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Re: Bonobo Genome Completed

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  • dons3148
    ... Hello Rob... ... If we were to substitute Pluralist, for Darwinist, I would say the difference is that Pluralists would look at an evolutionary trait and
    Message 1 of 111 , Feb 2, 2013
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      --- In AAT@yahoogroups.com, "Rob Dudman" wrote:



      Hello Rob...


      > Hello Bill......
      >
      > I'll leave the Heinlein quote and go straight to.....
      >
      > >
      > > sort of related:
      > >
      > > The great wrinkled finger debate.
      > >
      > > http://www.genomicron.evolverzone.com/2013/01/the-great-wrinkled-finger-debate/
      > >
      > > ...it includes this insightful quote:
      > >
      > > [quote]
      > >
      > > "...Many biologists favour the adaptationist approach to studying trait
      > > evolution. That is, they begin with ideas about why a certain trait might
      > > be adaptive and then proceed from there. Others (increasingly, myself
      > > included) may argue that there must be evidence that the trait is adaptive
      > > in the first place before such hypotheses are pursued. This may be a matter
      > > of preference or training or philosophical bent more than anything.
      > > However, it should be clear either way that there are good and bad ways
      > > to test adaptationist hypotheses."
      > >
      > > by the way, his entire article is worth a read... itself.
      > >
      >
      > What is the difference between 'an adaptationist' and 'a Darwinist'?
      >



      If we were to substitute Pluralist, for Darwinist, I would say the
      difference is that Pluralists would look at an evolutionary trait
      and ask… "What evolutionary mechanism caused this?" Whilst the
      Adaptationist would ask…"How can this be explained by natural
      selection?"

      In other words the Pluralists take the view that there is more than
      one evolutionary explanation for a particular trait, while the
      Adaptationist is only interested in a just-so-story explanation
      (an ad hoc fallacy) ... I would agree, and only add that the
      adaptationist "wading hypotheses" is probably a good example
      of such a just-so-story.

      This article from `79 by Gould and Lewontin is well worth a read:


      The Spandrels of San Marco and the Panglossian Paradigm: A Critique
      of the Adaptationist Programme (1979)

      Stephen Jay Gould and Richard c. Lewontin

      [quote]

      "...We fault the adaptationist programme for its failure to distinguish
      current utility from reasons for origin (male tyrannosaurs may have used
      their diminutive front legs to titillate female partners, but this will
      not explain why they got so small); for its unwillingness to consider
      alternatives to adaptive stories; for its reliance upon plausibility alone
      as a criterion for accepting speculative tales; and for its failure to
      consider adequately such competing themes as random fixation of alleles,
      production of nonadaptive structures by developmental correlation with
      selected features (allometry, pleiotropy, material compensation,
      mechanically forced correlation), the separability of adaptation and
      selection, multiple adaptive peaks, and current utility as an epiphenomenon
      of nonadaptive structures. We support Darwin's own pluralistic approach
      to identifying the agents of evolutionary change."


      http://rspb.royalsocietypublishing.org/content/205/1161/581.abstract

      related:

      http://sandwalk.blogspot.co.uk/2009/02/dawkins-on-chance.html

      http://jonfwilkins.blogspot.co.uk/2011/05/traffic-preterm-birth-and-adaptationism.html

      _________________________________________


      Whist it is likely to be a temptation to find and an adaptive story
      (a just-so-story) for everything under the sun, from the colour of
      blood to the shape of the human nose it is a dumb idea best, as is
      the adaptationist "survival of the fittest" twaddle, for when it
      comes to natural selection in the real world, it is more a
      question of "survival of the fittest enough".




      > > > AFAIK, there's no evidence for H.e/e using fire for cooking prior to a million
      > > > years ago although I'd think they were more than capable, but any explanation
      > > > that presupposes cooking with fire prior to 2 Mya needs a very critical second
      > > > look. You mention the fact that chimps regularly consume raw meat and this
      > > > indicates that this is an issue of degree.....prior to cooking our ancestors
      > > > could and undoubtedly did eat raw meat, but it's probable that raw meat was not
      > > > a very significant percentage of their diet.
      > >
      > > Agree... raw meat (from animals and fish) was probably just a few per cent
      > > at most of the content of the early hominin diet at best for millions of
      > > years, it would be interesting though to find out when it was they figured
      > > out, how to cook what they ate, as at the moment the date for the use of
      > > fire is less than a million years, while hunting or at least tool use, goes
      > > back almost 2.7 million years.
      > >
      >
      > C.2.7 Mya? D'you refer to the Gona tools associated with garhi? In that case
      > the use of the tools to butcher meat has to be a more than reasonable inference,
      > but I understand that it's their Mode 1 manufacture that makes them special at
      > that early date....even more so because they were found 'proximal' to A'pith
      > fossils, not Homo fossils. AFAICS, the reasonable inference from this is not
      > that H. is descended from an A'pith, but that like Homo, some A'piths produced
      > Mode 1 tools.
      >


      The ones at Bouri, Ethiopia are attributed to A'piths, Gona is a
      possibility, but there is a claim that they are habilis rather
      than A.garhi stone tools. This raises the question if Mode 1 tools
      were originally an a'pith innovation then that would seem to indicate
      that Homo copied the tools, from the a'piths, as both these early
      tool sites are within Ethiopia.

      (assuming a'piths are not direct ancestors)





      > > > http://news.discovery.com/human/human-bite.html
      > > > _________________
      > >
      > > Interesting article, but their claim that modern humans can crack a nut open
      > > is questionable. We may be able to crunch peanuts, but walnuts, brazil nuts,
      > > macadamia nuts?
      > >
      > > Combined with the small size of the human mouth, humans probably can only
      > > exert enough force to slice through the flesh of an apple or bite someone,
      > > but it is likely to be far short of that needed to slice through and swallow
      > > in one go a chunk of the raw muscle tissue of a bovine, or crack bone open...
      > >
      > > (early hominins, such as the P. boisei that could crack open nuts, had much
      > > larger teeth and jaws)
      > >
      >
      > Walnuts and bovine bones? Not likely, but then when I think about it, here in
      > Australia it's not uncommon for men to take the caps off beer bottles with
      > their teeth. Didn't Mike Tyson remove a large part of an opponent's ear in
      > one bite? I wonder what the Marquis of Queensbury would have thought of that! :-)
      >


      :-)

      An apple would have provided more of a challenge... than his opponents' ear.



      > The MSC.....
      > >
      > > > I think an important point re-emerges here......the extinctions and
      > > > opportunities for speciation that can follow massive geo/climatic
      > > > catastrophe are now taken for granted, yet the MSC remains apparently
      > > > unnoticed by paleoanthropologists. It's a very odd - and very big -
      > > > blind-spot.
      > >
      > > Odd it is... more so when paleoanthropologists go on to argue today that
      > > it may have been rapid climate fluctuations some two million years ago
      > > or so in northeast Africa that lay behind the shift to tool use and
      > > large-scale hunting among humans... climate shifts that occurred within
      > > as little as ten to a hundred human generations. If that was the case
      > > some two million years ago, why ignore the possibility of similar
      > > climate fluctuations five million years ago, following the MSC.
      > >
      > > [quote]
      > > "...A series of rapid environmental changes in East Africa roughly
      > > 2 million years ago may be responsible for driving human evolution,
      > > according to researchers at Penn State and Rutgers University."
      > >
      > > "...We show that the environment changed dramatically over a short
      > > time, and this variability coincides with an important period in
      > > our human evolution when the genus Homo was first established
      > > and when there was first evidence of tool use."
      > >
      > > http://www.sciencedaily.com/releases/2012/12/121226080906.htm
      > > ______________________________________
      > >
      >
      > AFAICS, for North Africa the 'dramatic' climate changes referred to here
      > were relatively tame when compared to the MSC. The water that evaporated
      > from the Med. Basin not only had to precipitate somewhere, it removed a
      > weight equivalent to a mile-high glacial ice sheet over an area about the
      > same as modern Europe.....those massive canyons were not only eroded by
      > river water, they were stretched as great cracks as the Basin rose when
      > relieved of the weight of the Med. Sea.


      Accounts of the amount of water removed by evaporation from the Med sea
      basin claim that it raised the level of the oceans worldwide by several
      meters... weight wise though the removal of the sea itself would have had
      somewhat less effect than burial of land under ice, as the bed of the
      sea basin is not continental rock. (the river canyons, were carved down
      into continental rock)

      The ice sheet at the last glacial maximum (about 20,000 years ago) in
      these parts was about two Km thick... an as you say, today Scotland, Norway
      and the rest of Scandinavia are still in the process today of bouncing back
      up from being buried under the ice...while the "opposite corner" of the
      UK - London and the S.East - is sinking.
      (some would say not fast enough).



      > (IIRC, the Highlands of Scotland
      > are the ongoing consequences of the most recent glacial retreat from northern
      > Europe....isn't Loch Lomond the deepest fresh-water lake in the world?)
      >


      Loch Morar at 310 m is our deepest freshwater Loch, Loch Lomond is larger
      in terms of surface area, but you may have in mind Loch Ness which in
      terms of freshwater volume, is our largest Loch.

      http://en.wikipedia.org/wiki/Loch_Ness

      ________________________________________





      > The Megalake Chad was shallow, but it was fresh water and it also covered
      > an area similar to that of the Med. Sea - the consequences for the flora
      > and fauna supported by that lake would have been rapid and catastrophic.....
      > and all this right next door to where we now find chimpanzees. AFAICS, the
      > MSC and its effect on northern Africa is probably the best kept most
      > obvious secret in paleoanthropology.
      >


      The land locking of the Mediterranean sea began at around 5.9 Mya, but it
      was only finally isolated about 5.6 Mya, which means the MSC as such lasted
      some 300,000 years before the rapid refilling of the basin at around 5.3
      Mya... the likely date at which the ancestors of the extant chimpanzee
      and Man went their separate ways.

      AMH (modern man) has been around for the last 200,000 years, so in a sense
      the MSC as such lasted somewhat longer than AMH has been around. Therefore,
      it is somewhat puzzling as to why the MSC does not feature in the thinking
      of anthropologists when it comes to human evolution.

      On the other hand they could be right in thinking that the somewhat later
      rapid climate shifts within periods of 10 to a 100 human generations (three
      generations per 100 years?),would have had more of a direct impact
      on human evolution, two to three million years ago.


      related:

      New research seems to indicate the climate favoured dry forest not
      rainforest for millions of years prior to and following the MSC...
      (deciduous trees predominate in dry forests) basically it is unlikely
      that there were extensive if any rainforests in north-east Africa in
      the last twelve million years...

      [quote]

      "...What came first: the bipedal human ancestor or the grassland
      encroaching on the forest? A new analysis of the past 12 million
      years' of vegetation change in the cradle of humanity is challenging
      long-held beliefs about the world in which our ancestors took shape
      -- and, by extension, the impact it had on them."


      Vegetation Changes in Cradle of Humanity: Study Raises Questions
      about Impact on Human Evolution

      http://www.sciencedaily.com/releases/2013/01/130131121304.htm

      http://worldwildlife.org/biomes/tropical-and-subtropical-dry-broadleaf-forests

      ________________________________________




      > > > > There is the possibility favoured by some anthropologists that the
      > > > > a.afarensis was the stem species, of both the a'piths and of those
      > > > > that became Homo, in the Pliocene. in other words the two lineages
      > > > > could simply have gone their separate ways 3.5 to 4 Mya.
      > > >
      > > > What evidence is there that afarensis had the MYH16 mutation, or is
      > > > this simply assumed because the A'pith descent theory requires it?
      > >
      > > In all probability the mutation does not figure in their thinking...
      > > basically as it appears there is no evidence of any other hominin species
      > > other than the a'piths and a'pith-like hominins some three to four million
      > > years ago(or outside of Africa, at that date), the assumption is that the
      > > a'piths are in a lineage that leads to AMH (modern Man)...........
      > >
      >
      > I think you're probably right in supposing that the MHY16 mutation doesn't
      > figure in their thinking, like the MSC doesn't and the same with Todaro's
      > baboon RV. I wonder how many other things I'm going to come across that
      > they ignore because there is no evidence of any other hominin species other
      > than the a'piths. This 'absence of evidence is evidence of absence' line
      > must be among the weakest arguments put forward in all science and this is
      > particularly so when theorists use it to avoid examining potentially
      > contradictory evidence.
      >
      > But y'know, I can use it too.....H.e/e is found in Asia earlier than in
      > Africa, there is no evidence of any hominin species that could have been
      > the precursors to H.e/e found between Asia and the Caucasus, therefore H.e/e
      > had to have arisen in Asia and that's how we avoided Todaro's RV. At this
      > Mad-Hatter's tea party the most parsimonious hypothesis is the one that
      > ignores the least amount of inconvenient evidence. :-)
      >



      :-)



      > > ..............an assumption recently reinforced by evidence that they
      > > walked upright and had similar foot morphology to modern humans. even
      > > though in all likelihood that they still climbed trees.
      > >
      >
      > AFAICS, similarity in foot morphology is evidence of similar foot use
      > over similar terrain and this certainly reinforces the idea that these
      > A'piths were bipedal. This similarity is consistent with the proposition
      > that H. is descended from these A'piths, but it's also consistent with
      > the proposition that the similarity in foot morphology is the result of
      > convergent adaptation and H. is not descended from any A'pith, so in terms
      > of A'pith descent, similarity in foot morphology is neutral evidence.
      >



      Perhaps, but that similarity in foot morphology faced with no evidence
      to the contrary would favour the a'piths or at least the earliest of them
      being direct ancestors… even if they were not, convergence would likely
      favour a direct ancestor who for all purposes was ... a'pith-like.




      > > Incidentally, humans can still climb trees today, and the open spaces (parks)
      > > created in our cities and towns tend to be filled swathes of grass, and trees.
      > > And in all likelihood early members of genus Homo, climbed trees to sleep in
      > > nests, at night, similar to the extant chimpanzee still do today.
      > >
      > > [quote]
      > > "...This is intriguing as it has long been believed that coming down from
      > > the trees was a crucial evolutionary shift. However, this chimpanzees'
      > > behaviour suggests a more deep-seated, gradual transition from tree-to-ground
      > > sleep."
      > >
      > > Chimpanzee "nests" reveal when hominids first left the trees
      > > http://io9.com/5902477/chimpanzee-nests-reveal-when-hominids-first-left-the-trees
      > >
      >
      > There are a few things about this article that leave me feeling uncomfortable.
      > The headline is a gross overstatement, but then journalistic headlines aren't
      > intended to be factual, they're designed to catch attention and as this one
      > caught mine I have to concede that it's effective even though it's balderdash.
      > Then the first sentence offers this completely unsupported proposition....
      >
      > 'When a chimpanzee goes to sleep, it first has to build a "nest", which allows
      > it to sleep safely up in the trees.'
      >
      > Such nests may well increase the safe surface area available for sleeping in
      > the branches, but to say nests 'allow' chimps to safely sleep in trees is to
      > say that they would be unsafe without them.....yet other primates manage to
      > safely sleep in the branches without sleeping-nests so why not apes?
      >



      A tree nest as you say could be more secure (and probably a lot warmer)
      than the ground, for a larger bodied primate such as a chimpanzee...

      Chimpanzees nesting in trees

      http://www.youtube.com/watch?v=JM9zZW7HdF0

      _________________________________________





      > Then we're told....
      >
      > 'Strangely, chimpanzees also build nests when sleeping on the ground, which
      > might reveal a secret about human evolution.'
      >
      > It takes a few paras for this secret revelation.....coming down from the
      > trees may not have been a 'really big deal'. Apparently we now know this
      > because sometimes a chimp will sleep in a nest on the ground and sometimes
      > the same chimp will sleep in a nest in the branches....the nest construction
      > being the same in both cases. The logic of that escapes me entirely.....no
      > matter what evidence may turn up about our past or how many other animals
      > may have done it, coming down from the trees was a 'really big deal' for
      > us and without it we'd be hooting at each other instead of writing to each
      > other.
      >


      Would agree the connection between tree nesting and ground nesting they are
      making is questionable, it reads like another dumb adaptationist just-so-story
      ... for starters, they are overlooking the fact that the ancestors of humans
      and those of the extant chimpanzee have been on very different evolutionary
      paths for the past few million years (comparisons with extant chimpanzees
      at best, are meaningless, whether it be gait or behavior).




      > All ground-apes build nests for both day and night use, with gorillas being
      > somewhat cavalier about the construction of their day nests. Not all arboreal
      > primates build nests...in fact it's only prosimians, but as this sub-group
      > is probably most similar to the primate LCA this opens the possibility that
      > the other arboreal primates have for some reason stopped building nests. (If
      > this is the case, then we can deduce that the nests are not primarily for
      > safety as it stretches credibility that monkeys would dispense with such a
      > fundamental survival capacity....it's a long drop.)
      >
      > Orangs weave day and night nests and this offers an intriguing disjunction...
      > either woven nest-building is shared by both African and Asian ground-apes
      > because this predisposition was inherited from a common ancestor, or it's
      > another case of convergent adaptation and we need to identify the selection
      > pressures that would result in this ground-ape similarity.
      >


      Probably it was inherited from their common ancestor some 14 million years
      ago, as gorillas, chimpanzees and probably early hominins build/built nests.
      The lesser apes (such as the gibbons) who split from the great apes some
      18 Mya apparently do not build nests (so it may have to do with body size
      – medium sized apes – gorillas, adult gorillas are little too heavy for
      the stoutest of trees).



      > The assumption being made in the article is that ape ground nesting is an
      > extension of arboreal nesting, but I think this assumption may need inversion....
      > great-apes are clearly not the immediate descendents of prosimians and that
      > means they are descended from a monkey-like LCA; monkeys don't build arboreal
      > nests and this opens the reasonable possibility that ground-apes reinvented
      > the nest to avoid sleeping in contact with the ground and then took their
      > reinvention back to the branches.
      >
      > What is there that apes across the world would try to avoid when sleeping on
      > the ground? Insects? Damp?
      >


      Probably both, plus less chance of being caught unawares by a large
      predator, or a rival...



      > BTW. I think that our fascination with trees has more to do with the shade and
      > resources they offer than some atavistic impulse that goes back to our arboreal
      > past.
      >


      Never climbed a tree when you were young?




      > > > Some A'piths clearly didn't have the mutation, so how would they explain it
      > > > in afarensis with a mutation date of c. 5.3 Mya? D'you suppose it even occurs
      > > > to them to explain our lack of the RV markers?
      > >
      > > Probably not, for whilst the RV three to four million years ago meddled with
      > > the genome of the extant chimpanzee. looking at it from the perspective of
      > > some of those dealing with hominin evolution, it was just another RV that
      > > infected the ancestor of the extant chimpanzee, but not hominins. (not all
      > > that unusual as far as RVs go)
      > >
      >
      > This may apply to the PTERV1, but not to Todaro's baboon RV.
      >


      Possibly, so...




      > > > Yes, our upright bipedal walking gait is impeded by mud, snow and water....
      > > > but so is a quadrupedal gait and probably more so because both silt and snow
      > > > would 'grip' four feet instead of two. As for our bipedal ancestors exploiting
      > > > the silt and mud at the edge of a lake, there is nutritious food to be found
      > > > in that silt and the bipedal forager has two free hands for digging and
      > > > scraping and only two feet in the silt. It seems self-evident that walking
      > > > through silt on four legs takes twice as much energy as walking through
      > > > silt on two legs.
      > >
      > > Wouldn't a biped simply sink somewhat deeper into the mud than a
      > > quadruped, as all the body weight would be on two feet, not displaced
      > > across four, an in a quadruped of similar weight?
      > >
      > > Think silt as such would be something most medium and large sized
      > > animals, quadruped and biped, would go out of their way to avoid, as
      > > it can be pretty treacherous.
      > >
      > > http://tinyurl.com/a33vurb
      > > _______________________________
      > >
      >
      > Isn't this all a bit extreme? I've walked in the silt/mud at the edge of
      > fresh water lakes and had no trouble at all getting about. There would be
      > places that would be treacherous and some of these may well be in locations
      > where animals could be caught, but as a rule the edges of lakes are the
      > safe playground of modern H.ss.
      >


      Harsh maybe, but realistically slithering around in mud, or faffing around
      wading waist deep in some forest swamp, would have added to the foraging
      costs for early hominins at a time when every kilo joule earned by
      foraging counted.

      (faffing = pointless, timewasting activity)




      > > > I hope that you weren't battered too much by the recent foul weather over
      > > > the UK.
      > >
      > > So far, it has been a mild winter here in the south-west, admittedly a
      > > very wet one... Jerusalem got the snow... Unfortunately the forecast
      > > is for a spell of colder weather starting tomorrow (Monday) that will
      > > last for next few weeks.
      > >
      > > See southeast Australia... has had it hot recently... 50C plus must
      > > be unbearably hot! Here 25C is hot...
      > >
      >
      > The +50C was in the less inhabited desert areas (it got to 54C in one place).
      > Sydney got to 43C, but this is as far away from me as Rome is from you.....
      > thankfully! Here is the subtropical 'Goldilocks' zone...we had a hot day
      > recently where the temp got to 33C, but then it settled back into its 28-32
      > summer range. We have the remnants of a cyclone sliding down the coast toward
      > us and we can expect some rain for a few days, but we'll all be in shorts and
      > bathers. When I heard the news of the floods in south-west England (where I grew
      > up), my first reaction was to think 'poor blighters, I know what they're going
      > through', but then it hit me that our flood in a subtropical summer is nothing
      > like a flood in an English winter....it had to be simply awful.
      >
      > Regards,
      >
      > Rob.
      >


      Not only serious flooding, the south-west (Eng.) and Wales were the worst
      hit when blanketed in heavy snow early this month. Winter winds, also
      toppled two wind turbines in Devon ... :-)


      http://www.thisisdevon.co.uk/Inquiry-second-wind-tower-topples/story-18021569-detail/story.html


      Here in the south-west (Scot.) it is a mild end to the month, admittedly a
      very wet and windy one. (we still have February to go, before we can say
      this has been a unusually mild winter)

      Regards,

      Bill
    • 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
      • 0 Attachment
        --- 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.

        http://sheilamishra.wordpress.com/2010/12/22/81/

        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;

        [quote]
        "...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.

        http://eichlerlab.gs.washington.edu/news/pix/PLOScommentary0305.pdf

        ____________________________

        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.
        >


        Perhaps...

        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.

        http://archive.archaeology.org/0403/newsbriefs/siberia.html


        related:
        A short paper on the early hominin diet...

        Stable isotope-based diet reconstructions of Turkana Basin hominins
        http://www.pnas.org/content/early/2013/05/31/1222568110

        [quote]

        "…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
        > _______________
        >


        [quote]
        "…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"

        [quote]
        "…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...

        [quote]
        "...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."

        quote]
        "...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
        http://phys.org/news/2013-06-chimps-humans-baseball-pitcher.html#inlRlv


        [quote]

        "…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."

        Nature:
        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

        http://www.nature.com/nature/journal/v498/n7455/full/nature12267.html

        ____________________________________

        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.


        :-)


        Bill.
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