Loading ...
Sorry, an error occurred while loading the content.

Re: Bonobo Genome Completed

Expand Messages
  • dons3148
    ... Hello Rob... ... Assuming the first outbreak of PTERV1 did not cross the Sahara desert some three million odd years ago, would not the early ancestors of
    Message 1 of 111 , Jul 28, 2012
      --- In AAT@yahoogroups.com, "Rob Dudman" <ausell@...> wrote:

      Hello Rob...

      > Hello Bill.....
      > >
      > > Yohn et al do go on to say in their paper that the baboons
      > > and the macaques succumbed to the chimpanzee virus/PTERV1
      > > at a much later date, than the first outbreak in which the
      > > ancestors of the extant chimpanzee and gorilla succumbed
      > > some three million odd years ago. Which raises the questions
      > > as to how early humans (Homo erectus) in this case evaded the
      > > RV (again?) nearly two million years ago, when the H.erectus
      > > (along with the habilis) would likely have been in north
      > > eastern Africa and probably in the Far east.
      > >
      > If the first PTERV1 couldn't cross the Sahara, then we'd have to
      > expect the baboons and macaques there to have remained vulnerable
      > while their southern and eastern cousins became immune. Why did
      > the African H.e/e remain unaffected? The obvious answer would be
      > that when they arrived in the areas where their fossils are found
      > the contemporary primates (c.2 Mya) carried the markers and not the
      > active RVs. The markers in Asian macaques would be best explained
      > by there being no Asian macaques at that time and when they did
      > spread there they took with them not the disease but only the markers.

      Assuming the first outbreak of PTERV1 did not cross the Sahara
      desert some three million odd years ago, would not the early
      ancestors of Man, have also evaded the RV by being isolated
      by the desert in north east Africa, similar to the baboons
      less than 2 Mya?

      Second time around when the baboons and the macaques succumbed
      to PTERV1 less than two million years ago, the H.erectus give
      or take a hundred thousand years or less, could have still
      been in Dmanisi at the time of the second outbreak, thus
      evading the RV for a second time.

      > > 'Divergent Patterns of Recent Retroviral Integrations in the Human
      > > and Chimpanzee Genomes: Probable Transmissions between Other
      > > Primates and Chimpanzees'
      > >
      > > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1346942/
      > > ___________________________________
      > >
      > > Should say that reading this paper, is like wading through treacle
      > > - as it is full of jargon - but it did throw up another scenario
      > > for the spread of the chimpanzee virus…
      > >
      > > [quote]
      > > "Chimpanzees frequently eat other primates, like baboons, geladas,
      > > and colobi which harbor ERVs similar to the PtG retroviral sequences.
      > > The probable cases of horizontal transfer of gammaretroviruses to
      > > chimpanzees thus agree with the predatory practices of chimpanzees.
      > > It is, however, intriguing that the human genome seems to have been
      > > spared from the PtG integrations. Human ancestors and chimpanzees
      > > may have been differentially exposed through differing hunting
      > > practices. Differences in ERV fixation due to population size and
      > > distribution could also be reasons."
      > >
      > > ______________________________________
      > >
      > Here we're told that there are 'cases of horizontal transfer of
      > gammaretroviruses to chimpanzees'......Ok, there undoubtedly are,
      > but this is the first hint that I've come across to suggest that
      > an RV named after P.t. didn't start in P.t. Did they toss a coin
      > when they named it PTERV1? Ah, but then it might be the case that
      > there were differences in hunting practices and/or population size/
      > distribution that kept H. free of the RVs? I've never tried to knit
      > with noodles, but this must be getting close to the experience.

      Think the horizontal transfer gammaretroviruses reference,
      was general, not a specific reference to how the ancestor
      of the extant chimpanzee may have succumbed PTERV1 ...

      The odds probably favor the ancestor of the extant chimpanzee
      getting infected by eating infected monkey kill...

      > > Would seem chimpanzees hunting practices were their downfall...
      > >
      > Chimps are known to eat young baboons when the opportunity arises,
      > although how often that would have been in the distant past is very
      > much up for question because modern human activity has tended to
      > squeeze them together. In cases where the two species have over-
      > lapping territories it seems that a quite hidden dynamic is at work
      > which must inevitably make the shared environment more baboon-
      > friendly, rather than the type where chimps can also flourish. When
      > chimps eat fruits the seeds pass through their digestive systems
      > to be defecated not only in a viable condition, but also packaged
      > in fertilizer; baboons digest both pulp and seed, so over time the
      > baboons turn forest into the more open environment to which they
      > are better adapted. I wonder if this is the reason for the emergence
      > of the 'savanna chimp'?

      Perhaps, but chimpanzees are more of a forest animal than the
      baboons, but then again some chimpanzees might be seeking new
      hunting grounds, new prey...

      A study last year into chimpanzee hunting practices, found
      chimpanzees have come close to hunting their favored monkey
      prey to near extinction.


      > > And on the infection of the macaques...
      > >
      > > [quote]
      > >
      > > "The macaque retroviral similarity was unexpected. African macaques
      > > are present in only a small North African population, remote from
      > > the ancestral chimpanzee habitats in forests and forested savanna.
      > > Consequently, they are unlikely to have been in close contact with
      > > the chimpanzees. However, the possibility that macaques and
      > > chimpanzees have overlapped geographically in the past should
      > > not be excluded."
      > >
      > No it shouldn't, but it's a red-herring in the context of PTERV1;
      > the macaques got the PTERV1 well over a million years after the
      > chimps got it, so even if the two species did mix during one of
      > the 'greening of the Sahara' periods, the RV wouldn't have been
      > active in the chimps to pass it on. It might be argued that the
      > PTERV1 not only leaves a genetic marker, but was also a dormant
      > virus that could reactivate and infect over more than a million
      > years later, but then fail to do this when macaques came into
      > contact with the other Asian primates who don't have markers?
      > Ah no, silly me....of course, it could be/may be/possibly be that
      > it's only in chimps that the PTERV1 can remain dormant for over a
      > million years, the other infected primates only got to keep the
      > marker!

      More likely there is a species that was or still is a species
      that is a reservoir for the PTERV1 RV, possibly a monkey or a
      bat species. The source of Ebola is suspected to be a bat
      species. (maybe all those old fears about being bitten by
      bats, have a factual basis... ).

      Bats: Important Reservoir Hosts of Emerging Viruses

      [Science Daily 24/07/12]
      "A vast international study(1), carried out in collaboration
      with IRD researchers and published in Nature Communications
      has led to the discovery of more than 60 new species of these
      dangerous infectious agents, almost double the number
      previously recorded. This family of highly diverse pathogens
      affects allanimals, from canines to fowl, cattle and humans.
      As a result, it is not always easy to determine which host is
      responsible for these viruses. Thanks to testing carried across
      the globe, the research team has recently discovered their
      source: bats."

      Bats, a Reservoir of Resurgent Viruses

      The original article, in Nature Communications...

      Bats host major mammalian paramyxoviruses


      > At every turn their speculations seem as implausible as those
      > ideas of the lost A'piths and humans bonking gorillas when they
      > were getting the PTERV1 and we just got the lice! And of course,
      > this is what happens when they ignore the obvious to engage in
      > special pleading....sooner or later they have to get tangled up
      > in the profusion of 'may have been', 'could have been' and the
      > endless 'it's possible that...'.
      > Todaro's solution remains the most plausible and the most
      > parsimonious by an astronomical order of magnitude.....H. was
      > not in Africa when the RVs were active. It's obvious why orangs
      > didn't get infected and it's obvious why gibbons didn't get
      > infected, yet in the case of H. there simply has to be another
      > explanation so that we can be descended from the A'piths? The only
      > reason to insist on ignoring the comparative evidence here is
      > to save the A'pith descent theory.....and that's science?
      > Todaro tested for the C-type marker in 23 sub-Saharan primate
      > species and found it present in all cases; he tested 18 Asian
      > primate species and found it to be absent in all cases. It is
      > also absent in modern humans and yet we're descended from an
      > African A'pith? What sort of inductive reasoning is that?

      > > > Tellier says that evidence of long distance infection implies
      > > > aerosol transmission, but this doesn't also imply that the
      > > > these RVs were blown for long distances. The aerosol spread of
      > > > interspecies RVs does not require that the RVs get blown for
      > > > hundreds of miles in one go, but just far enough to get from
      > > > one group of suitable hosts to another group of suitable hosts.
      > > > This wind mediated host-hopping could explain why the RVs didn't
      > > > cross the Med. or the Arabian deserts.....no potential hosts.
      > >
      > > Contact, species to species transmission would work in a similar
      > > way, as it too would spread as long as there were potential hosts…
      > > for example the pandemic of 1918 reached worldwide, reaching into
      > > the Arctic and to remote islands in the Pacific. (death toll has
      > > been estimated at 50 million)
      > >
      > > 1918 flu pandemic
      > > http://en.wikipedia.org/wiki/1918_flu_pandemic#Theories_about_source
      > >
      > > Pandemic
      > > http://en.wikipedia.org/wiki/Pandemic
      > > ____________________________________
      > >
      > This is mixing time-periods......the flu virus of the 1918 pandemic
      > spread in the context of the end of a world war when servicemen
      > were being demobbed to all parts of the globe. More recent epidemics
      > have occurred in the age of air travel. Prior to 3 Mya we need a way
      > for a virus to cross different biomes where many of (at least) 23
      > different species never come into short-range contact to pass it on
      > through sneezing/coughing/spitting or whatever. Wind mediated aerosols
      > is the most obvious answer according to Tellier and FWIW, I agree with
      > him.

      Well if you want to go further back before the age of mass transit,
      there is always the "Black death"... probably the most devastating
      of all pandemics … that spread across Asia from China, to Europe, in
      the 1300's ... Spreading fast, it killed one in three. Estimated
      death toll was between 75 and 200 million.


      > > As to there being no hominids (hosts) in Arabia that is uncertain…
      > > Arabia (a chunk of Africa, that is still breaking away) is one of
      > > those places where very little work (exploring) has been done by
      > > paleoanthropologists even though there were periods when it was
      > > green and fertile, hosted rivers and lakes. Arabia is also the
      > > `bridge' between Africa and Asia(and Georgia), while the Levant
      > > is the shortest route to Georgia…
      > >
      > > Hominin responses to Pleistocene environmental change in Arabia
      > > and South Asia
      > >
      > > http://tinyurl.com/7cf2n6x
      > > __________________________________
      > >
      > Unfortunately, this paper is about the Pleistocene and we're dealing
      with the climate a million years or more before the Pleistocene.

      Could be less than a million, as some studies date the mPWP from
      3.3 Mya to 3 Mya; others from 3.15 Mya to 2.85 Mya, the latter
      date would put the end of mPWP within a few hundred thousand
      years of the start of the Pleistocene epoch which starts
      at 2.58 Mya

      > There's now quite a lot of research going on into the mPWP climate
      > (it's thought to be a good proxy for anticipating the consequences
      > of the present warming trend) and although much of the discussion
      > is carried on using a seemingly endless list of acronyms (not as
      > confusing as the geneticists' jargon, but something of slog for
      > the casually interested), I'm able to glean that when those RVs
      > were active the central and western areas of the Sinai peninsula
      > had become 'open grassland' (savanna?), while the eastern areas
      > were much as they are today. I assume that the Red Sea would have
      > been much wider during the mPWP than it is today due to ice-melt
      > in both the northern and southern hemispheres causing sea-level
      > to rise.

      Which date are you using for when PTERV1 was active... a date
      within the mPWP?

      The mPWP and the final closure and the start of the glaciation
      in the north, overlap somewhat... sea levels however, would
      likely have been higher before the onset of glaciation
      in the northern hemisphere.

      Final closure of Panama and the onset of northern hemisphere glaciation

      Pliocene Global Warming

      > Sinai primates of the mPWP? I've found no information so far.

      Not much is known about Arabian primates, in general.
      Curiously though, Arabia 28 Mya did play host an intriguing primate
      one from close to the time that apes diverged from the OWM, namely
      the Saadanius hijazensis ... a primate possibly from the time
      of the common ancestor of the apes and old world monkeys...


      "The new fossil catarrhine, Saadanius hijazensis, dates from
      29 million to 28 million years ago and lacks the specialized
      features that distinguish modern apes and Old World monkeys,
      suggesting that the split had not yet occurred. The researchers'
      analysis of the fossil leads them to believe its physical
      features are much like those of the last common ancestor
      of Old World monkeys and apes."

      Fossil Find Puts a Face On Early Primates



      > > (Africa also has its deserts…)
      > >
      > I note the present tense.....what deserts d'you have in mind for
      > mPWP Africa when the RVs were spreading?

      Three of the major African deserts, as they have been around
      for more than a few million years, in the case of the Namib in
      south west Africa, it is estimated it has lasted for some 80
      million years... while the Kalahari desert in southern Africa
      has been around for sixty million years, while north of the
      equator the Sahara in one form or another has been around for
      some seven million years (from the time of Toumaï in Chad?).

      The geographical location and age of all three of those
      deserts, especially the two south of the equator, would
      seem to rule out a continental south-north wind pattern
      over Africa, even if the continent did not straddle
      the equator.

      > > Think it is the location of the African continent itself that
      > > it is problematic for a south north wind pattern over the
      > > continent... as it straddles the equator, and the equatorial
      > > zone is where winds from the north and south converge. In other
      > > words Earth's rotation seems to rule out a south north wind
      > > pattern over the entire African continent.
      > >
      > > Global winds:
      > > http://apesnature.homestead.com/files/fg09_05c.jpg
      > >
      > > Global climate:
      > > http://www.lordgrey.org.uk/~f014/usefulresources/aric/Resources/Teaching_Packs/Key_Stage_4/Weather_Climate/09.html
      > >
      > Again, all this about the present situation....the Global Winds
      > map shows Panama as closed and this wasn't the case during the
      > mPWP. The Global Climate page is also about the present situation
      > and I'm not sure what it can tell me about Africa during the mPWP
      > 3-4 Mya.

      Climate differences and the closure of the CAS (Panama) would
      have made little difference, as global wind patterns are in
      part shaped by the rotation of the Earth itself...

      If Africa had been further south of the equator some three
      million years ago it might have been different, but it seems
      it has straddled the equator for nearly twenty million
      years, if not longer.

      > > Have read that the aerosol particles from someone sneezing or
      > > coughing dry out within 10 to 15 cms of the mouth, this may
      > > increase the distance of an aerosol spread of these particles,
      > > but these same particles need to enter the respiratory tract
      > > of a healthy victim before they can be infected, or enter an
      > > open wound on their skin. Whereas contact spread only needs
      > > physical contact, a bite from a carrier (infected) animal or
      > > insect, or by eating recently killed prey or simply eating
      > > half-eaten discarded fruit.
      > >
      > This is from Tellier's paper.......
      > 'In experiments that used homogeneous aerosolized influenza virus
      > suspensions, virus infectivity (assessed by in vitro culture) at
      > a fixed relative humidity undergoes an exponential decay; this
      > decay is characterized by very low death rate constants, provided
      > that the relative humidity was in the low range of 15%--40%.
      > These results are consistent with those of an older study (admittedly
      > performed in a more rudimentary manner) in which infectious influenza
      > viruses in an aerosol could be demonstrated for up to 24 h by using
      > infection in mice as a detection method, provided that the relative
      > humidity was 17%-24%.'
      > 'Review of Aerosol Transmission of Influenza A Virus: Influenza
      > Virus Aerosols'
      > By Raymond Tellier.
      > http://rsif.royalsocietypublishing.org/content/6/Suppl_6/S783.full
      > ___________
      > This 15%-40% humidity range means that in the conditions that prevail
      > in the tropics for about half of the year (and there's no reason
      > to think this didn't apply to mPWP Africa during the dry-season),
      > there are viruses that could be carried for many miles on the wind.
      > You say that contact-spread 'only' needs physical contact between
      > all those different species as if this is a far more likely occurrence
      > than the necessarily ongoing business of inhaling whatever the wind is
      > carrying.
      > >
      > > Did Todaro give a date at which the baboons, were infected?
      > >
      > > I ask as it now looks like the RV the baboons (along with
      > > macaques) succumbed to less than 2 Mya, was a second outbreak
      > > the chimpanzee RV – PTERV1, so any other RV infection in the
      > > baboons would have had to have happened after the baboons
      > > and the gelada (Papio and Theropithecus) diverged some
      > > 3.5 Mya to 4 Mya ago...
      > >
      > Today at least, geladas are an exclusively Ethiopian baboon....
      > precisely where so many of those A'pith fossils are found. AFAIK,
      > only Hamadryas baboons share an environment with Barbary Macques
      > in North Africa.
      > Todaro's dating is frustratingly vague, in fact he doesn't address
      > the issue directly. But a deduction can be made now that we have
      > a probable date for the H/P divergence. The H/P LCA did not carry
      > the C-type marker (or along with the chimps we would have now have
      > it) and assuming our descent from an unaffected African H.e/e who
      > first appeared c.2 Mya, we have a 3 million year range in which the
      > baboon C-type could have occurred....this is the primary reason that
      > I take the line of least resistance and assume that H. left Africa
      > when they diverged from P., an exodus that would have been defined
      > by the MSC.

      Maybe a narrower range if we take into account the timing of when
      the baboons diverged from the gelada... 4 Mya to 3.5 Mya ... that
      would narrow the gap to 2 million or 1.5 million years. If it
      occurred in the baboons at the time they diverged, it may have
      coincided with the outbreak of the chimpanzee RV - PTERV1.

      If the ancestors of H left after they diverged from the ancestors
      of the extant chimpanzee... wouldn't that be a million to 1.5
      million years before the first outbreak of PTERV1 ?

      > > > AFAICS, in terms of fossil evidence it's the same gap from
      > > > c.2 Mya back to the H/P LCA and even then there are no
      > > > fossils, just genetic evidence. The first unambiguous
      > > > fossil evidence for H. then turns up in Asia (Mojokerto),
      > > > not Africa.
      > >
      > > Some would place the Ardi (Ardipithecus) in that initial gap
      > > following the divergence of the ancestor of the extant chimpanzee
      > > from those of Man (admittedly it does kind of fit into that gap).
      > >
      > Yes, some would.
      > >
      > > Think the H.erectus fossils from Dmanisi, are as old if not older
      > > that the Mojokerto which are dated to 1.6 Mya to 1.81 Mya.
      > >
      > The Dmanisi fossils are effectively the same age as those from
      > Mojokerto.....the difference being that Mojokerto is unambiguously
      > H., while the Dmanisi fossils also retain features that are more
      > primitive. Dmanisi and Mojokerto could well have had the same ancestor,
      > but the fact remains that neither of them were African and because of
      > this the clear inference is that neither carried the two markers.

      If they were both descendants of the ancestor of H.erectus, those
      that settled in Dmanisi would likely be older than those that
      settled in the far east...

      > Foot morphology and convergent adaptation....
      > >
      > > > > Convergent adaption is similar, but not identical.
      > > >
      > > > Would you say the same about the two knuckle-walkers, the
      > > > palm-walkers and the hopping in kangaroos and wallabies?
      > > > They all require a similarity in foot morphology commensurate
      > > > with the similarity between the afarensis arched foot and that
      > > > of modern humans.
      > >
      > > Yes I would... taking `knuckle-walking' as an example, gorillas
      > > do not knuckle-walk in the same manner as the extant chimpanzee...
      > > and the extant chimpanzee is more of a `knuckle-walker' than is
      > > the gorilla.
      > >
      > > http://zinjanthropus.wordpress.com/2010/01/11/so-did-knuckle-walking-evolve-twice/
      > >
      > There is one foot bone to establish that afarensis had arched feet,
      > yet you seem to be arguing that this (and I assume, the Laetoli
      > prints) made their feet identical to ours? The Laetoli prints are
      > very similar to those of a modern human, but then it takes an expert
      > tracker to tell the difference between a wallaby's tracks and those
      > of a small kangaroo.

      May not just be the foot, it may also include the shape of the
      shoulder and the length of the leg… `Kadanuumuu' (big man) is
      the name given to a new(2010) a.afarensis discovery in Ethiopia,
      an a'pith that lived and walked upright 3.6 Mya…...


      "Kadanuumuu's" legs were also surprisingly long—almost as
      long compared to the size of his arms as are those of modern
      humans. Elongating our legs was previously thought to be a
      pivotal change later in human evolution, and most observers
      thought "Lucy's" legs were very short.

      Human-like Walking Is Ancient: "Lucy's" Forebears were
      Advanced Upright-Walkers



      > A quote from the zinjanthropus blog....
      > 'As we've discussed before, knuckle-walking is a pretty weird thing
      > to do, which is why the idea that it evolved only once is hard to
      > shake.'
      > Now I'm not aware of his/her previous discussion, but to say that
      > knuckle-walking is 'weird' is a vacuous argument from incredulity.
      > All modes of terrestrial locomotion have to be related to the surface
      > type which has exerted the selection pressures; it would be a puzzle
      > if knuckle-walking had been adapted in any other situation than that
      > in which it is found....the relatively soft ground of the tropical
      > rainforest....and in that environment 100% of the resident great apes
      > have adapted to knuckle-walking. What could be 'weird' about that?
      > Even though the geladas' 'shuffle-walk' is quite unique, there's even
      > nothing weird about walking on your bum if that's the best way for
      > you to get your food.
      > I assume that the writer does not know that by a long shot the
      > majority of the dangers in a tropical rainforest are not easy to
      > see because they are small, have six or more legs and most are found
      > in the leaf-litter on the forest-floor. Knuckle-walking reduces the
      > surface area of the hand that would be exposed to these threats with
      > palm-walking and there's nothing at all weird about that. (I would
      > argue that the mandrill's 'finger-walking' has been adapted for exactly
      > the same reason.

      He probably should have used... unusual, instead of weird...
      which can have other connotations.

      As the early apes palm-walked (twenty odd million years ago),
      and the Ardipithecus probably used a mixture of bipedalism
      and palm-walking when down on the ground 4 Mya, and most extant
      monkeys today palm-walk when down on the ground today... the
      exceptions are gorilla and the extant chimpanzee which
      knuckle-walk ... which makes them unusual.

      > The MSC.....
      > >
      > > If it was a humid, hot, oxygen rich atmosphere down in the empty
      > > sea basin, one form of life that may have adapted quickly, could
      > > have been the insects, as the last time Earth had a rich oxygen
      > > atmosphere the insects were huge... possible prey for hominins
      > > down in the basin, or predators...
      > >
      > It's an intriguing idea.
      > >
      > > Would rivers like the Rhone and the Ebro that discharge large
      > > amounts of water into the north western Med today, have been same
      > > some five, six million years ago?
      > >
      > I understand that the Rhone flowed before the MSC, but recent evidence
      > suggests that this was not the case with the Ebro. (See http://tinyurl.com/bpez6f8)
      > This has surprised me because of the Ebro's position to collect run-off
      > from the Pyrenees and that mountain chain has been there from long
      > before the MSC.

      It is surprising as the Ebro is a large river, an of the Spanish
      rivers it discharges the most water, can only conclude it either
      did not exist before the MSC or that the river followed a
      different course (drained westwards?).

      Thanks for the link…

      > > Of interest:
      > >
      > > Toumaï, 10 years after discovery...
      > > http://blogs.smithsonianmag.com/hominids/2012/07/sahelanthropus-tchadensis-ten-years-after-the-disocvery/
      > >
      > Thanks for the link.....
      > 'Since 2006, the study of Sahelanthropus hasn't advanced all that much.'
      > Ah well.
      > :-)
      > Rob.


    • 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.


      Your message has been successfully submitted and would be delivered to recipients shortly.