Nucleotide sequence variation in ancient human mtDNA

dear All,Since Dr Page wanna play a tough game, I post here the published mtDNA sequences of ancient humans.Just a moment...(Maybe somebody can fit in the figure)I claimed that the mtDNA sequences:1) demonstrate NRM,2) that according to the presented sequences human and chimp have a common ancestor 150 ky BP.Now, I invite you to take an objective look at the sequences. The presented sequences are taken from ancient homo sapiens as excavated in Australia near Lake Mungo (abbreviated LM), and from Kow Swamp (abbreviated KS).In my opinion these date demonstrate clear NRM at postion 184, 223, 278, 301, 311, and 387. In addition there are less obvious NRM present in the sequences, namely 93 and 230.Furthermore, a careful look at the 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. Easy as that, you don't even require a calculator for such analysis.
Similarly, the presented bonobo demonstrates 29 differences compared to human, and the Neandertahler (Feldhofer) demonstrates 27 differences. So, they all have a common ancestor around 150 kY before present, according to these data.Or NOT Dr PAge?best wishes,
Peter

Dear Dr Page,I quickly skimmed down your analysis. For a layman it looks like science, that's true. However, I will show the board what tricks you apply and why they are highy questionable. As promissed, my dear friend, I will beat your nonsense.You've just found a friend who will join you in all the boards you participate in See you soon, Panomo pagensis Now I go for a morning swim,Best wishes,
Peter"I like it when the objecter of Truth gets mad"

Dear Page,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 presentPage: Sounds reasonable, right? Lets set up a simple ratio that we can use to extrapolate this method’s results to other issues.PB: Here we already start to understand how much understanding Page has about genomes. He must be still under the (ancient) impression that all positions in a genome are equivalent. Well, --as is known in the 21st century-- they are not. Although, Page doesn't seem to be aware of this he is able to show some maths tricks.Page: 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?).PB: That was my claim isn't it? If you had read the article you would have known that the age was dated 62 +/- 6 Ky BP, meaning 150-170 Ky BP. You are nitpicking.Page: So, I decided to take Borger’s results and apply to two other datasets.PB: So YOU decided? Based on what assumptions? That all mtDNA regions are equivalent in (ancient) human, chimp, and Neanderthaler.Page: 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.PB: Similar in lenght? So that is what DNA is about: LENGTH. Probably in your mind DNA is only lenght, Dr Page, but in my opinion DNA is not at all about length. It is about a coded function. FUNCTION.Page: Comparing one of the human with one of the chimp sequences, I discovered a difference of 48 nucleotides (it was, afterall, the hypervariable region).PB: So, this is the region that supposed to change with the highest rate, I presume. Than it would be the best region to compare, since according to your paradigm it changes so fast since there is NO constraint on this region I presume.Page: 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.9/62,000=24/150,000 truedoes 9/62,000 (or 24/150,000) = 48/150,000?9/62,000 = 48/xx= 330,666;24/150,000 = 48/xx = 300,000False.PB: And here we see Dr Page simple assumption that all regions of the mtDNA are equivalent are completely, entirely wrong. He demonstrates that the distinct mtDNA regions are not equivalent so you can not interchange them. If you wanna say somthing on this region you also have to demonstrate this region in ancient human LM3, Dr PAge, since now all you do is comapring apples and oranges. (I know that is allowed in evolutionism, but not in maths. It is first thing you learn in maths class)Page: Gee — what could be going on?Localized fluctuations in mutation rate maybe?PB: NRM?Page: Ridiculously simplistic "analysis" and unwarranted extrapolation?PB: The only one that introduced ridiculous oversimplification assumptions on DNA is Dr Page himself. He thinks that DNA is length. Well, Dr Page, DNA is NOT about length. For you: DNA is coded information. Welcome to the 21st century.Page: Demonstration of the shortcomings of pontificating in areas that you have limited knowledge in? All of the above?PB: Shortcomings? You demonstrated again that your discipline is completely, entirely outdated. Based on completely false assumptions.Page: Well, then I went ahead and downloaded the entire mtGenome for human, chimp, mouse.PB: And here we see LIVE the biggest trick present in the evolutionary toolkit. And Page doesn't even try to obscure it. Simply assume that human, chimp and mouse have a common ancestor.DEAR PAGE, from here your analysis is completely IRRELEVANT to our discussion. I know you want to compare apples and oranges, but I think it is not allowed. Here our paradigms clash. I’ve already demonstrated that before. I demonstrated that according to the known sequences in ancient human, chimp must have a common ancestor around 150 Ky before present. You CONFIRMED that.
For the rest your analysis is based upon assumption I do not agree with, since they are not present in my paradigm.Page: 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.PB: No, Borger demonstrated your oversimplification on DNA. DNA=lenght: don't let me laugh, Page. You demonstrate that DNA regions are not equivalent and therefor cannot simply be put on a pile.Page: 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.PB: Evidence? The usual evo-gibberish you mean.Page: I guess all that will need changing, too.Right Pete?Adios, Scheisskopf.PB: If you wanna continue in German, I don’t mind, I speak and write German, too. Page: And this time, I really hope for good.PB: We will meet again, since I will beat your nonsense on all fronts.Best wishes,
Peter

Dear Sonnike,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'. Best wishes,
Peter

Dear Dr Page,Quote:
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 presentPage: Sounds reasonable, right? Lets set up a simple ratio that we can use to extrapolate this method’s results to other issues.PB: Here we already start to understand how much understanding Page has about genomes. He must be still under the (ancient) impression that all positions in a genome are equivalent. Well, --as is known in the 21st century-- they are not. Although, Page doesn't seem to be aware of this he is able to show some maths tricks.Page: You start off with a lie. This shold be good.PB: Obviously you don’t know what a lie is. With your definition of a lie, you keep ‘lying’ to me that you will never again respond to me.Page: 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:PB: I already responded top that but you choose to ignore it. Here, specially, for you again: The sequences in ancient subspecies contain more information regarding mutations that your simplistic comparison of chimp and human mtDNA. It gives us information about the rate and the position where they are introduced: in the ancient subpopulations we are able to exactly follow mutations and mutation rates over a more accurate time scale. That the data don't fit with your evolutionary view is tale telling: evolutionism's conclusions based on comparison BETWEEN species are wrong.
Now we know that all info for variation is already preexistent in the genome we know that Darwin made an unwarranted extrapolation with respect to microbe to man evolution. If you take the contemporary observation on variation preexisting in the genomes as the mechanism that drives evolution from microbe to man (as Darwin did), than you talk about a mechanistically determined evolution, in other words creation.Page: 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?).PB: That was my claim isn't it? If you had read the article you would have known that the age was dated 62 +/- 6 Ky BP, meaning 150-170 Ky BP. You are nitpicking.Page: No, I am just trying to follow your.. "logic"...PB: No, even a child can see that you are nitpicking.quote:
Page: So, I decided to take Borger’s results and apply to two other datasets.PB: So YOU decided? Based on what assumptions? That all mtDNA regions are equivalent in (ancient) human, chimp, and Neanderthaler.Page: 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.PB: No Page, you don’t use the same logics. If you had used my logics than you had compared the SAME regions in human, ancient human, chimp, Neanderthaler and bobobo. Now, all you did was comparing apples and oranges, assuming that they are equal. They are not equal Page, and that is what you demonstrate below.quote:
Page: 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.PB: Similar in lenght? So that is what DNA is about: LENGTH. Probably in your mind DNA is only lenght, Dr Page, but in my opinion DNA is not at all about length. It is about a coded function. FUNCTION.Page: You really are beligerant and acting quite bizarre.PB: Why do you think I am belligerent? Because you are such a nice and charming guy? Or because I am dumb and dumber, a moron, schizoid, a fool, etcetera, etcetera. I am gonna show the board that evolutionism is false, and that you —-as a PhD-ed evolutionist-- are not able to defend it.Page: 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?PB: Because these sequences give us much more information.quote:Page: Comparing one of the human with one of the chimp sequences, I discovered a difference of 48 nucleotides (it was, afterall, the hypervariable region).PB: So, this is the region that supposed to change with the highest rate, I presume. Than it would be the best region to compare, since according to your paradigm it changes so fast since there is NO constraint on this region I presume.Page: 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.PB: ‘Back-mutations’ is nothing but a meaningless evo-word. If they exist at all, they seem to be introduced over and over on the same spot, and that makes me remind of something: NRM.quote:
Page: 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.
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.PB: And here we see Dr Page simple assumption that all regions of the mtDNA are equivalent are completely, entirely wrong. He demonstrates that the distinct mtDNA regions are not equivalent so you can not interchange them. If you wanna say somthing on this region you also have to demonstrate this region in ancient human LM3, Dr PAge, since now all you do is comapring apples and oranges. (I know that is allowed in evolutionism, but not in maths. It is first thing you learn in maths class)Page: I don't know what "maths" are.PB: Yes, that’s obvious (open goal, Page). Page: 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?PB: Let me once more reiterate:
The sequences in ancient subspecies contain more information regarding mutations that your simplistic comparison of chimp and human mtDNA. It gives us information about the rate and the position where they are introduced: in the ancient subpopulations we are able to exactly follow mutations and mutation rates over a more accurate time scale. That the data don't fit with your evolutionary view is tale telling: evolutionism's conclusions based on comparison BETWEEN species are wrong.Page: Someone else, Peter I think, mentioned that you seem to have this tunnel vision when discussing things. How right he is.PB: My tunnel vision? You mean your preconceived ‘NDT is all there is’, and ‘evolution did it’.quote:
Page: Gee — what could be going on?
Localized fluctuations in mutation rate maybe?PB: NRM?Page: So it is NRM that causes the hypervariability in the HVRs? Intriguing... Funny - I have seen nothing about that in the literature...PB: No? Better do a more extensive search. Besides, ‘localized fluctuations’ is another meaningless word. What do you think is the mechanism behind such fluctuations? No Mechanism involved, I gues? Well, Page even a hotspot has an underlying mechanism. Nothing on this earth just simply happens. Ever heard of laws of nature?quote:
Page: Ridiculously simplistic "analysis" and unwarranted extrapolation?PB: The only one that introduced ridiculous oversimplification assumptions on DNA is Dr Page himself. He thinks that DNA is length. Well, Dr Page, DNA is NOT about length. For you: DNA is coded information. Welcome to the 21st century.Page: 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.PB: It is very clear that you compared the two unequal stretches of DNA because they are of the same length. Next you demonstrated mathematically that they were not equal. It demonstrates the evolutionary method of analysis to be invalid.quote:
Page: Demonstration of the shortcomings of pontificating in areas that you have limited knowledge in? All of the above?
PB: Shortcomings? You demonstrated again that your discipline is completely, entirely outdated. Based on completely false assumptions.Page: My, you sure can extrapolate things that ARE NOT THERE.PB: That is allowed in evo-biology, isn’t it? So, what is your objection? You even compare thing that are not even equivalent. I’d call that POOR science.Page: 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.PB: I already noticed that you are VERY, VERY, VERY good in finding straw men. Maybe you could point out, where I used creatons in our discussions.Page: 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.PB: I do not even see a argument here to respond to. Your replies are getting weaker and weaker.quote:
Page: Well, then I went ahead and downloaded the entire mtGenome for human, chimp, mouse.PB: And here we see LIVE the biggest trick present in the evolutionary toolkit. And Page doesn't even try to obscure it. Simply assume that human, chimp and mouse have a common ancestor.Page: How else am I to test your methods? Are you trying to pull a switcheroo now?PB: By looking at SUBspecies and by comparing EQUIVALENT regions of course. How many times do I have to spell this out?Page: Yet another demonstration of your ignorance - the "assumption" of human - ape shared ancestry is warranted by many lines of evidence.PB: There is NOT such evidence. There is inferrence from soem data, that can easily be interpreted differently.Page: Your true colors are getting brighter and brighter.PB: Red, white and blue?Page: Whats next? Are you going to explain to us all that only 16,000 Kinds were on the ark?PB: Ark? Where do you get the ark from? Our discussion was on the ancient mtDNAs. What kind of debating tactic is this? Distraction? Off on a tangent?quote:
DEAR PAGE, from here your analysis is completely IRRELEVANT to our discussion. I know you want to compare apples and oranges, but I think it is not allowed. Here our paradigms clash. I’ve already demonstrated that before. I demonstrated that according to the known sequences in ancient human, chimp must have a common ancestor around 150 Ky before present. You CONFIRMED that.Page: You are an incompetent zealot, frankly.PB: I can add another word to Page’s coarse language dictionary: incompetent zealot. Well Page, your level is declining, going downhill by the second. Your credibility what was left of it has gone.Page: You have decided to totally IGNORE my solid refutation of your quackery - AGAIN.PB: No, Page I’ve just demonstrated that molecular evolutionary biology is founded upon POOR SCIENCE. You wanna keep it like that, I know, and that’s why outsiders are not ALLOWED to say something about evolutionism.Page: 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?PB: As mentioned before but you chose to ignore:
The sequences in ancient subspecies contain more information regarding mutations that your simplistic comparison of chimp and human mtDNA. It gives us information about the rate and the position where they are introduced: in the ancient subpopulations we are able to exactly follow mutations and mutation rates over a more accurate time scale. That the data don't fit with your evolutionary view is tale telling: evolutionism's conclusions based on comparison BETWEEN species are wrong.Page: 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.PB: No, Page, you demonstrated that the methods you apply are NOT valid. You are free to ignore that.Page: You are a crank and a charaltan, I have little doubt of that.PB: Although you are not able to spell charlatan correctly, I will add it to your coarse language dictionary.quote:
PB: For the rest your analysis is based upon assumption I do not agree with, since they are not present in my paradigm.Page: Then how was it that you did your analysis in the first place?PB: I demonstrated the analysis in ancient human mtDNA. It is an INTRAspecies comparison and completely valid, since it accurately demonstraes what is going on WITHIN species. It tells me that your extrapolations are NOT valid.Page: Creationists always like to pullout that gem when their back is against the wall. I'm eagerly awaiting the bible verses...PB: Back against the wall? Get real, Page; everyone on the board can see from your intonation that you are the one that is cornered.quote:
Page: 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.PB: No, Borger demonstrated your oversimplification on DNA. DNA=lenght: don't let me laugh, Page. You demonstrate that DNA regions are not equivalent and therefore cannot simply be put on a pile.Page: 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?PB: I simply quoted you. You think DNA is about length; otherwise you wouldn’t have performed this analysis in public. Once more for you: DNA is coded (functional) information. If you are going to compare DNA and make proper conclusions you better analyze equal regions.Page: 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?PB: If you don’t know the function of a region and you wanna make an analysis better be sure that you compare the same regions. Otherwise you will introduce unknown artifacts. Taking that upfront in account is called: Science.quote:
Page: 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.PB: Evidence? The usual evo-gibberish you mean.Wow, Petey. You is so smart....PN: Thanks, at last a friendly word Page: 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.PB: I meant, the usual non-scientific comparison of unequal things.Page: Predictable and pathetic.PB: If it were so predictable why did you show this analysis the way you did? I could point out all your tricks in public.quote:
Page: I guess all that will need changing, too.Right Pete?
Adios, Scheisskopf.PB: If you wanna continue in German, I don’t mind, I speak and write German, too.Page: 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.PB: Than, for the umpteenth time you ‘lie’. And if anybody can do a scientific discussion it’s me, NOT you. As proven on this board (even in this letter).Page: This really took the cake. You display in this thread nearly every underhanded, sleazy, cretin trick (with the exception of out of context quoting!).PB: Point them out. I will respond scientifically, as usual.Page: What a waste of sperm.PB: You’re to kind by wishing me dead. (Is this really you Page?)Best wishes,
Peter

dear Page,In response to my excellent scientific rebuttal of his mail Page continues:--------------------------------------------------------------------------------
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.Borger says:I will miss Page. I really loved our little discussion.Anybody to take it over from Page?Otherwise, it can be concluded that evolutionary theory can NOT even be defended by PhD-ed evolutionary biologists.Propagating the theory in its current form is NON-SCIENCE. QED.best wishes,
Peter

Peter,P: In your world view do humans and chimps have a common
ancestor?PB: Both human and man have common ancestors. Man has the original human MPG ancestor, chimp have the original chimp MPG ancestor.P: If there is no common ancestor what was there, and how long ago?PB: GUToB point 5.P: Do you accept speciation as occurring?PB: MPG has plenty of room for subspeciation. For instance, the famous Darwin finches are still able to interbreed and would classically have to be defined as one species (Nature/Science?, last year? I have the reference somewhere. I will look into it). Wallibi's? Probably one diverging MPG. Stone corals? One interchanging MPG. Bacteria? Probably one/few interchanging MPG?My guess would be that to define borders for MPGs extensive research is required.Best wishes,
Peter

Dear Peter,Concerning your questions: Go sit in a bus in a metropolitan city and look around you. Human MPG.Best wishes,
Peter

Dear Andya,AP: Please. As far as I know, even Michael Behe acknowledges common ancestry.PB: Behe is a catholic, I am not a catholic. As mentioned, even if the pope agrees on evolution, I wouldn't for scientific reasons.best wishes,
Peter

Dear Andya,You say:
Please answer my question on archetypes.I say:
To everything there is a season. A time to ask and a time to aswer.In the meantime you could ponder the questions yourself and provide a possible explanation from the GUToB. Then I will think about it. Of course, I will try and address your question. But not now.Best wishes,
Peter