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Re: [AAT] Re: Bonobo Genome Completed

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  • Jack Barnes
    Rob, The genetic record actually fits perfectly with a non-african origin for Homo Erectus and it explains the lack of the retroviral record in Homo and why we
    Message 1 of 111 , Jul 9, 2012

      The genetic record actually fits perfectly with a non-african origin for
      Homo Erectus and it explains the lack of the retroviral record in Homo and
      why we are morphologically closer to Orangutan than the chimpanzee. See
      these slides from the Hammer lab which traced the point of origin of the
      human genome. Our oldest genes are from Asia not Africa. Before 2.4
      million years ago there is a complete blank slate. (see attached).

      Also Humans show signs of Neoteny, hairlessness, shorter arms... We are
      without a doubt in the process of self-domestication, just like the dog to
      the wolf. That explains why all 7 billion humans have less genetic
      diversity than two chimps from the same troupe in Africa.

      You must be referring to the genes expected on the RAR replacement model.
      Modern Human genes come from Africa but they are very recent indeed. 500k
      to 1.5 million years old. So homo erectus arrived without any doubt in
      Africa 1.5 million years ago.

      [image: Inline image 1]

      On Sun, Jul 8, 2012 at 9:23 PM, Rob Dudman <ausell@...> wrote:

      > **
      > Hello Bill.....
      > >
      > > Lineage-Specific Expansions of Retroviral Insertions within the
      > > Genomes of African Great Apes but Not Humans and Orangutans
      > >
      > >
      > http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0030110
      > >
      > > (they appear to be saying-that PTERV1 - was unusual)
      > >
      > It's good to be able to agree with them...if most RVs go back to more
      > than 25 Mya, then the PTERV1 at 3-4 Mya is indeed unusual, but it's not
      > unique - there's also a baboon type-C and a colobus RV to take into
      > account. Here at least it's acknowledged that it's unlikely that H. once
      > had the markers which have since been deleted and this removes one line
      > of special pleading that I've come across.
      > Whenever I come across this issue, the discussion is always about the
      > PTERV1 as if Todaro's work simply doesn't exist...where almost any
      > information at all is available on the internet, the one thing that seems
      > to
      > be missing (other than behind Nature's paywall), is Todaro's paper on the
      > baboon type-C RV. Why this should be is a puzzle to me, after all the paper
      > was published over three decades ago and it's hardly a matter of anyone's
      > national security. And it's not as though Todaro is a nonentity....he's a
      > leading researcher in the genetics of cancer and AIDS.
      > Having just completed yet another unsuccessful web-search for the Todaro
      > paper, I'll quote from the copy Elaine sent to me a few years ago....
      > 'Cell-culture studies show, for example, that cells from related African
      > primates resist infections by the baboon virus, while the Asian primate
      > cells are sensitive to baboon viral infections. Similarly the domestic cat
      > and members of the Felis species from Africa are resistant to viral
      > infection, while members of the Felis species from Southeast Asia or the
      > New World are susceptible. This again argues that the genes which provide
      > resistance against baboon viruses have had a selective advantage in the
      > African environment. Humans clearly do not have such genes, while the
      > chimpanzee, gorilla, colobus monkey, and even prosimians, such as the
      > gallago and bush baby, do have these gene sequences.'
      > And this carefully worded warning against special pleading...
      > 'As I see it, one of our major functions in this area of research is to
      > act
      > as historians - to report what actually happened rather than what we
      > would have liked to happen. The basic assumption of the classical
      > field of anthropology is that a record of our history as a species may
      > possibly be buried in the ground. Even though it is widely scattered and
      > one can only look in certain places, if one is skillful enough, or
      > fortunate
      > enough, to find the right pieces, one will be able to put together a
      > plausible
      > solution. But one still would not know if it is correct. I would suggest
      > a complimentary approach; that there is in fact a record of our history,
      > however tortured and tortuous, that is recorded in all of us in our genes
      > and we are beginning to "read" that history. I have described one set of
      > genes, and would expect there are others, that give information about
      > geographic origins.'
      > 'Evidence Using Viral Gene Sequences Suggesting an Asian Origin of Man'
      > By Todaro, G.
      > Over thirty years later the discovery of the missing PTERV1 markers
      > emphatically corroborated Todaro's work and supported his comments
      > about genes giving us a record of our species with regard to geographic
      > origins. Yet the work by Yohn et al. is treated as a one-off hitch to the
      > A'pith Descent theory that can be waved away with special pleading. If
      > Todaro's work can't be refuted, then it's best to ignore it....this is
      > simply appalling science.
      > >
      > >> It's known that African primates got the RVs because there's genetic
      > >> evidence that this was the case, but the idea that nonAfrican primates
      > >> 'evolved resistance' to all the RVs seems an odd suggestion...they'd
      > have
      > >> needed to get the bloomin' RVs in order to adapt a resistance and if
      > this
      > >> was the case they'd have the markers. The obvious reason why Asian
      > primates
      > >> didn't get the infections is simply that the infections didn't reach
      > Asia.
      > >> In fact it's more than just obvious, it's whacking them over the noggin
      > with
      > >> a sledgehammer!
      > >
      > > That may not be the case, as in rereading their paper; I noted they
      > > mention the macaques (Asian) could have been infected outside of
      > > Africa, possibly from a reservoir of the RV in Asia. (they did so
      > > at a much later date than the ancestor of the extant chimpanzee in
      > > Africa, which would be an argument in favour of there being a
      > > reservoir for this particular RV ).
      > >
      > > [quote]
      > >
      > > "Furthermore, both Asian (macaque) and African (baboon) Old World
      > > monkeys show evidence of PTERV1 proviral integrations less than 2
      > > million years ago, indicating that the exogenous source virus is
      > > either endemic to both continents or that ancestral populations
      > > frequented both continents."
      > >
      > The baboon is an exclusively African primate;
      > The macaque is found in both Africa and Asia;
      > Both have the markers for the PTERV1;
      > No other Asian primates have the markers.
      > To conclude from these four premises that there was a PTERV1
      > 'reservoir' in Asia that then only infected macaques, would result in a
      > failure at a first-year undergraduate level in Logic. They might just
      > sneek
      > through with a conditional pass for mentioning the most probable
      > situation...ancestral populations of macaques frequented both
      > continents. If it was an undergraduate course in the Philosophy of
      > Science, then even this mention wouldn't have saved them from a Fail
      > (or just being shown the door). It's simply atrocious reasoning.
      > D'you suppose that they think the infected Asian macaques then
      > migrated to Africa and once there (on the Barbary Coast) infected
      > only baboons? If it hadn't come from a scientific paper published in
      > a peer-reviewed journal, I'd think that someone was pulling my leg!
      > >
      > >>> '....While geographic isolation of the African and Asian ape
      > >>> lineages during the Miocene might account for part of this difference,
      > >>> the ancestral habitat of early hominids is generally thought to have
      > >>> overlapped, in part, with the African apes.'
      > >>
      > >> It's broadly worded and this allows maximum ambiguity, but it remains
      > >> vacuous. The RV evidence argues against what is 'generally thought'
      > about
      > >> the early habitat of H., so to counter this with 'it's generally
      > thought'
      > >> does no more than ignore the RV evidence. This low standard of argument
      > in a
      > >> scientific paper is very disappointing and it's little wonder that many
      > in
      > >> the 'hard' sciences look down their noses at paleoanthropology. This
      > quality
      > >> of argument in physics or chemistry would be laughable.
      > >
      > > Yep, paleoanthropology has not earned itself a good reputation...
      > > probably as a result of too many tv and books deals being signed
      > > the moment the `dig-up' a new fossil. Though it should be said there
      > > are paleoanthropologists who do the science - before releasing news
      > > of their discovery, like those involved with the Ardi.
      > >
      > Thar's gold for the retirement fund in them thar tv and book deals! And
      > I think that if there is a place for opinionating (even when it flies in
      > the
      > face of good reasoning), then tv docos and general interest books would
      > be appropriate. The paleoanthropologists you mention must cringe when
      > their colleagues sprinkle it into papers that aspire to be scientific.
      > (Mind
      > you, in the case of popular books and tv docos by far the worst offenders
      > in terms of muddled thinking must be the cosmologists and their endless
      > references to God...Stephen Hawking even accepted a medal from the
      > Pope for providing a gap into which God could be squeezed and I'll refrain
      > from any further comment on that bit of mummery!)
      > >
      > > One possible explanation for the much later infection of the
      > > macaques and baboons, is that the RV was spread by physical
      > > contact, and the there was a `reservoir' for this particular
      > > RV on both continents...
      > >
      > > Wikipedia:
      > > Natural reservoir or nidus (the latter from the Latin word for
      > > "nest") refers to the long-term host of the pathogen of an
      > > infectious disease. It is often the case that hosts do not get
      > > the disease carried by the pathogen or it is carried as a
      > > subclinical infection and so asymptomatic and non-lethal.
      > >
      > > http://en.wikipedia.org/wiki/Natural_reservoir
      > > ______________________________________
      > >
      > Yes, this is what I understand such a 'reservoir' to be. I also assume
      > that even though they show no symptoms, the host/s of this reservoir
      > would carry the markers? So far only the Asian macaques are known
      > to carry the markers, so they must be assumed to be this reservoir..
      > special pleading by any other name smells just as sour.
      > >
      > > A later date, and there being a possible source for the RV on both
      > > continents could be problematic in the sense that early H.erectus
      > > could have been present on both Africa and Asia when the RV infected
      > > both the baboons and macaques less than two million years ago (an
      > > alternative scenario: would be to say it was the H.erectus carried
      > > the RV eastwards - and infected the macaques in Asia - these Asian
      > > H.erectus not being ancestral to modern Man, leaving no markers
      > > in the human lineage!)
      > >
      > I don't think the core issue here is what may be possible, after all,
      > special pleading relies on being possible or it's no more than an
      > ad absurdum rebuttal of the position it's supposed to support. The
      > issue here is evidence or the lack of it, not the capacity of intelligent
      > people to think up possible scenarios that would support an otherwise
      > falsified theory.
      > Given the presence of H.georg outside Africa and our lack of the RV
      > markers, the reasonable conclusion has to be that the African H.e/e
      > was a variant of a Eurasian H.e/e and the A'piths finally became extinct
      > with the demise of habilis.
      > >
      > > > > Also from rereading their paper, I am also starting to wonder if
      > PTERV1
      > > > > was spread by contact... not as we previously discussed, airborne.
      > > >
      > > > I'd be most interested to know your reasons.
      > >
      > > A contact spread of the RV. could better explain the disparity in
      > > dates between the infection that hit the ancestors of the chimpanzee
      > > some 3.Mya, and that which later hit the baboons in Africa and
      > > macaques in Asia some two million years ago or less.
      > >
      > > One possible scenario could be that some 3.5 Million years ago the
      > > ancestors of the extant chimpanzee in penetrating deeper into the
      > > west African rainforest - they encounter an old world monkey species
      > > that was effectively the RVs reservoir, in hunting, killing and eating
      > > some of those monkeys the ancestors of the extant chimpanzee
      > > sealed their own fate.
      > >
      > Do you think the same happened with Todaro's baboon type-C RV
      > which even got to African 'prosimians such as the gallago and bush baby'?
      > It's getting complicated enough when we only deal with the PTERV1, but
      > this isn't the only missing RV marker in question.
      > >
      > >> These morphological characteristics are to be expected in a human
      > ancestor,
      > >> however, they would be just as unsurprising in a species that did not
      > have
      > >> ancestral relationship with H., but evidence that some A'piths had to
      > deal
      > >> with similar selection pressures. All other things being equal, these
      > >> features would corroborate such a relationship between H. and the
      > A'piths,
      > >> but all other things are not equal..we don't have the markers.
      > >
      > > That could be the case, however no other fossils have been found from
      > > that period that could be alternatives to a'piths . even if there were
      > > any, they at that date. would themselves probably be a'pith like
      > >
      > It's certainly the case that removing the A'piths from the human story
      > leaves us with a 'gap'. But then the RV evidence as it stands dictates
      > that a 'gap' is precisely what we've got and using it as a midden is a very
      > poor way of filling it. (I put the quotes around 'gap' because this is just
      > a euphemism for lack of evidence.) Yes, our nonAfrican ancestors 3-4 Mya
      > may well have looked something like afarensis and H.georg may also have
      > looked something like afarensis. Our ancestors may have looked like Lucy's
      > twins, but they still didn't get those RVs. Who would have predicted
      > H.georg
      > at Dminisi? No-one, yet the evidence turns up.
      > >
      > >> Did H.e/e walk to Africa? Beside the RV evidence suggesting very
      > strongly
      > >> that this is precisely what they did, there's also the corroborating
      > evidence
      > >> of the Dmanisi fossils showing that a probable relative of H.e/e lived
      > >> outside Africa. The dates in this case are also contemporary with
      > African
      > >> H.e/e, but at least they didn't co-exist in the same habitat as was the
      > case
      > >> with habilis.
      > >
      > > The Dmanisi fossils are a far better candidate than those of the habilis.
      > > though it would be more an Eurasian origin for Man, rather than one
      > > originating in east Asia...
      > >
      > If I'm to be consistent I have to consider an African origin of H. as the
      > legitimate null-hypothesis and the Megalake Chad as the probable final
      > location of the H/P LCA. Because of the RV evidence I can't include the
      > A'piths in the H. line, so it seems most probable that H. emerged as a
      > distinct genus after geographically separating from P. in Africa 5-6 Mya.
      > >
      > >> A north-east route for H. would have eventually encountered the
      > mile-deep
      > >> Nile canyon and this would have turned them either north and eventually
      > back
      > >> on their previous route, or south toward A'pith country and into the
      > area of
      > >> RV infection 2 million years later, but then of course, we're back with
      > the
      > >> problem of the missing markers.
      > >
      > > Alliteratively in heading north east, they could have negotiated
      > > the Nile somewhat to the south of Aswan (an in doing they would
      > > have avoided the canyon) then trekked up the eastern side of the
      > > canyon, then crossing into the Levant... (would be the shortest route
      > > to Dmanisi)
      > It's a reasonable speculation.
      > >
      > >> A northerly route west of the Eosahabbi canyon would have ended at the
      > >> biggest empty hole that may ever have existed and from there the route
      > >> (other than down into the hole) would have been further west toward the
      > >> Gibraltar land bridge. If they had followed the river from Chad along
      > the
      > >> bottom of the Eosahabbi canyon, then they'd have found themselves well
      > down
      > >> the southern rim of the Med. Basin and from there they could have
      > walked to
      > >> Sicily, on to Italy and then across the empty Adriatic, or maybe around
      > the
      > >> rim to Cyprus and then on to the Caucasus. These are just two possible
      > ways
      > >> in which an empty Med. Basin could have opened routes out of Africa.
      > >
      > > The Gibraltar and Sicily land "bridges" could have been negotiable,
      > > probably the Gibraltar one would have avoided venturing down into
      > > the near empty sea basin (the "hole"), but it would have entailed
      > > trekking north west from Chad, or westward along the southern
      > > edge of the "hole" ...
      > >
      > When I was learning about the MSC and its consequences it became
      > very clear to me that although much of the Med. Basin would have
      > been a no-go zone for any sort of life (Hsu et al.), there was much of
      > it around the bottom of the rim that would have been an attractive
      > and resource-rich environment for a ground-ape. There was an
      > enormous amount of fresh water pouring back into the Basin from
      > both Europe and Africa and at a mile below sea level the atmosphere
      > would have been oxygen-rich. These factors are almost certainly going
      > to result in some degree of gigantism in the colonising plants, insects
      > etc. Over a few hundred thousand years there could well have been a
      > population explosion of the H. side of the divergence - most of whom
      > would have died when the Basin refilled.
      > >
      > >> They use special pleading to explain away evidence because they've got
      > a gap
      > >> to fill? I think you may well be correct, but it simply emphasizes my
      > >> suspicion that these researchers have lost sight of the fact that
      > they're
      > >> supposed to be scientists. They can't fill their gaps in any way that
      > suits
      > >> them, they have to do it with scientifically acceptable evidence, not
      > >> special pleading to save a theory.
      > >
      > > The accumulating fossil evidence from that period seems to be in
      > > favour of the a'piths being ancestral to Man, as they were bipedal
      > > species, and recent discoveries seem to indicate they also are likely
      > > to have walked on arched feet as they had a bone in their feet that
      > > is almost identical to the one in the feet of modern humans.
      > >
      > > [quote]
      > > A fossilized foot bone recovered from Hadar, Ethiopia, shows that
      > > by 3.2 million years ago human ancestors walked bipedally with a
      > > modern human-like foot, a report that appears Feb. 11 in the journal
      > > BScience, concludes. The fossil, a fourth metatarsal, or midfoot bone,
      > > indicates that a permanently arched foot was present in the species
      > > Australopithecus afarensis, according to the report authors,
      > >
      > > [Science Daily 2011]
      > > http://www.sciencedaily.com/releases/2011/02/110210141215.htm
      > > ______________________________
      > >
      > To claim these feet as belonging to human ancestors is leading the
      > evidence in a way that would be unacceptable in any other field of science
      > (maybe with the exception of cosmology?). Why on earth would they
      > conclude that only human ancestors could have had arched feet?
      > >
      > >> I understand that presently maggot meal is used in cattle and fish
      > farming,
      > >> but with those nutritional values there's a lot of under-nourished
      > people
      > >> who might be interested.
      > >
      > > Or it could be they are trying to find another cheap way to feed
      > > beef cattle... you never know what kind of muck they are chucking
      > > into cattle feed these days. (a few years ago in the UK, they had
      > > to slaughter tens of thousands of cattle when they got a disease
      > > that may have resulted from what may have been added to their feed...)
      > >
      > I think it's beyond doubt that reducing cost is as much a factor as the
      > high
      > nutritional value, but then these are precisely the limiting factors in
      > getting
      > nourishing food to those in such desperate need around the world. There's
      > one positive result from that catastrophe in the UK..the health
      > authorities
      > will now be very much more alert to any shonky practices of the meat
      > growers.
      > >
      > >> Then there's this....
      > >>
      > >> 'Given their inherent resistance to food-poisoning bacteria, maggots
      > >> can be used to create an antibacterial food additive to increase the
      > >> safety of the meat supply.'
      > >>
      > >> http://nutritionfacts.org/video/maggot-meat-spray/
      > >
      > > Weird... Would have thought their inherent resistance would die, with
      > > them (once they themselves start to decompose)...
      > >
      > > Houseflies as such can also play host to pathogens, such as typhoid,
      > > cholera .
      > >
      > Do they in fact 'host' these diseases, or just vector them by contact?
      > >
      > >> These conversations do reach into some interesting and quite unexpected
      > >> corners!
      > >
      > > :-)
      > >
      > > Certainly makes for far more interesting posts....
      > >
      > And that's good enough for me.
      > Rob.
      > [Non-text portions of this message have been removed]

      [Non-text portions of this message have been removed]
    • dons3148
      ... Hello Rob... ... If those in the Caucasus were `lost , what does it say for those who possibly left evidence of their tool use at Riwat (Pabbi hills,
      Message 111 of 111 , Jun 30, 2013
        --- In AAT@yahoogroups.com, "Rob Dudman" <ausell@...> wrote:

        Hello Rob...

        > Hello Bill......
        > >
        > There are always differing opinions, but H.georg are classified as
        > Homo as the null hypothesis. That the H.georg dated to c.1.8 Mya are
        > the remnants of a population that previously diverged to become H.e/e
        > is the proposition that IMO seems to best fit the evidence....the
        > contentious issue is this idea that they 'somehow got lost in the
        > Caucasus'. Reminds me of the idea that Abel is an A.afarensis that
        > 'somehow got lost in Chad'! These silly animals didn't just get lost
        > by wandering away from their familiar areas....they got lost by
        > wandering thousands of kms!


        > It would take numerous generations to travel these sorts of distances
        > and to call either Abel or H.georg 'lost' either stretches the word
        > beyond any useful meaning, or it reflects a determination to maintain
        > that H.'had' to have 'belonged' in East Africa where they 'had' to have
        > diverged from an A'pith.

        If those in the Caucasus were `lost', what does it say for those
        who possibly left evidence of their tool use at Riwat (Pabbi
        hills, Pakistan) some 1.9 Mya.


        This `they had to be in a certain place' attitude probably also
        has a lot to do with the OoA just so story of how humanity first
        expanded out of Africa (apparently it was just "60,000 years ago"),
        an adaptationist just so story that was heavily promoted at the
        end of the last century.

        > That H.georg was the ancestral Homo population
        > some of whom went to Africa (where they came into contact with P.reich
        > malaria), is far more sensible than the 'lost' proposition.

        It certainly makes a lot more sense than the `lost' proposition...
        for example following the unfortunate encounter t an ancestor of the
        extant chimpanzee and P.reich, a number of them as H.ergaster they
        could have headed for Morocco and history, while the H.erectus
        headed east into Asia and extinction.

        > Those RVs......
        > > Yohn C.T et al. searched the chimpanzee genome for ERV traces, they
        > > only found evidence for one - PtERV1.
        > >
        > > [quote]
        > > "...Based on analysis of finished BAC chimpanzee genome sequence, we
        > > characterize a retroviral element (Pan troglodytes endogenous retrovirus 1
        > > [PTERV1]) that has become integrated in the germline of African great ape
        > > and Old World monkey species but is absent from humans and Asian
        > > ape genomes"
        > >
        > I could find nothing in Yohn et al. that indicates they only found
        > evidence for one ERV. In fact they write.....
        > '....we identified several members of a full-length endogenous retrovirus
        > family that were present in chimpanzee but absent in corresponding human
        > genome sequence.'
        > They concentrate on the PTERV1 marker, but I couldn't find where they
        > say it's the only ERV marker to be found and Todaro provides unambiguous
        > evidence that chimps also carry the marker for the C type baboon RV.

        In the first sentence of the following quote they say that they found
        one marker in the chimpanzee genome that is not shared with humans...
        From the summary of Eichler's paper;

        "...In a new study, Evan Eichler and colleagues scanned finished
        chimpanzee genome sequence for endogenous retroviral elements,
        and found one (called PTERV1) that does not occur in humans.
        Searching the genomes of a subset of apes and monkeys revealed
        that the retrovirus had integrated into the germline of African
        great apes and Old World monkeys—but did not infect humans and
        Asian apes (orangutan, siamang, and gibbon). This undermines
        the notion that an ancient infection invaded an ancestral
        primate lineage, since great apes (including humans) share
        a common ancestor with Old World monkeys.



        On the other hand we share something like 98,000 other
        markers with the extant chimpanzee and other primates.

        > > > Todaro OTOH, does present sufficiently compelling evidence to shift the
        > > > burden of proof onto the A'pith-descent hypothesis to show that the C type
        > > > baboon RV did not reach East Africa.....and so far every attempt at this
        > > > that I've come across has been constructed on special pleading.
        > >
        > > Not so certain. Africa is a somewhat large continent; and the respective
        > > numbers of a'piths, gorilla and the extant chimpanzee around three million
        > > years ago would likely have numbered in the thousands or tens of thousands
        > > at most, and most of the primates if not all that succumbed would have been
        > > rainforest species.
        > >
        > Certainty is not the issue for me, it's about the burden of proof and a
        > defensible null-hypothesis. Todaro tested 23 African primate species only
        > four of which are strictly rainforest species - mandrill, chimpanzee,
        > gorilla and the mangabey....the patas is a savanna/open woodland monkey,
        > colobus are widespread and are found in East Africa, galagos are native
        > to southern Africa. This and paleoclimatic evidence indicating that a
        > viable airborne vector was present during the early and mid-Pliocene
        > Warm Periods is enough to shift the burden of proof onto those who would
        > claim that East Africa was not reached by the baboon RV.


        However, I still think that the odds of a successful airborne
        spread of a RV three to four million years ago are at best
        on the low side, when you take into account that the African
        continent straddles the equator and amounts to about
        11 million sq. miles in surface area (or about 20 per cent
        of the total land surface of the planet)… when you combine
        that with the likely number of infected individuals at the
        height of an RV outbreak three to four million years ago,
        the odds would likely worsen.

        (gorilla, chimpanzee an hominin numbers at three to four
        million years ago, would be in the tens of thousands –
        sparse populations concentrated in a few locations)

        Extrapolating backwards so to speak from the present (in terms
        of habitat, behaviour and more) also has a few difficulties,
        for example hominins have certainly changed somewhat over the
        last four million years, and the sole surviving example -
        ourselves - has changed considerably)...in all likelihood the
        behaviour and niche preferences' of the ancestors of extant
        monkey, baboon and ape species you mention has also changed
        somewhat over the last few million years.

        > > There are also questions about timing and location, for example the
        > > origins of the baboon as such are thought to have been in southern Africa
        > > and South Africa with the northern clade of the baboon estimated to have
        > > diverged from there southern kin at around two million years ago, so it
        > > could be argued that the baboon has only been present in northeast Africa
        > > in the last two million years (even today, they are not present in a large
        > > part of north Africa).
        > >
        > > Then there are divergence dates themselves, the Papio-Theropithecus divergence
        > > was about 1.4/1.5 Mya after the ancestor of the extant chimpanzee and that
        > > of Man went their separate ways, then there are the divergence dates among
        > > the baboons.
        > >
        > > [quote]
        > >
        > > "...Our divergence age estimates indicate an initial separation into
        > > southern and northern baboon clades 2.09 (1.54-2.71) million years ago
        > > (mya). We found deep divergences between haplogroups within several
        > > species (~2 mya, northern and southern yellow baboons, western and
        > > eastern olive baboons and northern and southern chacma baboons), but
        > > also recent divergence ages among species (< 0.7 mya, yellow, olive
        > > and hamadryas baboons in eastern Africa)."
        > >
        > > http://www.biomedcentral.com/1471-2148/9/83
        > >
        > A southern African origin of the baboon seems most likely with an
        > original divergence from Theropithecus between 3 & 4 Mya (the period
        > of the RVs and a tropical climate in most of Africa). The conclusion
        > here is that the C type RV infected the original baboon species and
        > then crossed to the other primate species with the marker then being
        > inherited by all subsequent subspecies. For the first inter-species
        > spread of the RV it was not at all necessary that the baboon had to
        > have spread from southern Africa that early....along with the wind,
        > the other primate species would have done the job.

        Possible, but a horizontal (contact) spread between species
        would have same result... though it may have not spread
        as far north.

        > The CMAH mutation....
        > > > And the genetic evidence indicates that it was significantly prior to
        > > > c.2 Mya...despite the previously mentioned verbal obfuscation by Chou
        > > > et al. that would make c.2.8 Mya 'just before' c.2 Mya.
        > >
        > > That discrepancy in timing would seem to break any potential link between
        > > the inactivation of CMAH at 2.8 Mya and an expansion human brain.
        > > at around 2 Mya
        > >
        > > Energetics and the evolution of human brain size
        > > http://www.nature.com/nature/journal/v480/n7375/full/nature10629.html
        > >
        > > Human brain expansion
        > > http://www.nature.com/nature/journal/v480/n7375/fig_tab/480043a_F1.html
        > >
        > > Intriguingly over 50% of the `expansion' in the human brain occurred
        > > between 800,000 and 200,000 years ago which would coincide with the
        > > exaptations for language (the use of spoken sounds) in the human lineage.
        > > on the other hand there appears to have been no expansion of the human
        > > brain over the last 200,000 years( its relative size has reduced), so
        > > those AMH who some think ate shellfish by the bucket load on the shore
        > > were clearly wasting their time, they would have been better off tucking
        > > into a juicy steak (on taste grounds).
        > >
        > AFAICS, the CMAH mutation was only incidentally connected with an
        > increase in brain-size and then only after some considerable time.
        > Neu5Ac is a neural nutrient and this would lead to an increase in
        > neural density, not to an increase in the overall size of the brain....
        > for this I assume an abundant and readily available dietary DHA
        > would have been required. It seems most likely to me that the H.e/e
        > brain was the result of both the CMAH mutation and a subsequent
        > period of high DHA intake (along with a cascade of related genetic
        > changes - see below re the SRGAP2 duplication).

        As you say the CMAH mutation could simple have been a precursor to
        what followed somewhat later, as a surplus of Neu5Ac in itself would
        not have led to an increased neuron density, as it is better seen
        as an available resource rather than a nutrient (IMO the same
        applies to DHA).

        The likely difference in humans following the CMAH mutation was
        that there would have been a sufficient Neu5Ac available if
        there was a need for it...

        IMO, something else was driving the demand for more processing power
        in the brain of humans just under a million years ago. (the acquisition
        of a spoken language could have been one possibility)

        > > `Cooking' the uniquely human innovation of cooking what they hunted or
        > > gathered as food, was probably one of the major factors in the expansion
        > > of the human (in increasing its neuron count that is.) as `cooking' their
        > > food enabled humans to pre-digest a wide range of foods, and in doing
        > > ensured they received the nutrients they needed to develop and sustain a
        > > uniquely `large' brain (however among AMH it has become an all too
        > > efficient way of getting the nutrition, modern man needs. to extant
        > > some food "experts" now advocate returning to what our distant
        > > ancestors ate a couple of million years ago. namely raw food).
        > >
        > In their defense....salads do combine healthy food with good taste
        > and a pleasing range of colours (not sure that the latter is apropos
        > of much, but y'never know). Trouble is for those who live in colder
        > climates salads don't warm you up as much as a good stew. :-)


        Probably human ancestors would not have moved into cold climes, if
        they had to rely on a diet of raw food… I would guess 30,000 years
        ago north of the Arctic Circle a bellyful of hot stew would have
        been a lot more satisfying (an appetising), than several
        bucketfuls of cold shellfish.


        A short paper on the early hominin diet...

        Stable isotope-based diet reconstructions of Turkana Basin hominins


        "…Hominin fossil evidence in the Turkana Basin in Kenya from
        ca. 4.1 to 1.4 Ma samples two archaic early hominin genera and
        records some of the early evolutionary history of Paranthropus
        and Homo. Stable carbon isotopes in fossil tooth enamel are
        used to estimate the fraction of diet derived from C3 or C4
        resources in these hominin taxa. The earliest hominin species
        in the Turkana Basin"


        Seems to fit well with what Cerling and colleagues (2011)
        said a couple of years ago.

        > >
        > > Sort of related.
        > >
        > > Extra gene drove instant leap in human brain evolution
        > >
        > > http://www.pasthorizonspr.com/index.php/archives/05/2012/extra-gene-drove-instant-leap-in-human-brain-evolution
        > >
        > Thanks for the link.
        > As usual when reading papers about genetic research brain-fog was
        > almost instantaneous, but I was able to see how important this
        > particular research could be for understanding human brain evolution.
        > Dennis et al. (http://tinyurl.com/mc3x2h8) estimate the dates of the
        > three duplications at 2.8-3.9 Mya, 2-2.8 Mya and 0.4-1.3 Mya and
        > isn't that an interesting trio of dates.....with the CMAH mutation
        > right between the first and second duplications and heidelbergensis
        > at the later end of the estimate for the third duplication.

        The heidelbergensis link(the duplication around a million years ago)
        was the first thing that stood out for me, as the third duplication
        occurred around the time when encephalization in humans underwent a
        remarkable change in matter of a few hundred thousand years,
        ceasing sometime between 400,000 and 200,000 years ago,

        They identify the second as occurring during the `transition' from
        a'pith to Homo 2.4 Mya… However they don't appear to given a
        reason for the first at around 3.4 Mya.

        The latter two duplications are unique to humans.

        > It's one thing to identify the nutritional role of Neu5Ac and its
        > abundance after the CMAH mutation, but these SRGAP2 duplications
        > seem show the nuts and bolts of the way that neural nutrition works
        > to feed the growth of dendrites (and I presume, axons)......

        Can only but agree...

        > 'We used in vitro and in vivo approaches to determine the function
        > of SRGAP2 and its human paralogs in the neocortex region of the
        > brain, the evolution of which is thought to underlie the emergence
        > of human cognitive abilities. Our results uncover a new function
        > for ancestral SRGAP2 in promoting dendritic spine maturation and
        > indicate that expression of a human-specific paralog of SRGAP2 in
        > mouse pyramidal neurons extends the phase of spine development and
        > leads to an increased density of longer spines in vivo, a feature
        > characterizing pyramidal neurons in the human neocortex.'
        > Inhibition of SRGAP2 Function by Its Human-Specific Paralogs Induces
        > Neoteny during Spine Maturation.
        > By Charrier C. et al.
        > http://tinyurl.com/kt4n3c5
        > _______________

        "…Taken together, our results suggest that the expression
        of SRGAP2C in the human brain inhibits the function of
        ancestral SRGAP2 and thereby reduces the rate of spine
        maturation, leading to changes in spine morphology and
        density that could have important implications for
        cognition, learning, and memory"

        "…We may have been looking at the wrong types of mutations
        to explain human and great ape differences," Eichler says.
        "These episodic and large duplication events could have
        allowed for radical – potentially earth-shattering – changes
        in brain development and brain function."


        > > > If the inactivation of Neu5Gc conversion resulted from a catastrophic
        > > > epidemic of P.reich malaria, then that contact with chimps (and/or
        > > > gorillas) would be fairly accurately dated by the CMAH mutation. After
        > > > all, how long would it take for the vulnerable to die or become seriously
        > > > debilitated as a result of malaria and thus be removed from the reproductive
        > > > equation?
        > >
        > > Not long... if hominins some three million years ago, had not previously
        > > encountered malaria.
        > >
        > > Assuming the CMAH mutation happened around 2.8 Mya, then the hominin
        > > ancestors of Man would have had to return to mainland Africa prior to
        > > that date if they had been absent entirely from Africa between four and
        > > three million years ago, as they would have had to returned prior to
        > > that date to have that disastrous encounter with the ancestor of the
        > > extant chimpanzee that `introduced' them to an infection (malaria) that
        > > still plagues mankind today. (2010 - Worldwide death toll from malaria,
        > > 1.2 million)
        > >
        > > Which in itself raises the question, did they remain in Africa after
        > > that disastrous encounter with the ancestor of the extant chimpanzee,
        > > or did they leave again, only to return again at around 2.4 Mya?
        > >
        > The first indisputably H. fossils in Africa are less than 2 Mya, so I
        > see no reason to think that they had to have returned around 2.4 Mya.
        > Given that fossilisation is not a common occurrence I would have
        > thought a return around 2 Mya would take taphonomic bias into account.

        The habilis (2.33 – 1.4 Mya) may not be generally accepted, but it
        highly unlikely that the H.erectus was the first member of genus
        H., in north east Africa… so I would go with the earlier date
        (2.3 - 2.4 Mya, based on evidence for tool use and meat eating.

        This is sort of related, and intriguing...

        "...Recent research indicates that stone points – the oldest kind
        of spear point – are about 500,000 years old," he said. "But people
        have been killing animals for at least 2 million years, and eating
        animals for about 2.6 million years."

        "...That means that for about 1.5 million years, when people
        hunted, they basically had nothing more lethal to throw than a
        pointed wooden stick," he continued. "If you want to kill something
        with that, you have to be able to throw that pretty hard, and you
        have to be accurate. Imagine how important it must have been to our
        ancestors to throw hard and fast."

        Researchers say ability to throw played a key role in human evolution


        "…Some primates, including chimpanzees, throw objects occasionally,
        but only humans regularly throw projectiles with high speed and
        accuracy. Darwin noted that the unique throwing abilities of humans,
        which were made possible when bipedalism emancipated the arms,
        enabled foragers to hunt effectively using projectiles."

        Elastic energy storage in the shoulder and the evolution
        of high-speed throwing in Homo
        Neil T. Roach, Madhusudhan Venkadesan, Michael J. Rainbow
        & Daniel E. Lieberman



        Found this brilliant piece of research intriguing for two reasons,
        firstly for the insight into how the human ability to throw developed,
        and secondly because it firms up the date at which hunting became the
        way human ancestors procured their food.

        > > Either way it does not seem very parsimonious that early hominins would
        > > have migrated en masse once out of Africa far less migrate en masse in
        > > an out of Africa several times.
        > >
        > They moved en masse from somewhere to either Central or West Africa
        > c.3 Mya (to catch P.reich malaria and leave no Neu5Gc producing
        > survivors), they then moved away again en masse to evolve into H.e/e
        > either in eastern or southern Africa or somewhere out of Africa.
        > The question is not how many times they moved, but how far. In terms
        > of parsimony the c.3 Mya move to either Central or West Africa is
        > required by the A'pith-descent hypothesis, as is the move away again
        > after the infection as there's no evidence or reason to think that
        > H.e/e emerged in either of these places.

        The difficulty for any other hominin decent theory is that other
        than a'piths in north and eastern Africa from four and two million
        years ago there is no fossil evidence for any other hominins in
        or out of Africa at that time… yet the a'piths left plenty.

        (That the A'piths could
        > make this sort of journey is undeniable; but Abel, poor lost thing,
        > was in Central Africa c.3.5 Mya when the RVs were active so it's
        > unlikely that it was them who later caught P.reich malaria and then
        > adapted into H.e/e sans Neu5Gc.)

        The long lived a.afarensis (3.9 Mya to 2.9 Mya) a long lived a'pith
        species, as its name suggests it hailed from the Afar like the earliest
        members of AMH… they would have been in north east Africa when the
        ancestor of the extant chimpanzee succumbed to PtERV1. ("Lucy" an her
        kin were a.afarensis, as probably was "abel "who went walkabout
        in Chad some 3.6 Mya)

        Also the disastrous encounter some hominin unfortunately had in the
        jungle around 3.0 Mya with an ancestor of the extant chimpanzee, seems
        to have occurred at around the time the a.afarensis gave way to the
        a.africanus in Africa.

        > The A'pith-descent hypothesis then has to propose a move out of East
        > Africa by the newly emerged H.e/e as their fossils are found in East
        > Asia dating to shortly after the first African fossils. OTOH, the
        > proposal that our ancestors left Africa immediately after the P.reich
        > epidemic suggests that around 2 Mya H.e/e radiated from somewhere
        > between East Asia and Africa and this is in accordance with the
        > dates for the earliest H.e/e fossils from both places. In terms of
        > parsimony between the two proposals it seems to me to be 'half a
        > dozen of one and six of the other'.

        As you say, neither proposal provides a satisfactory answer...

        > > Something nasty that came out of the sea...
        > >
        > > History of Malaria Parasite and its Global Spread (2011)
        > > http://www.malariasite.com/malaria/history_parasite.htm
        > > ___________________________________
        > >
        > Interesting. Thanks.
        > >
        > > > You say that the PTERV1 probably changed how the chimpanzee evolved, but
        > > > other than leaving a genetic marker, I'm aware of no evidence for this.
        > > > Gorillas also carry the PTERV1 marker and AFAIK, there's no evidence for
        > > > it having any substantial effect on their evolution either. Likewise with
        > > > the later infection of macaques and baboons.....it left a marker and that's
        > > > about it. Whatever symptoms that the PTERV1 caused we can reasonably assume
        > > > that it had no reproductive repercussions....those who had the disease were
        > > > successful enough at reproduction to leave the marker in all descendants.
        > >
        > > It had the potential to, and may have changed how the ancestor of the
        > > extant chimpanzee subsequently evolved . the following quote is from
        > > the abstract of the PtERV1 paper;
        > >
        > > [quote]
        > >
        > > ".Retroviral infections of the germline have the potential to
        > > episodically alter gene function and genome structure during the
        > > course of evolution. Horizontal transmissions between species have
        > > been proposed, but little evidence exists for such events in the
        > > Human/great ape lineage of evolution. Based on analysis of
        > > finished BAC chimpanzee genome sequence, we characterize a
        > > retroviral element (Pan troglodytes endogenous retrovirus 1
        > > [PTERV1]) that has become integrated in the germline of African
        > > Great ape and Old World monkey species but is absent from humans
        > > and Asian ape genomes."
        > >
        > Yes, such RVs do have great potential to alter an evolutionary trajectory
        > because of the way they can penetrate the genome, but that being said
        > there appears to be no evidence at all that this in fact happened with
        > the PTERV1 or the baboon C type.
        > What does intrigue me is the fact that like every other living thing,
        > the virus is first and foremost concerned with survival, then with
        > reproduction and proliferation. Viruses that kill their hosts quickly
        > are self-limiting in these objectives, while others that don't adversely
        > affect their hosts have an advantage in these objectives.

        Not certain, that a virus can be defined as living (as apparently they
        cannot replicate themselves)… probably they are the real `undead' -
        being neither one nor the other.

        > This raises the question of why it is that we don't find viruses that
        > act to make their hosts healthier with the best chance to reach maximum
        > longevity? Surely this would maximise the virus' chances in reproduction
        > and proliferation, yet the bloomin' things don't seem to do this....
        > why no virus that boosts the immune system, or increases healing
        > capacity? I wonder if there are genetic researchers who are trying
        > to genetically alter viruses to have positive rather than negative
        > consequences. Spontaneous remission of cancer appears to be some sort
        > 'delayed' immune system reaction that suddenly recognises the cancer
        > cells as 'foreign'....it seems to me that a genetically manipulated
        > RV would be able to trigger this reaction.

        Probably viruses are the last thing if ever that `scientists' should
        ever tamper with... as one mistake could have dire consequences.

        Viruses themselves can be likened to parasites, in that they use the
        host's cells to reproduce themselves, then when they have finished
        they can end up killing the host.

        > > > The fact that the later infection also left a marker in Asian macaques is
        > > > intriguing given that it did not also get to orangs and gibbons....and both
        > > > were in East Asia at that time. IIRC, the oldest Asian macaque fossil dated
        > > > at c.3 Mya was found in northern India so maybe they took it there from Africa
        > > > and it got no further as an active RV.
        > >
        > > It would have had to have infected macaques in east Asia, and the
        > > baboon in Africa. less than two million years ago - different species
        > > on different continents.
        > >
        > > From the PtERV1 paper;
        > >
        > > [quote]
        > >
        > > "...Furthermore, both Asian (macaque) and African (baboon) Old
        > > World monkeys show evidence of PTERV1 proviral integrations
        > > less than 2 million years ago, indicating that the exogenous
        > > source virus is either endemic to both continents or that
        > > ancestral populations frequented both continents.'
        > >
        > Ok, but why did it have to have infected macaques in East Asia rather
        > than the marker being carried east from India as the macaques spread
        > and diverged?

        As far as I know the macaques in Asia diverged into four or five
        species some 3 Mya, a million and so years before PtERV1 infected
        the Asian macaques. (however there is also a second question, the
        question of how the baboons in Africa came to be infected less
        than two million years ago – and more than a million or so
        years after an ancestor of the extant chimpanzee
        was infected in Africa?)

        It seems that neither the orang, gibbon nor other Asian
        > monkeys came into contact with the PTERV1 and while this is not conclusive
        > evidence that the RV didn't reach East Asia, it is indicative evidence
        > that the RV was never active in eastern Asia.

        Seemingly humans, in the shape of the H.erectus also seem to have
        evaded that second outbreak less than two million years ago, even
        though they were present on both continents when both the baboon
        and the macaques would have succumbed to PtERV1.

        > Bipedalism......
        > >
        > > > The fact that an obligate striding bipedal gait was in East Africa c.3.6 Mya
        > > > is usually seen as evidence that our ancestors were there c.3.6 Mya and all
        > > > they have to do now is deal with the RV evidence in a scientifically rigorous
        > > > manner and I for one will readily accept that as the null. But until this
        > > > is done I see those prints as evidence of probable common ancestry....a
        > > > bipedal A'pith/H/P LCA.
        > >
        > > The other way of seeing it, would be to say that it is simply evidence that
        > > the hominins in east Africa more than 3.6 Mya were obligate bipeds, whether
        > > any of the hominins in east Africa at that date were the direct ancestors
        > > of Man that would be a different question... though the more that is known
        > > about the a'piths, the more it favours that a least one or more a'pith
        > > species as being forerunners of genus Homo.
        > >
        > Yes, I agree....now all they've got to do is deal with the lack of the
        > C type baboon RV marker in a scientifically rigorous way and I'll take
        > a ride on the A'pith-descent bandwagon toot sweet, but bearing in mind
        > that all refuted scientific hypotheses fit all the facts except the one
        > that refutes them, I have to consider the A'pith-descent hypothesis as
        > refuted. :-)
        > Rob.


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