The ‘founder effect’ for prehistoric human migration, colonisation and evolutionary descendence

1 Aug

My conclusion on the evidence submitted thus far is that Jokodo did not provide us with convincing reasons, given what Biologists know about how mutations take place in reality and how natural selection is supposed to have acted upon it in human history, that mitochondrial DNA and nuclear DNA generate a theoretical mechanism-based framework for designing genetic clocks that can reliably be used as models for ascertaining when prehistoric migration, colonisation and lineage descendance of humans took place over the past 2 million years through the so-called ‘founder effect’. Until such evidence is forthcoming the circumstantial evidence that East Asian Homo erectus survived and led to the modern Han Chinese population cannot be dismissed – this also despite the lack of the discovery of human fossils in China during 100,000-40,000 years ago that some might cite as evidence that an extinction of all existing humans had taken place around 100,000 years ago.

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50 Responses to “The ‘founder effect’ for prehistoric human migration, colonisation and evolutionary descendence”

  1. Jokodo August 1, 2012 at 12:41 pm #

    “… the circumstantial evidence that East Asian Homo erectus survived and led to the modern Han Chinese population…” – such as?

    I’m not a native speaker of English, but as far as I know “dismissing” implies that something has been presented. And, no, “may gut feeling says that X” doesn’t count as evidence for X, circumstantial or otherwise.

  2. shantanup August 1, 2012 at 1:49 pm #

    Ask yourself this: would you have been able to do any better had you been a native speaker of English?

  3. Jokodo August 1, 2012 at 2:00 pm #

    I’m not the one who has failed to present a single coherent argument for his main claim for 17 blog posts straight (+discussion in comments), so I guess the answer is “no”.

    • shantanup August 1, 2012 at 2:27 pm #

      Back there at your 12.41 pm post, you seemed not to know what I had cited as my ”circumstantial evidence that East Asian Homo erectus survived and led to the modern Han Chinese population”. Have you now given further consideration that I have in fact presented ample coherent arguments for my assertion from the very beginning of this blog?

      • Jokodo August 1, 2012 at 2:44 pm #

        Could you repeat one of your ample coherent arguments, my memory seems to be failing me.

        What I do remember is stuff like “but they’re so much more docile, that can’t have arisen in 50,000 years”, which is not a coherent argument (not even a coherent claim since you haven’t really clarified what docility is supposed to mean in this context, or how it is to be measured). A coherent argument along these lines would have something like the following structure:

        1) clarify what you mean with docility.
        2) provide reason to believe that it is a biological rather than a cultural measure.
        3) provide a way to quantify (the biological component of) docility.
        4) provide a reasoned estimate for how much difference in docility can be realistically expected to arise over a timeframe of 50,000 years, as measured by (3).
        5) measure the actual observed difference in (the biological component of) docility between extant populations, using the same measure.

        Only *after* you’ve done all of this, and only *if* you’ve found that the measured differences in docility between different extant populations far exceed the degree of difference that can be expected to arise over 50,000 years do you have an argument that humans must have started to diverge earlier than the out-of-Africa hypothesis suggests. Same goes for all your other would-be arguments. Without that, you’re not making an argument when you say that the differences seem to you to exceed what you would expect to accumulate over 50,000 years, you’re at best stating your gut feelings, and have no more right to be taken serious than someone whose gut feeling says that the Chinese are _so_different_ they must be from a different planet. You would probably find that claim ridiculous too, but you have not given more reason to trust your gut feeling that the differences are so big that they warrant assuming a divergence going back two million years despite the evidence than he has given to trust his gut feeling that different populations are from different planets.

  4. shantanup August 1, 2012 at 3:13 pm #

    I do not wish to add to what I wrote earlier since you will only find the argumentation semantic:
    https://dispersalofhumanityfromhomoegaster.wordpress.com/2012/07/28/species-and-speciation-in-human-evolution/#respond

    • Jokodo August 1, 2012 at 3:28 pm #

      Exactly where in that post do you (a) quantify the differences between extant populations, (b) give an estimate for what you think is a plausible level of differences to arise within 50,000 years, and motivate your estimate, such as to (c) compare the two values?

      If *that* post is your single best example of a coherent argument you believe you have given in this blog, I can safely rest my case.

      • Jokodo August 1, 2012 at 3:33 pm #

        In other word, that post *at*best* provides an argument that, *if* it turns out that East Asians are the direct descendents of Asian homo erectus, we may have to reconsider our classification of homo fossils into different species (h. neanderthalensis, h. erectus, h. floresiensis, h. heidelbergensis, etc.) and/or generally our definition of species/subspecies, but it does nothing to motivate that premise.

      • shantanup August 1, 2012 at 3:34 pm #

        We will have to wait for someone-else to come along and ratify ‘the founder effect’ scientifically then.

  5. Jokodo August 1, 2012 at 3:42 pm #

    “We will have to wait for someone-else to come along and ratify ‘the founder effect’ scientifically then.” Whatever that’s supposed to mean.

    In the meantime, you could start with “(a) quantify[ing] the differences between extant populations, (b) giv[ing] an estimate for what you think is a plausible level of differences to arise within 50,000 years, and motivat[ing] your estimate, such as to (c) compar[ing] the two values” – what you should have done in post #1 of this blog, and without which nothing you say amounts to an argument.

    • shantanup August 1, 2012 at 3:45 pm #

      And I thought back there you have rested your case finally.

      • Jokodo August 1, 2012 at 3:51 pm #

        I’m feel no need to provide any new arguments since you still haven’t made a case for your claims in the first place. I preserve the right to keep reminding you of this state of affairs. So, when will you “(a) quantify the differences between extant populations, (b) give an estimate for what you think is a plausible level of differences to arise within 50,000 years, and motivate your estimate, such as to (c) compare the two values?” Then, and only then, you *might* have an argument.

  6. shantanup August 1, 2012 at 3:57 pm #

    Do you still believe that my thoughts are the result of a ‘Revelation’, or were the result of smoking some kind of dope that you wanted me to provide to you?

    • Jokodo August 1, 2012 at 4:26 pm #

      In case you missed the sarcasm, I never believed that your thoughts were the results of Revelation. I was trying to express my dismay at your style of argumentation – expecting everybody to take your claims at face value without ever providing rational reasons, *as*if* you knew that stuff from a higher source. That hasn’t changed, as far as I can see.

      • shantanup August 1, 2012 at 4:37 pm #

        So you believe that there exists a higher source?

  7. Jokodo August 1, 2012 at 4:46 pm #

    Not what I’m saying. I’m saying that *your* rhetorics indicate that *you* seem to believe that you’re in touch with a higher source that is reveiling The Undiluted Truth to you personally, and thus not required to state the reasons for your claims unlike the rest of us mere mortals. That’s how your constistent refusal to provide any reasons (other that what could most favourably be called your gut feeling) for any of your claims comes across. Wheter or not there *is* a higher source is rather irrelevant to this point of mine – even if there were, we’d have no reason to believe that he/she/it has chosen you as its channel of communication with humanity.

    • shantanup August 1, 2012 at 4:53 pm #

      And it did not occur to you that my ‘rhetorics’ are the result of 35+ years of painstaking research in the Biological Sciences, so that I do not have to look up things like you have just now (3.43 pm in ‘what does the genetic evidence say’ thread) agreed you need to do in order to be able to post such as to try and save your face in forums and other internet sites?

      • Jokodo August 1, 2012 at 5:12 pm #

        I don’t know what you did in those 35 years, or which areas of “the Biological Sciences” you researched, painstakingly or otherwise, but with the kind of basic errors that even a moderately interested laymen can easily spot (and I am a bit more than an interested layman, coming from a neighbouring discipline and having been seriously considered for positions which were meant to be filled with a biologist) which you’ve committed on this blog and elsewhere, it obviously doesn’t qualify you to proclaim Truths about an area such as human genetics.

        Examples? Your equivocation between the concept of “mitochondrial Eve” and an ancestral population, when you claimed that it was a problem for the out-of-Africa hypothesis that the timeframes don’t coincide; your expectation that mitochondrial Eve and Y-chromosomal Adam lived at the same time; your consistent refusal to look at the probability-theoretic underpinnings of genetic drift; your consistent refusal to quantify the alleged differences between extant populations and compare them with what might be a reasonable amount of differences to arise within a few tens of thousands of years.

        Maybe you should look up things before making claims a bit more often. It’s not a sign of ignorance, it’s a sign of caring about whether what you claim actually has any chance of being true.

  8. shantanup August 1, 2012 at 5:31 pm #

    You are indeed a very sick human being and should see a doctor about your annoying addiction that you wrote to me about on July 26, 2012 at 8:04 pm in the thread ‘Has the hypothesis suggested in this blog been reported earlier’.

  9. Jokodo August 1, 2012 at 5:44 pm #

    I think it would help the quality of this blog if you refrained from ad hominems and used your time to finally provide actual arguments for your claims. Proclaiming your opinion, based on your gut feeling, some outdated data, and a number of assumptions you refuse to make explicit, as fact isn’t how science works, as you should no. Referencing earlier research (i.e. looking up stuff), whether you agree with the results or not, and making explicit what you think the results are unreliable if its the latter, is how science works (and the biological sciences and elsewhere), as you should know. If you want a quality discussion about a scientific topic on this blog, that’s where you should start.

    Of course, this is your blog, and if you want it to stay crappy, that’s entirely your decision.

    • shantanup August 1, 2012 at 6:12 pm #

      Wikipedia states that ”an ad hominem (Latin for “to the man”), short for argumentum ad hominem, is an attempt to negate the truth of a claim by pointing out a negative characteristic or belief of the person supporting it. Ad hominem reasoning is normally described as a logical fallacy, more precisely an informal fallacy and an irrelevance”. http://en.wikipedia.org/wiki/Ad_hominem
      I referred you to your own comment. Can you explain why it is ‘ad hominem’ that I said you should see a doctor about your problem of posting incessantly in this blogsite despite a number of attempts I made to stop you for you were posting rubbish?

  10. Jokodo August 1, 2012 at 6:25 pm #

    So you’ve decided not to discuss the issue of human origins and not to give any arguments for your view that modern East Asians are the descendents of Asian homo erectus which you keep claiming without providing reason?

    Fine with me. I’m not going to discuss your or my persona on this blog. Whether or not I need a doctor is a perfect irrelevance when discussing human origins, and calling my contributions “rubbish” because I’m asking you to make your premises explicit isn’t a good sign that you want to discuss the actual content.

    • shantanup August 1, 2012 at 6:50 pm #

      I am prepared to discuss the issues with someone who knows the subject matter or I will be wasting my precious time. You say you are not a Biologist or a Geneticist but indicate that you have some kind of qualifications in an adjoining subject. Going by your earlier interest in Genetic Drift that we discussed at FRDB which you will recall you abandoned when my evolutionary biological facts were coming out, you cannot be mathematician/statistician either. But it is possible that you have done some computer modelling work in these fields and started reading up about genetics from the internet at a superficial level. Since you post anonymously I have no way of checking out your credentials. So can you spell out precisely which discipline you are a specialist in?

      • Jokodo August 2, 2012 at 8:27 am #

        Suffice it to say that until such time as you choose to actually look at the evidence, and specifically point to where, and why, you think it’s flawed, my expertise is sufficient to tell you that handwaving and ignoring results because they contradict your gut feeling without even trying to point to where you think the logic leading to those results may be flawed does not make an argument. Anybody who has an idea of how science work, whatever discipline they’re hailing from, is qualified to tell you that much. If and when you start to actually discuss the fine details of the analysis and make objections that demonstrate that you’ve understood the workings of the arguments being made, and point to specific assumptions which you think you’ve found to be flawed based on such an understanding, then it may require a geneticist to judge whether your objections have any merit. You haven’t even started to go there.

        (Incidentally, no, again. I didn’t abandon that discussion because of any “evolutionary biological facts” that were “coming out”, I abandoned it because your consistent *refusal* to let facts bear on the argument made it look like a pointless waste of time.)

  11. shantanup August 2, 2012 at 1:08 pm #

    So you will not give my readers your full list of scientific publications in international refereed journals, and specifically, you will not tell us whether you have had any review articles on the ‘genetics of human origin’ published within the past 2 years?

    • Jokodo August 2, 2012 at 4:19 pm #

      As long as you’re not even trying to make an argument and plainly dismissing the scientific consensus on the subject without as much as demonstrating that you understand how that consensus was reached in the first place, it doesn’t take an expert to tell that you’re almost certainly wrong, so none of that would be relevant for this discussion.

      • shantanup August 2, 2012 at 4:50 pm #

        I am the moderator of this blogsite so I decide what is relevant and what is not. You failed to answer the direct questions posed to you in the last two comments of mine. It proves to me that you do not have the interests of the readership that this blogsite is aimed at in your dealings with me.

  12. Jokodo August 2, 2012 at 4:59 pm #

    Anyway, if you’re interested in the positions taken by the authors of recent review articles on human evolution from the perspective of genetics, couldn’t you do something crazy like *read* those papers?

    Start here: http://scholar.google.at/scholar?start=0&q=review+article+human+evolution+genetics&hl=de&as_sdt=0&as_ylo=2010

    (That is, searching Google Scholar for the following set of keywords: ‘review article human evolution genetics’, limiting the search to articles that appeared since 2010.)

    Here’s some relevant papers I found skimming the results, and I’m only using ones that are freely available online in full length:
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010284
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945812/
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2994553/
    http://www.pnas.org/content/107/17/7853.full

    None of these are perfectly on point of this discussion, but the reason for this is mainly that all of what we’re talking about is old news, so let’s drop our superfluous restriction on articles since 2010, which gives us two very relevant and freely accessible papers from 2000 and 2003 respectively – on the first page of the results:

    http://www.nature.com/ng/journal/v33/n3s/full/ng1113.html (if you only read one, read this!)
    http://server2.icav.up.pt/AP/120010/6.pdf

    I somehow doubt that you’ll actually read any of these. Last time I pointed you to a paper, it took you a week before you even had a look at it, and then you misrepresented it and came back to me with questions that were answered either in the paper itself, or where you could have simply followed up on the references provided.

    • Jokodo August 3, 2012 at 9:38 am #

      How are you getting on with the papers?

      • shantanup August 3, 2012 at 1:39 pm #

        I have made a start but am struggling to find the review sections that deal with the following problems that bother me about the standard (consensus) hypothesis:

        (1) is an assumed natural mutation rate crucial to determination of human origins in the form of the mitochondrial Eve at 200,000 years ago? If so, I would have liked to see some kind of scientific evidence for the rate that is used in the computations. The type of science that I feel is necessary is scientific observations from 20+ generations of human beings that would demonstrate the so-called natural mutation rates in mtDNA and nuclear DNA for the ova, sperm, and somatic tissues of individuals. In vitro studies on DNA maintained in culture perhaps over 10 years may yield usable figures in the absence of in vivo studies, but at this stage I need to know what has already been done in these areas.

        (2) if the founder effect states that the geographical areas of lower DNA variation (East Asia, for example) must have originated from the area of high variation (Africa), what is the basis for such an argument? We know Africa was the continent for the Apes to Humans evolution over 7 million years so the genetic variation will naturally be considerable in this continent, but how would it be possible to say that the Chinese population today derived from African ancestors is concomitantly less variable to make its presence only 40,000 years in that continent. I would like to see a review article focussing on this point.

        (3) which paper gives us the DNA-sequence of mitochondrial Eve at 200,000 ago and its geographical distribution and what does it state about the relationship of this individual to African Homo erectus.

        (4) if DNA-sequences and genes are conserved in some specific areas of the genome what is the biological process of this conservation and how does this affect the standard model for the derivation of the ancestral populations.

        Edit at 7.20 pm:
        Are you going to respond to these issues today or will you wait for my next post to do so?

  13. Jokodo August 3, 2012 at 8:04 pm #

    I’m not going to respond today because I have other thingst to do (and you have no right to give me ultimata when to respond). Will come back to this, though.

    • shantanup August 3, 2012 at 8:22 pm #

      You only have another two hours to make your comments and failing that it will be ‘Auf Wiedersehen’ because all your future comments will be trashed.

      • Jokodo August 4, 2012 at 8:55 am #

        I don’t know about you, but I have a live beyond this blog. I have a job and a kid, and currently I’m writing an abstract for a conference. You’ll have to wait a bit. This habit of yours of giving me ultimata when to respond is extremely annoying, and if this is how you react to contentful contributions, it doesn’t reflect well on your “truth-seeking”.

        Just wait a bit, will you?

      • Jokodo August 4, 2012 at 9:06 am #

        If you want to have someone whose available to extensively respond to everything your write at all times, we’ll need to talk about a salary.

  14. shantanup August 4, 2012 at 9:23 am #

    Auf Wiedersehen

  15. Jokodo August 4, 2012 at 9:46 am #

    I was going to respond more extensively, but if you’d rather have a quick and dirty response, so it be. Don’t complain about the quality, though:
    (1) ” is an assumed natural mutation rate crucial to determination of human origins in the form of the mitochondrial Eve at 200,000 years ago?” estimating mutation rates is indeed needed, and there are various ways to do this:
    a) family studies – if you compare the mitochondria of two people who are joined through their maternal great-great-great-grandmother who lived 150 years ago, you’re effectively looking at 300 years of evolution of mitochondria (150 years down one leg, and 150 years up the other leg). If you do the same trick with 100 families, you are effectively measuring 15,000 years of mitochondria evolution.
    b) reference to historical events which can be dated
    c) comparison with interspecific differences for pairs of species whose divergence can be reliably dated from the fossil record.

    “The type of science that I feel is necessary is scientific observations from 20+ generations of human beings that would demonstrate the so-called natural mutation rates in mtDNA and nuclear DNA for the ova, sperm, and somatic tissues of individuals.” – that’s what the above methods do in effect.

    If all of these methods yielded widely disparaging results, we’d have a problem. But they reconfirm each other.

    “In vitro studies on DNA maintained in culture perhaps over 10 years may yield usable figures in the absence of in vivo studies” – that would be useless – in real organisms, with their complex interactions between different molecules, there’s a ton of factors that encourage or inhibit mutations, or that lead to a repair of mutaded DNA to restore the originial version. At our current level of understanding, any in vitro model is almost certain to miss out on some of them, and we have no way to estimate by how much the rates observed in vitro will diverge from rates in the wild, or indeed in which direction.

    (2) I think this paper I linked addresses this: http://www.nature.com/ng/journal/v33/n3s/full/ng1113.html

    (3) “which paper gives us the DNA-sequence of mitochondrial Eve at 200,000” – none, and that’s the way it should be. Any paper claiming to know the exact DNA-sequence of any specific individual 200,000 years ago can be assumed to be bullshit without looking at the rest of what it says. Genetic drift is a probabilistic process: If two alleles have a distribution of 70:30, there’s (absent selection) a 70% chance that the first will come to predominate, and a 30% chance that the second will, over the course of time. The same works in reverse: If we observe a 70:30 distribution today, there’s a 70% chance that the first is the older variant and the second arose through a mutation through it, and a 30% that it was the reverse. Since we’re talking about a lot of genes and a lot of mutations, the uncertainty accumulates, and the best we can hope to state is which variant is the single most likely one to have been present originally, but the chance that it was exactly that is still rather slim.

    “and its geographical distribution” – individuals don’t have geographical distributions.

    “what does it state about the relationship of this individual to African Homo erectus.” – nothing, not least because we don’t have the latter’s genome.

    (4) “if DNA-sequences and genes are conserved in some specific areas of the genome what is the biological process of this conservation and how does this affect the standard model for the derivation of the ancestral populations.” – unsure what this means.

    • Jokodo August 4, 2012 at 10:16 am #

      Short summary: You need to learn some probability theory soonish.

      • shantanup August 4, 2012 at 12:32 pm #

        Why would I need to learn some probability theory soonish?

  16. Jokodo August 4, 2012 at 12:13 pm #

    Am I now entitled to say “if you don’t answer with a clarification of the above questions within an hour, we can conclude that you’ve realised how wrong you are and ignore any future posts”? You seem to be under the impression that this kind of ultimatum is an acceptable tactique for online discussions.

    • shantanup August 4, 2012 at 12:34 pm #

      So you have completed your extensive comprehensive response, clarifying all the questions that I have asked you concerning the standard (consensus) theory?

  17. Jokodo August 4, 2012 at 3:15 pm #

    “Why would I need to learn some probability theory soonish?”
    The questions you ask – let’s take (3): Anyone who expects that this kind of research should be able to determine a precise DNA sequence of an individual tens or hundreds of thousands of years ago, implying that if we can’t assert that, we can’t assert anything, needs an update on probability theory. If you toss a coin 1,000 times, I cannot predict whether you’ll get a head or a tail on the 345th trial. I nonetheless can reliably predict that the total number of heads will almost certainly be between 400 and 600. Or your implication that we need to observe 20+ generations unfold in real time, as if the result of that were qualitatively different from observing the *outcome* of of a known number of generations of separation

    • shantanup August 4, 2012 at 9:30 pm #

      So you cannot tell us:
      (a) What the most probable and least probable DNA-sequence portions or the most probable and least probable full DNA composition of mitochondrial and nuclear DNA are as predicted for the original Eve of 200,000 years ago by the standard (consensus) model; and
      (b) how these predicted sequences entirely rule out a possible genetic linkage of Eve with the East Asian Homo erectus?

      • Jokodo August 4, 2012 at 9:54 pm #

        (a) I guess that information could be calculated from the data; I guess nobody has done it because it would be a waste of time since the information would be rather meaningless. If you toss a coin 1,000 times, the single most probable number of heads to show up is 500, but the chance that it will be no more or less than exactly 500 is quite small, so only someone who doesn’t understand probability theory will claim to be able to predict the exact number of heads. Conversely, the chance that it will be between 400 and 600 is almost a certainty, so only someone who doesn’t understand probability theory will conclude that therefore, we don’t know anything.

        (b) What on Earth is a “linkage of mitochondrial Eve with the East Asian Homo erectus”? Why would we want to “entirely rule out” anything – you’re the one making a claim, it’s up to you to present positive evidence for it.

  18. shantanup August 4, 2012 at 10:24 pm #

    Can you describe the options-nature of this coin that you imply that the standard (consensus) model is tossing for the purposes of determining which is likely to have been the common human ancestral option and when and where in human history this ancestral option is to be located?

    • Jokodo August 4, 2012 at 11:19 pm #

      Can you repeat this question in a way that actually makes sense in light of what has been discussed?

      • shantanup August 5, 2012 at 6:40 am #

        There were several aspects to my previous comment:

        (1) You said, ‘I was going to respond more extensively, but if you’d rather have a quick and dirty response, so it be. Don’t complain about the quality, though’, and did not respond to my question of whether ‘you have completed your extensive comprehensive response, clarifying all the questions that I have asked you concerning the standard (consensus) theory’, so I was giving you another opportunity to review the entirety.

        (2) Specifically, I was examining the logic of your assertion that the mitochondrial DNA analysis for the detection of Eve can be subjected to a neat proability theory analysis for the derivation of human origins. You clearly gave the analogy of the tossing a coin 1000 times and seeing how many times a head comes up. I was therefore asking you is what is the totality of all the options that could come up when you toss the human genome coin in order for the probability theory to be based. I assumed that the entire human genome coin of 6.8 billion people was being examined by taking a random sample from this population for mitochondrial and nuclear DNA-sequence analysis, but if some other kind of coin is being tossed (only the female DNA-sequences) you still need to tell us what all the possible options are for a probability theory to be suitably based. If a coin is being tossed with unlimited and unknown DNA-sequence possibilities how can the probability of one of these option be calculated?

        (3) When I asked you about the DNA mutation rates for mitochondrial DNA and nuclear DNA, you said, ‘family studies – if you compare the mitochondria of two people who are joined through their maternal great-great-great-grandmother who lived 150 years ago, you’re effectively looking at 300 years of evolution of mitochondria (150 years down one leg, and 150 years up the other leg). If you do the same trick with 100 families, you are effectively measuring 15,000 years of mitochondria evolution’. Are you saying that examining the structure and biochemical functions of the mitochondria gives us the same answer on conservation and mutation as given by an examination of the mitochondrial DNA-sequence so that this DNA is entirely connected to the functioning of the mitochondria? If so, on what biological evidence do you base this assumption? Thus, I am not clear on whether by family studies you meant variations in mitochondrial DNA rather then the mitochodria as a whole as you words showed. This needs clarification.

        (4) What does the standard (consensus) model say to the question why humans waited from 200,000 years ago that Eve is known to have existed to only 65,000-70,000 years ago before migrating out of Africa?

        In summary, as I understand your presentation, you are now using the word ‘Genetic Drift’ to characterise the entire process of this human origins analysis. Please bear in mind that the subject of this blog-post requires you to clearly expose the nature of this genetic clock in a way that demonstrates that the method of computation is not grossly flawed in conception for the use of natural mutation rates for specific genetic markers among the current world population (and b and c in your 9.46 am 4 August post) to generate the options that will then be subjected to probability theory analysis to arrrive at the timing of the last common human ancestor, which my hypothesis states was a Homo ergaster of 2 million years ago that bifurcated into the Homo sapiens and Homo erectus lines (with the latter migrating to East Asia) but which the standard (consensus) hypothesis says was a Homo sapiens of only 200,000 thousand years ago that overran all existing human species through competition and annihilation rather than through genetic assimilation.

  19. Jokodo August 5, 2012 at 10:53 am #

    (1) I did unintendedly end up giving a pretty long and complete, reply, didn’t I?
    (2) I don’t understand what you’re getting at. What genomics does is look at the patterns of genetic variation and calculate how likely a pattern like the one observed is to arise under a range of different scenarios. Turns out that the pattern observed is what we’d expect under a recent immigration out of Africa, and extremely unlikely under your scenario. The total number of possibilities is irrelevant to that. I don’t need to ennumerate all possible sequences of heads and tails to tell you the probability of the total number of heads to be between 400 and 600 on 1,000 trials, there are formula to calculate these probabilities directly.
    (3) Of course I was talking about mitochondrial DNA. Context!
    (4) Why is for theologists. Anyway, what does your “model” say on why humans, after hanging in Asia for ~1,500,000 years, waited until 50,000/13,000 years ago before migrating to Australia/the Americas? If that’s supposed to be a problem for the out-of-Africa hypothesis, it’s an even bigger problem for you.
    (“summary”) It doesn’t actually matter how large the role of drift vs. selection has been in bringing about current variation – since the genetic clocks aren’t based on lab studies but on actual observations, whatever the relative impact of selection, it’s part of what has been measured all along. If selection has a stronger role, reducing variation, this will be true on the timescales of thousands of years (historical reference points) or millions of years (interspecific comparisons) as much as on the timescales of tens or hundres of thousands of years, so the observed rates that are used to set the molecular clocks implicitly take this effect into account. What you’re essentially claiming is that they fail at a tens to hundreds of thousands of years timescale despite being verified for both shorter *and* longer timescales. That’s like saying “it may well be true that you can walk 500 meters in just over 5 minutes, and 30km in a day, with extensive breaks in between, but this doesn’t imply that you can walk 10km in a few hours.” See how ridiculous that is?

    • shantanup August 5, 2012 at 11:58 am #

      We are getting there but we are not in full control of the facts yet.

      Let us start with how many different samples of what biological tissue or fluid were taken from individuals worldwide by the standard consensus study; how did the sampling method used ensure that sample number was representative of the entire 6.8 billion population (that is the total world population at the time of the study); and how many different ‘patterns’ of genetic variations in the DNA were identified by the study?

      • Jokodo August 5, 2012 at 1:28 pm #

        “how many different samples” – that’s right there in the papers.
        “of what biological tissue or fluid” – that may be there as well, but it’s irrelevant.

        You won’t get around reading the studies if you’re interested in what experts say and how they came to their conclusions. I can’t take that burden from you.

  20. shantanup August 5, 2012 at 9:06 pm #

    Good luck with your abstract for the conference.

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