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Author | Topic: Nucleotide sequence variation in ancient human mtDNA | |||||||||||||||||||||||||
derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
Being the masochist I am....
quote:You supply a link to several ~350 bp fragments of the mtDNA from several primate species, including ancient humans. quote: Lets look at position 184. The only discernible pattern at that position is that there is no pattern. Most of the sequences have a "T" at that position. Bonobo has a "C", common chimp has an "A". Feldhofer has a "C", insert has an "A". What about this distribution demonstrates non-randomness? At 223, We see an assortment of Ts and Cs. What of it? Seems NRM's evidence is as arbitrary as its definition .quote: According to your simplistic 'analysis' of a ~350 bp fragment of mtDNA, sure. Let us ask these questions: 1. How big is the mitochondrial genome? (ans: ~ 16,000 bp) 2. How big is the human genome? (ans. ~ 3,200,000,000 bp) 3. How much of the mtGenome has been used in phylogenetic analyses of primates? (ans.: all of it. I just did it this afternoon). 4. How much of the nuclear genome has been used in such studies? (ans.: all of the single-copy genome(DNA-DNA hybridization); individual loci, on the order of 60-70 kp or more. I personally have done about ~14,000 bp) 5. What happens when much more extensive datasets are used? See, for one example: Mol Phylogenet Evol 2001 Jan;18(1):14-25 Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade. Page SL, Goodman M. Maximum-parsimony and maximum-likelihood analyses of two of the serum albumin gene's intron sequences from 24 catarrhines (17 cercopithecid and 7 hominid) and 3 platyrrhines (an outgroup to the catarrhines) yielded results on catarrhine phylogeny that are congruent with those obtained with noncoding sequences of the gamma(1)-gamma(2) globin gene genomic region, using only those flanking and intergenic gamma sequences that in their history were not involved in gene conversion. A data set that combined in a tandem alignment these two sets of noncoding DNA orthologues from the two unlinked nuclear genomic loci yielded the following confirmatory results both on the course of cladistic branchings (the divisions in a cladistic classification of higher ranking taxa into subordinate taxa) and on the ages of the taxa (each taxon representing a clade). The cercopithecid branch of catarrhines, at approximately 14 Ma (mega annum) divided into Colobini (the leaf-eating Old World monkeys) and Cercopithecini (the cheek-pouched Old World monkeys). At approximately 10-9 Ma, Colobini divided into an African clade, Colobina, and an Asian clade, Presbytina; similarly at this time level, Cercopithecini divided into Cercopithecina (the guenons, patas, and green monkeys) and Papionina. At approximately 7 Ma, Papionina divided into Macaca, Cercocebus, and Papio. At approximately 5 Ma, Cercocebus divided subgenerically into C. (Cercocebus) for terrestrial mangabeys and C. (Mandrillus) for drills and mandrills, while at approximately 4 Ma Papio divided subgenerically into P. (Locophocebus) for arboreal mangabeys, P. (Theropithecus) for gelada baboons, and P. (Papio) for hamadryas baboons. In turn, the hominid branch of catarrhines at approximately 18 Ma divided into Hylobatini (gibbons and siamangs) and Hominini; at approximately 14 Ma, Hominini divided into Pongina (orangutans) and Hominina; at approximately 7 Ma, Hominina divided into Gorilla and Homo; and at approximately 6-5 Ma, Homo divided subgenerically into H. (Homo) for humans and H. (Pan) for common and bonobo chimpanzees. Rates of noncoding DNA evolution were assessed using a data set of noncoding gamma sequence orthologues that represented 18 catarrhines, 16 platyrrhines, 3 non-anthropoid primates (2 tarsiers and 1 strepsirhine), and rabbit (as outgroup to the primates). Results obtained with this data set revealed a faster rate of nucleotide substitutions in the early primate lineage to the anthropoid (platyrrhine/catarrhine) ancestor than from that ancestor to the present. Rates were slower in catarrhines than in platyrrhines, slower in the cheek-pouched than in the leaf-eating cercopithecids, and slower yet in the hominids. On relating these results to data on brain sizes and life spans, it was suggested that life-history strategies that favor intelligence and longer life spans also select for decreases in de novo mutation rates. Germane to this discussion, I took Borger’s simplistic pseudo-analysis and used his results to see if they had merit when applied to larger datasets. One thing that can be done to test a method is to use a known, then use the same method on an unknown; or if the unknown had been tested first, use the method on a ‘known’ and see if the results have merit. In Borger’s world, a simple proportion of nucleotide substitutions in a small fragment of mtDNA is sufficient ‘evidence’ that an entire framework is falsified. Borger explains: ancient human (LM3) and modern human (CRV) demonstrate 9 nucleotides differences. LM3 has been dated at 62 Ky BP. Counting the differences between modern human and chimp demonstrates 24 differences, and that would make a common ancestor around 150 Ky before present Sounds reasonable, right? Lets set up a simple ratio that we can use to extrapolate this method’s results to other issues. 9 nucleotide changes = 62,000 years (9/62,000)so 9/62,000 = 24/x Solving for x, we get roughly 165,000 years (maybe Borger should have used that calculator after all?). So, I decided to take Borger’s results and apply to two other datasets. First, I went to Pubmed and downloaded several mtDNA sequences from the D-loop hypervariable region I. These included human samples, chimp, baboon, and Neanderthal. This dataset was similar in length to the dataset used in the Adcock paper that Borger cites. Comparing one of the human with one of the chimp sequences, I discovered a difference of 48 nucleotides (it was, afterall, the hypervariable region). This gives us the following proportion: 48 (nucleotide changes) in 150,000 years, ala Borger. We can then set up a simple equation to see if there is equivalence. Borger: 9/62,000=24/150,000 true does 9/62,000 (or 24/150,000) = 48/150,000? 9/62,000 = 48/x x= 330,666; 24/150,000 = 48/x x = 300,000 False. Gee — what could be going on? Localized fluctuations in mutation rate maybe? Ridiculously simplistic "analysis" and unwarranted extrapolation? Demonstration of the shortcomings of pontificating in areas that you have limited knowledge in? All of the above? Well, then I went ahead and downloaded the entire mtGenome for human, chimp, mouse. Using the same proportion (ala Borger), I tested it against the entire mitochondrial genome differences. The human and chimp genomes differed by 1351 bp in this alignment.Human and mouse by 4,436. The overall lengths were not the same, so I truncated the alignment to 14, 789 bp. So, what is the date inferred using the Borger method using the entire mtGenome? 24/150,000 = 1351/x x = 8,443,750 8,443,750 does not equal 150,000 There is not equivalence, Borger’s method is flawed. Just for fun, let’s see where Borger’s method places the split between mouse and human: 24/150,000 = 4436/x x = 27,725,000 mya. Fossil evidence indicates a split between Galagos and other primates at 63 million years ago. I guess all that will need changing, too. Right Pete? Adios, Scheisskopf. And this time, I really hope for good.
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
quote: Intellect and common sense are obviously not yours. All humans are animals, so all animals are human! Brilliant! Go back to your hole, Son.
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
PB:
I think Page tries to get expelled from the board, since he is loosing all discussions. But what would the board be without Page? If Page leaves the board, they'd better change their site into 'Creation versus evolutionism' It would appear that Borgers lithium is out again....
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
quote: You start off with a lie. This shold be good. By the way, Petey - if what you write is so true, why on earth did you insist that that one ~350 bp locus in the Adcock paper is somehow superior to all others? Why is the results form that locus more 'right' than any other? Do tell...quote:No, I am just trying to follow your.. "logic"... quote: No, I decided to use the same "logic" you did - that the numbers of base substitutions in a locus can be used to infer divergence times. If the ratio in one locus can be used in that way, as you did, it stands to reason that the same ratio should be applicable to the entire mt genome and with some tweaking, the nuclear genome as well. If not, then your "analysis" was worthless from the word go.quote: You really are beligerant and acting quite bizarre. If you are so concerned with function, why on earth did you make such a big deal about the nucleotide differences in the Adcock paper's locus? Can you not even remain consistent in your argument for one post?quote:Gee, surely a genetics expert like you knows all about the HV regions? The problem with hypervariability, as I am sure an expert like you must know, is that it is subject to back mutation. So it is only useful for certain timeframes. However, since you made no mention of any of this in your brilliant analysis, I did not either. I assumed you knew all about it. Guess I was wrong. quote: I don't know what "maths" are. But I was proving a point. I see such subtle things are lost on you.If there are such differences WITHIN the mt Genome, why on earth would you insist that one ~350 bp locus trumps analysis of other regions of the mt Genome or the nuclear genome as well? Someone else, Peter I think, mentioned that you seem to have this tunnel vision when discussing things. How right he is.quote: So it is NRM that causes the hypervariability in the HVRs? Intriguing... Funny - I have seen nothing about that in the literature... quote: DNA is length? What are you talking about? Do you even know? I mentioned the length of the locus I used to show that it was about the same size as the Adcock locus. Is that so terribly hard for you to get? Or are you just tossing out Red Herrings to cover your failed "analysis"?Your bizarre - and quite misplaced, not to mention totally irrelevant - strawman is duly noted. quote: My, you sure can extrapolate things that ARE NOT THERE. Must be like those mythical creatons. You just make stuff up as you see fit.What assumptions are you talking about? I extrapolated YOUR numbers and methods. I guess you are too deluded ot see even that. It is funny - you are not the first creationist to be wholly unable to see their own arguments thrown back in their face, nor are you the first to argue against it.quote:How else am I to test your methods? Are you trying to pull a switcheroo now? Yet another demonstration of your ignorance - the "assumption" of human - ape shared ancestry is warranted by many lines of evidence. Your true colors are getting brighter and brighter. Whats next? Are you going to explain to us all that only 16,000 Kinds were on the ark?quote:You are an incompetent zealot, frankly. You have decide dto totally IGNORE my solid refutation of your quackery - AGAIN. Do you really want us - well, Sonnike, at least - to believe that your extrapolation from a ~350 bp mt DNA locus is more informative, all encompassing, and trumps an analysis of the ENTIRE mitochondrial genome? Are you for real? Are you sane? I confirmed that your analysis was flawed and overly simplistic. Now, you are simply handwaving away a much, much larger analysis that cements the flaws in yours. You are a crank and a charaltan, I have little doubt of that.quote: Then how was it that you did your analysis in the first place? Creationists always like to pullout that gem when their back is against the wall.I'm eagerly awaiting the bible verses... quote:You have a strange tendency to basically make stuff up. What on earth are you talking about with this "DNA=length" crap? Do you even know? Or are you consciously making diversions? If you are so concerned about function, what is the function of the locus from the Adcock paper? And why didn't you mention it? quote: Wow, Petey. You is so smart.... You have come full circle. YOu started out sounding like a semi-rational, semi-literate 'professional' with a legitimate skepticism, now you are little more than a common gutter-cretin.Pathetic. Predictable and pathetic.quote:I should hope so. Maybe that would be better, as you clearly cannot converse in the language of science. But, for that umpteenth time, I am done with you. This really took the cake. You display in this thread nearly every underhanded, sleazy, cretin trick (with the exception of out of context quoting!). What a waste of sperm. [This message has been edited by SLPx, 01-27-2003]
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
If I did my math correctly, according to borger, Anya,
human and drosophila split some time last week....
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
quote: What is deceitful or misrepresntative about my quote of your "logic"?
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
quote:The point of satire - which a caricature is a kind of - is to have a truth behind it. Just because you are personally offended by the facts does not make them untrue. You were soundly amd repeatedly utterly refuted on that issue, yet being a creationts, you refused or were unable to see that, and so used that silly 'caricature' (which you insisted was accurate). By any defintion - excpet, apparently, yours - humans are animals. By no stretch of logic would it therefore be ratinal to claim - even iun a caricature - that therefore all animals are human. Yet you did just that to try to 'prove some point.' What point? Who knows...quote: No, it is not. Other than subjective pleas regarding appreciation of music and such, you have yet to offer anything of substance which removes Man from the Aniamla Kingdom. If you actually have something that is not based on emotional pleading and subjective assertion, I suggest you start a new thread laying it all out. Until then, I see nothing deceptive of misrepresentative about getting a fun diug now and then using your own "logic" - and yes, despite what you are claiming now, you DID present that as a 'logical' argument. ------------------"The analysis presented in this study unambiguously shows that chimpanzees are our closest relatives to the exclusion of other primates. This is an important point that cannot be discounted. Further, the functional genetic differences that are represented by nonsynonymous sites also show this relationship. The notion that the great apes form a functional and evolutionary grade is not supported by our analysis. Rather, humans and chimpanzees are a functional evolutionary clade." Page Not Found | University of Chicago
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derwood Member (Idle past 1907 days) Posts: 1457 Joined: |
Borger spins his wheels, like a good little creationist.
He offers nothing of substance, nothiung worthy of breaking my vow of tuning him out. Makes a few utterly asinine extrapolations, though. I was especially tickled by his last bizarre extrapolation - equating a waste of sperm with wishing he were dead. Only a demented megalomaniac could make so foolish an extension. I can only stomach so much nonsense, and I am getting nauseous. Bye bye Borger.
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