Neanderthal DNA Among Modern Humans? How About the Denisovans' DNA ?

In a post two years ago, I noted research conducted at the University of Colorado- Boulder, and UC-Denver, that appeared to scotch two common theories: 1) that the Cro-Magnon exterminated the mentally slower Neanderthals, or 2) that they out -competed for resources by higher reproduction rates.   Based on detailed computer modeling, as well as genetic analysis (from the human genome) the research showed instead that Neanderthals were simply absorbed into modern humans. By "absorbed", I mean that their unique phenotype (see image, e.g. for the skull) became non-existent after extensive interbreeding with the modern humans.

Supporting this was the finding  from a year earlier that 1 to 4 percent of modern human genes, mainly in Eurasian peoples, were "leftovers" from Neanderthals. (Evolutionary biologists consider that residual gene percentage the proof of breeding between the two distinct species before the Neanderthals died out roughly 30,000 years ago)    The computer models had been run over 1,500 generations, based on estimated samples of humans and Neanderthals roving across Europe and Asia. One parameter in the model included the researchers' knowledge that the last ice age forced Neanderthals and modern humans to widen their search for food. The computer models showed interaction, but because there were far more Cro-Magnon (something like a 10:1 ratio) over time than the mating- diluted Neanderthals,  until they emerged as just a minor fraction of our DNA.

Since then the proportions, mating frequencies have been more refined. We now know that 2.5 percent of Neanderthal DNA is found in Asians and Europeans. Two Swiss geneticists - Matthias Currat and Laurent Excoffier - researched how much interbreeding would be needed to end up with so little Neanderthal DNA today and concluded it would require one Neanderthal to mate with a human (Cro-Magnon) to create a child every 30 years.

To have been preserved into modern times, clearly the hybrid offspring would have had to have been accepted - but no one can say how they emerged (in what context) in the first place. It might have been by way of rapes during violent battles between humans and Neanderthals or (more benevolently) when Neanderthals were welcomes into one or more human communities.

A new strategy has been adopted by David Reich, in terms of following the directionality of gene flow.  This is made possible given that human females have two X chromosomes and males have one X and one Y. If Neanderthal females mated with male humans more prominently  Reich notes - they'd provide an X- chromosome to all their children. If Neanderthal males predominated in relations with human females they'd impart  an X chromosome to daughters but none to sons.

Reich hypothesizes that if he were to find an unusually low amount of Neanderthal DNA on the X chromosome, say compared to the other chromosomes, it would be a prime clue that Neanderthal males impregnated human females. Conversely, a high ratio would point the other way, i.e. to Neanderthal great-great grandmothers.

Readers may also recall that roughly a year ago, another specimen hominid was unearthed, packed with DNA (which was then sequenced) and found to be not quite human and not quite Neanderthal.  Geneticists concluded the DNA belonged to yet another hominid group hitherto unknown to science and they dubbed it "Denisovan".  Reich and colleagues applied their same methods (as they did to Neanderthal DNA) to the newcomer genome and discovered the genes were closest to Neanderthals  - but the genome also included many mutations not found in either humans or Neanderthals.

Evidently, Denisovans had diverged from the ancestors of Neanderthals somewhat more recently than the split between Neanderthals and modern humans.   Knowing this, Reich and colleagues looked carefully for Denisovan DNA in the genomes of modern humans. They found it in genomes of two populations, one from New Guinea and another from the nearby island of Bougainville. Reich et al found that at least 5 percent of their DNA came from the Denisovans.

By contrast, Reich et al could not find any trace of Denisovan DNA in Africans, or Europeans or mainland Asians.  They did, however, find vestiges in the genomes of Australian Aborigines and in a people known as the Mamanwa in the Philippines.

The picture that's now emerged is that by the time Neanderthals and Denisovans encountered modern humans their genes had been evolving separately for hundreds of thousands of years.  Despite that, it's possible their DNA is still influencing the health of billions today.  Reich, however, is not ready to take a firm stand because the draft genomes of both Denisovans and Neanderthals still have too many gaps and errors to allow for anything more than conjecture.

More research is in the works, including experiments. As Reich puts it, we can actually perform an experiment to decide, say, whether people with a particular chunk of Neanderthal DNA are faster runners than those without it. Just parse the genetic profiles of different people beforehand, turn 'em loose, then draw conclusions after the race. In the same way experiments can be done to determine, say, whether people with a particular chunk of Denisovan DNA are better at logic puzzles .....or more likely to be atheists.

Stay tuned!

Clearing the Air on "Missing Links"

The use of the term "missing link" has exposed Darwinian evolution to a host of specious criticisms from the Rightist religious wackos and creationist crazies - who somehow believe they know the theory more intimately than bona fide Darwinians! At the same time, I believe it has retarded a fuller understanding of what evolution is actually about.


Look back the past twenty years through any media archives, say The New York Times or The London Telegraph or The Barbados Advocate, and you are likely to see at least 15-20 headlines with references to "missing links" - in terms of discoveries to do with evolution.  Indeed, two of the most noteworthy were: (1) the report from the April 3, 2010 London Telegraph on the discovery of an almost-complete fossilized skeleton belonging to a previously-unknown type of early human ancestor that may have been a intermediate stage as ape-men evolved into the first species of advanced humans, Homo habilis, and (2) the May, 2009 report (in numerous papers) of a lemur fossil dubbed "Ida' described as "the first link to all humans," and "the closest thing we can get to a direct ancestor".

Well, uh.....yeah....but.....

Big BUT.... What IF another fossil is then discovered predating Ida by even a couple million years, then what?

The problem is the whole template vastly oversimplifies the nature of fossil finds, as well as the biological importance and meaning. In a way, the use of the term "missing link" in any context, is simply a copout by either scientists or media to try to simplify a complex notion for people who may never even have taken a single high school biology course. (As in most Americans).


Who can blame them? When I attended a conference in Fairbanks, Alaska in January, 1986, on the role of the Media in Science, I was appalled at the lengths of simplification of ideas resorted to, as told by a former NPR reporter. Across the whole spectrum from astronomy to physics, to biology, vast complex ideas were reduced to cartoons or caricatures simply for the consumption of would -be readers. Thus, as the NPR reporter also noted, was the term "missing link" also invoked by science reporters- starting with Richard Leakey's finds in the 70s- to transmit in a concise form complex evolutionary ideas.


Problem is it doesn't work! Let me show why: take the line below to denote a path of evolutionary development for some species, with the time increasing to the right:


(A)--------------------------(B)---->--------------->(C)  (+T)


In this simplified format, an original species - say a root -eating shrew at (A), evolves over time to become a leaf -eating shrew at (C) (with different taxonomic adaptations). The time differential is maybe twenty million years. In this linear unfolding or sequence of a linear development, it makes eminent sense to look for a "missing link" (B), say somewhere in between. Maybe this is a shrew that eats roots, but is also developing a taste for large leaves.


Now, mentally, the word "link" evokes the image of a chain, i.e. a chain typically has links and the more links the longer the chain. A "missing link" therefore refers to one piece or link missing in the putative long, linear chain. In the context shown, therefore, identifying (B) as a "missing link" makes eminent sense. However, in real world evolution of species, it doesn't.


To grasp this, consult the diagram above which displays the realistic algorithmic development of two hominid families, called A and A' - initially. Note here the primary differentiating characteristic is not a uniform linking in a linear sequence, but rather a TREE-like branching. The tree-like branching fits the evidence we have that while a 'shoot' of the evolutionary lineage starts off, it often quickly hits a dead end, then stops. Others continue to develop before they branch off...or don't. What if a small branch is "missing"? Generally, the train of evidence that led to that branch in the first place was based on some previously found fossil. If that fossil later happens to be misdated, or attributed to a different branch (due to a dearth of ample data) it doesn't vitiate the whole sequence nor does it amount to a "missing link". In most cases it amounts to a simple time delay in locating the fossil remains that fit with the proposed hominid for that branch. Even if the whole branch is later removed (e.g. C-D in the top sequence of  Fig. 1), for whatever reason, this doesn't vitiate the entire sequence leading to the more evolved hominid at the end! (A similar branching algorithmic sequence is depicted in the lower part of Fig. 2)


In this case, the use of the term "missing link" is totally inappropriate since it skews perceptions of what is really happening in evolution. Indeed, use of the term implies a causal break, and hence that the hominid line itself is in question because the putative earlier cause is absent. Thereby, people are led to believe or think of evolution as a simple linear unfolding process rather than a complex path of integrated branching trees, at differing times with many speciation attempts coming to dead ends, or non-causal contributions. They then question the concept of some "missing link" when either multiple ones are found (or claimed to be) or expected finds don't materialize within the sequence. In either case, the wrong expectations are used to attempt to fault evolution, when the real problem is that an oversimplistic template is being employed which skews perceptions and judgment.


Here's where it stands in terms of hominid evolution: As of this writing more than 240 hominid individuals have been found and classified, one of the most recent being Ardipithecus kadabba or 'Ardi' as noted in a previous blog. The research that went into the composition of Ardi's fossil structure took nearly 15 years before it could be published. Even before that extensive pre-publication preparation, diligent work at the particular digs had to be completed. Even with dozens of fossils excavated the work wasn't finished, since CT scanners then had to be used on them and advanced computer imaging employed to digitally restore the crushed skull. The good news is that the effort was worth it. In the words of one Ardi worker:


"You crawl on your hands and knees, collecting every piece of bone, every piece of wood, every seed, every snail, every scrap".


So, much for the classic (fundie)  simpleton belief or assumption that one just walks out into a closed canopy or escarpment and pulls out complete fossils at will, as if the dynamic Earth itself would cooperate with this. No freaking way. The brute fact here is that the deeper one goes into the paleo-anthropological record, the more difficult it is to not only recover intact evidence - but to assemble what one does find in ONE piece! (In the case of Ardi, she was assembled from 125 separate pieces of skeleton.)

Let's use common sense here. The ancient hominids that pre-existed us didn't have the benefit of embalming methods (say like used on the Pharaohs in Egypt) and certainly weren't able to preserve themselves against the ravages of fearsome natural forces, including shifting tectonic plates, earthquakes, etc. Thus, the bodies and skeletons of most ancestors decayed or were otherwise ravaged, and left few traces. To expect more then, say complete fossil finds over time, and at any time, would border on the imbecilic.


It would be as idiotic in this case to shout "You have no evidence!" as it would be for a crime scene inspector to assert the same (to an undertaker) for an exhumed body whose key features had completely decayed when the person had requested a "green burial" beforehand. (A green burial means no extenuating preservatives are used, and the body basically rots into the ground where it is as bacteria gain access).


Despite these obstacles, we have tens of thousands of hominid fossils in museums around the world that stand as an evidentiary testament supporting our current knowledge of human evolution (see, e.g. the photo snapshot shown). Moreover, the pattern that emerges from this vast array of hard evidence is consistent across thousands of independent investigations - which means all the key steps are confirmed. This means two things of overriding import:


(1) No new "missing link" is needed to validate the amassed evidence, and no subsequently claimed "missing link" will invalidate it. The evidence is what it is, fitting into an algorithmic skein, and in that mode it is consistent ...plus


(2) All myths or fairy tales based on any instantaneous "creation" of humans are resoundingly invalidated because the amassed, consistent, independently verified fossil finds support no such outlook or belief. If people (like fundies) wish to believe that humans are special creations, they can of course do so, but no empirical evidence supports that belief. Thus, they are no more secure in their assumed "scientific" support than say, flat Earth believers. Their best bet, rather than appealing to fraudulent claims, is simply admit they are making religious claims.


Now, those ancient "biblical" or other fables that originated with semi-literate sheep herders and nomads thousands of years ago are, of course, useful artistic or fictional metaphors available to people who have trouble grasping technical concepts like DNA, speciation, allele fitness & survival value, or gene frequency. But in that light, those crude cartoonish perspectives belong rightly in the context of religious studies, not any claimed "scientific research". (And indeed, "creation science" is itself an oxymoron, like "military intelligence")


The bottom line here? The invocation of "missing links" advances no case for or against the existing evidence we have for hominid evolution- speciation leading to Man. "Missing links" represents a term fraught with basic misconception (often misused to identify intermediary fossils) and largely adopted by the media to try to relate difficult evolutionary concepts to a scientifically illiterate public. This term, while partially useful in a limited context, is too overused in the real panorama of algorithmic development - as shown.

In the end, the denial of evolution, however motivated (and the fear of evolution by fundamentalists -who tie their purpose to meaning and special creation -can be well appreciated) is a denial of evidence and a retreat to the backwaters of ignorance.

As someone said once before, people are entitled to their own opinions (and even beliefs) but not their own evidence!