these factors could have been exacerbated in past environments. You and Bluegenes were stating that a factor of 2 is not enough to prove my position, I have now shown that is all I need.On the other hand evolutionists need a factor of 4 in currently measured mutation rates to explain divergence between apes and humans. I throw down the gauntlet to you and to bluegenes, can you explain why current rates of mutation are far slower than that required by evolutionary timeframes?Edited by mindspawn, : No reason given.

The way I read the article is that 8.97 mb of the Y-chromosome had high coverage in 35 individuals. This 8.97 Mb is the region that the information was extracted from for that study:
"We have identified variants present in high-coverage complete sequences of 36 diverse human Y chromosomes from Africa, Europe, South Asia, East Asia, and the Americas, representing eight major haplogroups. After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants"
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence), including both SNPs and indels, from 8.97 Mb of unique Y sequence"The 36th individual was the haplogroup A individual. They only had high coverage in 3.2 Mb of the haplogroup A individual. (restricted the region considered to the 3.2 Mb with high coverage in the haplogroup A individual). They had to make do with a smaller region with the 36th guy, but the first 35 guys had 8.97 Mb of high-coverage.So I believe your original estimate stands.

lol, just like that? I don't think so.If 36 individuals have 6662 mutations detected in 8,97 Mb, how then can figure 2 be claiming that 36 individuals have 12240 mutations in 3.2 Mb?? This makes no sense.
'After restricting our analysis to 8.97 Mb of the unique male-specific Y sequence, we identified 6662 high-confidence variants, including single-nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs), and indels. '
"After QC and validation, we extracted 6662 high-confidence variants (i.e., sites that differ from the Y chromosome reference sequence), including both SNPs and indels, from 8.97 Mb of unique Y sequence"
"We assigned ancestral states to 6271 of the variants and then constructed a rooted parsimony-based phylogenetic tree containing all 6662 variants (tree 1) (Supplemental Fig. 1)"(note - tree 1 has no 3.2 Mb restrictions)6662 mutations are found in 8.97 Mb , if we divide that among 36 individuals we get 185.06 mutations in each individual. Multiply this by 6.58 to represent the whole Y chromosome, and we have 1217 germline mutations per Y-chromosome per individual.At 225 generations, and at a mutation rate of 4.6 per generation in the Y-chromosome, we get to 1025 expected mutations. 1217 found, 1025 expected. Obviously we can get a better match if we adjust the generation time or the 1.5 x 10(-8) mutation rate, both variables are uncertain.I'm not swearing by this either because various areas of even the y chromosome collect mutations at far higher rates and so this whole study is not a definite reflection on germline mutations in the rest of the genome.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.Edited by mindspawn, : No reason given.

There are 36 individuals, and they do have about 340 mutations each. The link isn't clear whose DNA was tested against to count the variations.Here are some general questions I have regarding the certainty of your claims:A) Knowing that they do not have the DNA of Y chromosome Adam , they must have defined variants as variations between humans within the study. Which focuses my attention on the 285 differences and 185 differences between the Haplogroup A individual and the rest. This is where the bulk of the differences lie, but compared against what ancestral DNA? If compared with eachother, surely the number of differences would be the same between two individuals. ie 285 differences. Why 185/285? Could you kindly explain that to me , because that is where the bulk of your differences lie.They refer to a chimpanzee as a reference point, if this is the source of the variation, that makes the first 185/285 variants completely irrelevant. (Figure 1 "chimpanzee reference F")
"First, we used all the 6662 sites in 36 individuals to construct a haplogroup tree, which was rooted using the chimpanzee Y sequence. "B) They included non-Germline mutations in their study, which distorts the figures. Even in those where they could have logically eliminated the somatic mutations, they still chose to include them in the study:
"An additional source of biological error is the mutations that occur somatically in the donor or during cell culture, which are relevant here since all sequences were derived from lymphoblastoid cell lines. We can estimate this number from the sequences of the three-generation family. The grandfather and father carry 13 and 11 specific variants, respectively, two of which are absent from the grandfather but present in the father and transmitted to all his sons and are thus likely to represent in vivo de novo mutations, while the remaining 22 are likely to be somatic"C) I quoted a Wikipedia article indicating that mutations on the Y-chromosome are about 4.8 times more common in the Y-chromosome. This was approximate, but it is generally known that Y-chromosome germline mutations are far more prolific than elsewhere. Have you any definitive studies on mutation rates specifically in the Y-chromosome that can help your case? It seems to be general consensus that Y-chromosome mutation rates need to be more fully established.D) Some regions of the Y-chromosome are more prone to mutations than other regions, are you sure that the following sequences do not contain excessive mutation rates:M32, M190, M220, M144, M202, M305, M219, P97http://www.uni-koeln.de/...ertation/diss/khalid_arhzaouy.pdf
"Up to now, more than 20 unique p97 missense mutations have been identified with codon 155 being a mutation hot spot"http://www.accessexcellence.com/WN/SUA05/ychrom.php
"We hope to be able to confirm an African origin by looking at another segment of the Y chromosome that is mutating slightly faster than our original segment, which could reveal subtle regional genetic differences," he said."Your link from the opening post was an accurate reflection of population movement. I believe it is premature to use it as a reflection on the number of generations since the common male ancestor, given the uncertainties surrounding the variations detected and the uncertainties of generation times and mutation rates. Mutation rates are especially fickle taking into account that even lifestyle can effect germline mutation rates. The lifestyles of early man (eg Neanderthal) were vastly different. Hoping you can provide more definite information.Edited by mindspawn, : No reason given.

What nucleotide diversity would reflect a bottleneck? Have you or Jar any estimate or evidence of the type of nucleotide diversity that would reflect a bottleneck? Anything?

My bad, I should have phrased the question, what evidence would reveal a long term bottleneck 4500 years ago, considering that the number of alleles would increase over time. I agree that short term bottlenecks a few hundred years old are detected (cheetahs/bison), but how would one detect long-term bottlenecks?