The skull in the cave

"If humans came from monkeys, why are there still monkeys?"

If there is one phrase that makes me want to throw a chair across the room, it's that one.  (Oh, that and, "The Big Bang means that nothing exploded and became everything.")  Despite the fact that a quick read of any of a number of reputable sites about evolution would make it clear that the question is ridiculous, I still see it asked in such a way that the person evidently thinks they've scored some serious points in the debate.  My usual response is, "My ancestors came from France.  Why are there still French people?"  But the equivalence of the two seems to go so far over their heads that it doesn't even ruffle their hair.

Of course, not all the blame lies with the creationists and their ilk.  How many times have you seen, in otherwise accurate sources, human evolution depicted with an illustration like this?

It sure as hell looks like each successive form completely replaced the one before it, so laypeople are perhaps to be excused for coming away with the impression that this is always the way evolution works.  In fact, cladogenesis (branching evolution) is far and away the more common pattern, where species split over and over again, with different branches evolving at different rates or in different directions, and some of them becoming extinct.

If you're curious, this is the current best model we have for the evolution of hominins:

The cladogenesis of the hominin lineage; the vertical axis is time in millions of years before present  [Image licensed under the Creative Commons Dbachmann, Hominini lineage, CC BY-SA 4.0]

The problem also lies with the word species, which is far and away the mushiest definition in all of biological science.  As my evolutionary biology professor put it, "The only reason we came up with the idea of species as being these little impermeable containers is that we have no near relatives."  In fact, we now know that many morphologically distinct populations, such as the Neanderthals and Denisovans, freely interbred with "modern" Homo sapiens.  Most people of European descent have Neanderthal markers in their DNA; when I had my DNA sequenced a few years ago, I was pleased to find out I was above average in that regard, which is undoubtedly why I like my steaks medium-rare and generally run around half-naked when the weather is warm.  Likewise, many people of East Asian, Indigenous Australian, Native American, and Polynesian ancestry have Denisovan ancestry, evidence that those hard-and-fast "containers" aren't so water-tight after all.

The reason all this comes up is because of a new study of the "Petralona Skull," a hominin skull found covered in dripstone (calcium carbonate) in a cave near Thessaloniki, Greece.  The skull has been successfully dated to somewhere between 277,000 and 539,000 years ago -- the uncertainty is because of estimates in the rate of formation of the calcite layers.

The Petralona Skull  [Image licensed under the Creative Commons Nadina / CC BY-SA 3.0]

Even with the uncertainty, this range puts it outside of the realm of possibility that it's a modern human skull.  Morphologically, it seems considerably more primitive than typical Neanderthal skulls, too.  So it appears that there was a distinct population of hominins living in southern Europe and coexisting with early Neanderthals -- one about which paleontologists know next to nothing.

Petralona Cave, where the skull was discovered [Image licensed under the Creative Commons Carlstaffanholmer / CC BY-SA 3.0]

So our family tree turns out to be even more complicated than we'd realized -- and there might well be an additional branch, not in Africa (where most of the diversification in hominins occurred) but in Europe.  

You have to wonder what life was like back then.  This would have been during the Hoxnian (Mindel-Riss) Interglacial, a period of warm, wet conditions, when much of Europe was covered with dense forests.  Fauna would have included at least five species of mammoths and other elephant relatives, the woolly rhinoceros, the cave lion, cave lynx, cave bear, "Irish elk" (which, as the quip goes, was neither), and the "hypercarnivorous" giant dog Xenocyon.  

Among many others.

So as usual, the mischaracterization of science by anti-science types misses the reality by a mile, and worse, misses how incredibly cool that reality is.  The more we find out about our own species's past, the richer it becomes.

I guess if someone wants to dismiss it all with a sneering "why are there still monkeys?", that's up to them.  But me, I'd rather keep learning.  And for that, I'm listening to what the scientists themselves have to say.

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A singular scientist

Science has become the realm of specialists, and I am by nature a thoroughgoing generalist.  (Less kind words like "dilettante" and "dabbler" have also been applied to me.)  The result is that although I have a decent background in a good many areas of science, my knowledge of most of them is shallow at best by today's standards.  Even though I taught biology for over three decades, papers in peer-reviewed journals in most realms of biological science -- immunology and biochemistry come to mind -- lose me after the first couple of sentences.

One exception is the field of evolutionary biology and its sibling, evolutionary genetics.  These subjects have been something of a fascination of mine since I was in college, and looking back, I rather wish I had pursued them as a career.  My AP Biology students always reacted with tolerant amusement at my obvious excitement once we got to those topics, so at least my background was put to some good use.

This love for evolution and genetics is why I was absolutely thrilled when I heard that the winner of this year's Nobel Prize in Medicine and Physiology was the eminent Swedish researcher Svante Pääbo.  Pääbo is the founder of the field of paleogenetics -- the use of DNA from fossils to reconstruct the evolutionary history of a species.

[Image licensed under the Creative Commons The Royal Society, Professor Svante Paabo ForMemRS, CC BY-SA 4.0]

Pääbo is best known for his accomplishing something no one thought was possible: extracting DNA from fossilized bones.  His attitude when told something is impossible is, "Watch me."  Working at the Max Planck Institute for Evolutionary Genetics in Leipzig, Germany, he developed a pioneering technique to extract DNA from bones, first the mt (mitochondrial) DNA, which is passed only through the maternal line, and finally the nuclear DNA.

It was Pääbo's technique that allowed researchers to determine the placement of our near relatives the Neanderthals and Denisovans, the latter using only eight fossil fragments from sites in Russia, China, and northern Laos.  Without Pääbo's work, much of what we know about our own prehistory would still be a mystery.

Pääbo is also a remarkably humble, genial man.  When he received the call of his win, he was incredulous, and thought he was the victim of a prank by his friends.  A bit of questioning established that no, he had in fact clinched the highest honor in the scientific world.  Characteristically, in a press conference shortly afterward, he directed the attention outward from himself to the subject he loves.  "The thing that is amazing to me," he said, "is that we now have some ability to go back in time and actually follow genetic history and genetic changes over time."

Others were more effusive about the contributions of this soft-spoken gentleman.  "Nobody believed him [about extracting fossil DNA]," said Leslie Vosshall, neuroscientist at Rockefeller University.  "Everyone thought it was contamination or broken stuff  from living people.  Just the mere fact that he did it was so improbable.  That he was able to get the complete genome sequence of a Neanderthal was viewed, even up until he did it, as an absolutely impossible feat...  He's a singular scientist."

Indeed.  I remember reading papers by Pääbo and his colleague, the late Luigi Luca Cavalli-Sforza, when I was in graduate school, and being absolutely fascinated by the light they shone on the genetic underpinnings of evolutionary biology.  That one of my science heroes won the Nobel Prize makes me very, very happy.  

I congratulate him, and wish him many more years of blowing our minds with his groundbreaking research into our own deep past.

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Out of Africa

In a rather startling coincidence, just yesterday I wrote about how much the course of human evolution was constrained by our evolving in a place that had large predators, scarce resources, and seasonal drought, and almost simultaneously a paper was published in Nature Geoscience about exactly that.

A huge interdisciplinary team of geoscientists, sedimentologists, micro-paleontologists, geologists, geographers, geochemists, archaeologists, chronologists, evolutionary biologists, and climate modelers led by Verena Foerster of the University of Cologne set themselves a mammoth task -- to correlate shifts in climate in East Africa over the past 620,000 years with patterns of population growth, evolution, and dispersal amongst the hominin species that lived there. 

Starting with two 280-meter-long continuous sediment cores from the Chew Bahir Basin in southern Ethiopia, the team was able to analyze not only the sediment geology and chemistry, but such things as pollen and seed types, fossil content, and rate of deposition to infer what the climate was doing at the time.  What they found was that from 620,000 to 275,000 years ago, the climate was amazingly stable -- warm and humid -- but that interspersed through that time were short, abrupt, extreme drought phases.  These "arid pulses" led to sudden habitat fragmentation, as the climatic shifts didn't hit everywhere at once (nor with equal severity).  Some areas remained relatively wetter, while other areas not that far away were experiencing catastrophic drought.

When this happens -- a large swath of relatively uniform habitat becomes unstable and/or patchy -- it generally has two results; (1) animals become more mobile, migrating in search of resources that are now less reliable; (2) organisms less capable of moving undergo strong selective pressure to adapt to "the new normal."  Both of these affected our ancient relatives.  Some began to disperse more widely, presumably seeking out food and water, while others diversified in response to their new local climatic conditions, leading to rapid speciation.

Following this, the East African climate began to undergo more regular oscillations between congenial and hostile.  Wet phases, with abundant vegetation and deep freshwater lakes, alternated with dry phases during which the lakes evaporated almost completely, leaving only highly saline, alkaline ponds.  During this time, the Acheulean hand axe culture of the Lower Paleolithic (associated with our predecessor species Homo ergaster) was superseded by more sophisticated technologies and the emergence of modern Homo sapiens about sixty thousand years ago.

An Acheulean hand axe [Image licensed under the Creative Commons José-Manuel Benito Álvarez (España) —> Locutus Borg, Bifaz cordiforme, CC BY-SA 2.5]

Things only got dicier from there.  Between sixty and ten thousand years ago -- the highest layers of the sediment cores -- East Africa saw the most arid phase in the entire record.  This had two effects -- driving our ancestors out of Africa in search of better conditions, and triggering the extinction of virtually all our near relatives.  We won, apparently, by dint of our mobility and large brains, allowing us to cope with hostile and rapidly fluctuating conditions, eventually leading to our dispersing to every habitable land on Earth.

It's fascinating to me that we owe our own existence to fluctuations in the climate -- that the conditions in one part of the world molded us into the species we currently are.  Now that we have technology to avoid many of the caprices of the environment, we are also shielded from their evolutionary effects; you have to wonder how (or if) our distant descendants will be altered by climate shifts, more specifically those we ourselves are perpetrating.  It once again brings home the truth of the perspective that each species is not a separate entity, but is part of an intricate tapestry of life.  Pull on one thread, and the others will inevitably, and irrevocably change -- for good or ill.

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The climatic teeter-totter

I remember how blown away I was when I first saw British science historian James Burke's documentary After the Warming, shortly after its release in 1991.  Its intent was ambitious, to say the least; to trace the effects of climate on humanity, from prehistory up to and beyond the point where (in Burke's words) "the climate stopped doing things to us, and we started doing things to it."

What struck me most is something that at this point is much more widely known; that the periodic warming and cooling had dramatic effects on sea level.  Up during warm periods, down during cold ones, enough to open and close land passages from one place to the other.  The most famous is the "Bering Land Bridge" between what are now Siberia and Alaska, but similar pathways existed across what are now the English Channel and the Gulf of Carpentaria (between Australia and New Guinea).

It shouldn't have been surprising, science geek that I am, but I'd honestly never thought that much about it.  The idea that climatic shifts affected history in such a profound way was an eye-opener.  Take, for example, the Little Ice Age, that started in the mid-fourteenth century and continued into the eighteenth, which had dramatic effects on the climate of northern Europe.  Prior to this, it'd been warm enough that shipping lanes to places like Iceland, Greenland, and Svalbard were open all year long; very quickly, they became impassible ice in the winter, and plagued by devastating storms in the summer.  All of this shut down what had been a thriving avenue for commerce and colonization.  The Icelanders survived okay; but the Greenlanders weren't so lucky.  All of the Viking era Greenland settlements were frozen out by 1400.

The idea was such a poignant one to me -- thinking about what it would be like to be one of the last settlers left alive, knowing you were stranded -- that it inspired me to write a poem called "Greenland Colony 1375," which is not only one of the very few poems I've ever written, but is the only piece of writing I've ever won a prize for -- second place in the 1999 Writers' Journal national poetry contest, an honor that still kid of blows me away when I think about it.

The reason all this comes up is a new study that appeared this week in Proceedings of the National Academy of Science suggesting that major impacts on the human species have been happening for a lot longer than even Burke's documentary covered.  A climatic teeter-totter called the "Wake Circulation" caused a back-and-forth swing of wet and dry from the east to the west part of the African continent, much as the monsoons do on a yearly basis.

But this oscillation has a period of 100,000 years.

That's enough time for an entire ecosystem to form.  Then when the climate changes, what were great adaptations for that habitat suddenly aren't any more, and either you move or you die.  But one other possibility is to live in an ecotone -- the transitional area between two climatic regions.  Since the rainfall didn't disappear from the continent as a whole, just shifted from one side to the other, the ecotone regions didn't move much.  The organisms that made it through the climate shifts tended to be ones that lived in ecotones.

Guess where humanity evolved?

"This alternation between dry and wet periods appeared to have governed the dispersion and evolution of vegetation as well as mammals in eastern and western Africa," said Stefanie Kaboth-Bahr of the University of Potsdam, who led the study.  "The resultant environmental patchwork was likely to have been a critical component of human evolution and early demography as well."

[Image licensed under the Creative Commons Bjørn Christian Tørrissen, Serengeti-African-Elephants, CC BY-SA 3.0]

"We see the archaeological signatures of early members of our species all across Africa," said Eleanor Scerri, of the Max Planck Institute, who co-authored the study.  "Innovations come and go and are often re-invented, suggesting that our deep population history saw a constant saw-tooth like pattern of local population growth and collapse.  Ecotonal regions may have provided areas for longer term population continuity, ensuring that the larger human population kept going, even if local populations often went extinct."

So we may owe our success -- and possibly even our existence -- to our evolving in an ecological borderland, and surviving while other, more specialized, species became extinct when their biome's climate shifted.  

All of this, of course, makes me wonder what the long-term outcome of our current idiotic, la-la-la-la-not-listening climate policy will be.  Will our long-standing flexibility save us -- or will we be, like the tragic last settlers in Greenland, done in by our own short-sightedness?

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Astronomer Michio Kaku has a new book out, and he's tackled a doozy of a topic.

One of the thorniest problems in physics over the last hundred years, one which has stymied some of the greatest minds humanity has ever produced, is the quest for finding a Grand Unified Theory.  There are four fundamental forces in nature that we know about; the strong and weak nuclear forces, electromagnetism, and gravity.  The first three can now be modeled by a single set of equations -- called the electroweak theory -- but gravity has staunchly resisted incorporation.

The problem is, the other three forces can be explained by quantum effects, while gravity seems to have little to no effect on the realm of the very small -- and likewise, quantum effects have virtually no impact on the large scales where gravity rules.  Trying to combine the two results in self-contradictions and impossibilities, and even models that seem to eliminate some of the problems -- such as the highly-publicized string theory -- face their own sent of deep issues, such as generating so many possible solutions that an experimental test is practically impossible.

Kaku's new book, The God Equation: The Quest for a Theory of Everything describes the history and current status of this seemingly intractable problem, and does so with his characteristic flair and humor.  If you're interesting in finding out about the cutting edge of physic lies, in terms that an intelligent layperson can understand, you'll really enjoy Kaku's book -- and come away with a deeper appreciation for how weird the universe actually is.

[Note: if you purchase this book using the image/link below, part of the proceeds goes to support Skeptophilia!]

A new twig on the family tree

My long-ago professor of evolutionary biology, Dr. Andrew Collins, once said, "The only reason humans came up with the concept of species as little air-tight boxes is that we have no near relatives still alive."  After a pause, he added, "And it's also the reason why evolution isn't completely self-evident to everyone."

I've always remembered that -- the word "species" is an artificial construct, and is the hardest concept in biology to come up with a consistent definition for.  No matter how you define it, you come up with exceptions and qualifications (something I dealt with a while back in my post "Grass, gulls, mosquitoes, and mice"), and it's only our determination that nature should be pigeonholeable (to coin a word) that keeps it in the textbooks.

We had a lovely example of that announced this week, when we learned that a stunningly well-preserved 3.8-million-year-old skull from Ethiopia had been identified as Australopithecus anamensis.  This species had been thought ancestral to A. afarensis (the species to which the famous Lucy belonged), but the Ethiopian skull (nicknamed MRD after Miro Dora, the site where it was discovered) is the same age as the earliest clearly A. afarensis remains.

So it looks like the two coexisted at least for a while, which is actually a much more common thing than the textbook one-species-slowly-morphing-into-another model.  Take, for example, our own (much more recent) ancestry, when only fifty thousand years ago there was enough interbreeding between Neanderthals, Denisovans, and anatomically-modern humans that we still find significant traces of each of those lineages in our own DNA.  (When I had my own DNA sequenced, I was proud to find out that I had 284 clearly Neanderthal markers, putting me in the 60th percentile and possibly explaining why I eat my t-bone steaks rare and like running around with little to no clothing on.)

The current discovery, though, is awfully cool.  Here's the skull itself, and a reconstruction of what its owner might have looked like, by the amazing John Gurche:

[Images courtesy of Jennifer Taylor, Dale Mori, and Liz Russell (right); and John Gurche and Matt Crow (left)] 

As an aside, John Gurche lives in the same little upstate New York village that I do, and I was privileged to teach all three of his kids.  His son, Loren, is now a paleontologist in his own right, and even when he was an eleventh grader in my AP Biology class he so clearly knew more about extinct animals than I did that I gladly asked him to contribute every time the topic came up in class.

Anyhow, the whole thing is wicked cool.  Picture it; an African savanna with not just one, but several different kinds of proto-hominins running around, some of them quite human-like and others more similar to our ape ancestors.  I'm always a little astonished at people who find the idea of our non-human ancestry demeaning -- I think it's grand that we're connected, in a series of unbroken links extending back three billion years, to every other life form on Earth.

And the whole thing took place, for the most part, in a smooth set of small changes, almost indistinguishable without the advantage of a huge time scale.  As Charles Darwin put it in The Descent of Man, "In a series of forms graduating insensibly from some apelike creature to man as he now exists, it would be impossible to fix on any definite point where the term 'man' ought to be used."

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This week's Skeptophilia book recommendation is about a subject near and dear to my heart; the possibility of intelligent extraterrestrial life.  In The Three-Body Problem, Chinese science fiction writer Cixin Liu takes an interesting angle on this question; if intelligent life were discovered in the universe -- maybe if it even gave us a visit -- how would humans react?

Liu examines the impact of finding we're not alone in the cosmos from political, social, and religious perspectives, and doesn't engage in any pollyanna-ish assumptions that we'll all be hunky-dory and ascend to the next plane of existence.  What he does think might happen, though, makes for fascinating reading, and leaves you pondering our place in the universe for days after you turn over the last page.

[Note: if you purchase this book from the image/link below, part of the proceeds goes to support Skeptophilia!]

A journey with the Denisovans

Every once in a while, I'll run across a piece of research that will make me think, "Ha!  How will the creationists explain that?  They'll have to admit that the evolutionary model is correct now!"

I am always wrong.

Assuming your conclusion, apparently, means never having to say you're sorry.

Take, for example, the recent study by Emilia Huerta-Sánchez et al., that showed that altitude adaptation in the Tibetan people was likely to be due to the presence of a specific gene from a group of Siberian proto-hominins called the Denisovans.  The gene, called EPAS1, protects the individuals who have it against hypoxia when the oxygen concentrations are low, is are not found in surrounding groups (the Han Chinese) but is found in the DNA of the now-extinct Denisovans.  Huerta-Sánchez et al. write:

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes.  These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations.  One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans, and was shown to be associated with differences in haemoglobin concentration at high altitude.

Re-sequencing the region around EPAS1... we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese.  Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression.

Put more simply, the scientists found that because of the distribution of the gene, the presence of EPAS1 in Tibetans was much more likely to be due to introgression (hybridization between two distinct species followed by repeated backcrossing to one of the parent species) rather than common ancestry followed by strong selection for phenotype.

Given that the Denisovans are otherwise genetically distinct from modern humans -- work by paleontologist Svante Pääbo supports the conclusion that the Denisovans represent a group whose ancestors left Africa, and have been separate from, both Neanderthals and modern humans for half a million years -- you'd think this would lead anyone who thinks that all humans come from a single family who miraculously survived the Great Flood less than 6,000 years ago to have some serious second thoughts.

Denisova Cave, southern Siberia [image courtesy of the Wikimedia Commons]

Nope.  Should have known better.  Turns out the creationists, for some reason, love the Denisovans, although I'm still at a loss for why.  Take, for example, what they have to say about all of this over at Creation.com:

It was easy to compare the [Denisovan DNA] to modern man, but in order to make comparisons to Neanderthal they needed more and better Neanderthal DNA to be sequenced.  The results were startling, for the Neanderthals turned out to be very close relations to each other, and this includes individuals from Spain, Germany, Russia and Croatia.  They were closer as a group than any of the modern populations used in the study.  That is a very large area for a very closely related group of people to cover.  The authors used the phrase “drastic bottleneck” to describe what they believe must have happened in the early years of the Neanderthal family line.  We do not feel it is ‘drastic’ to believe the Neanderthals were one family group who spread out into western Eurasia in the years after the Flood, who intermingled with other people groups as they also spread out, and who eventually died out as many other people groups have done in history... 

As with Neanderthals (from whom these Denisovans probably were a further splitoff), the evidence from hybridization scotches any notion that these were other than post-Babel descendants of Adam.

Or if you've a taste for even more bizarre pretzel logic, there's this, over at New Discoveries & Comments About Creationism:

How could have ancient humans who lived in a Siberian cave who were considered lower than Neanderthals interbreed with modern humans?  Before the sequencing of the genome took place it would have been considered, impossible!  But in human evolution, falsifications are confirmations... 

Rather than admitting their evolutionary story had been wrong with real-time observations, it’s now a race to get to the finish line. Not only that but it is implausible that this bone contained 70% of its original DNA after 82,000 years!  Who would believe such preservation of soft tissue?  It’s a stretch to say the least.  It’s much more likely that this individual lived a few thousand years ago at most... 

While a new sequencing technique now available to researchers that can be used to discern a genome from one DNA strand rather than both is quite remarkable but trying to explain it in historical terms which is forced into a particular framework known as human evolution, is not remarkable, it’s not even science. 

We live in an exciting time, since the earth is actually thousands of years old, we are able to learn more about the past rather than loosing [sic] valuable information which comes from DNA if the earth was older!

So... because the Denisovans interbred with some human populations, they had to be modern humans, and therefore less than 6,000 years old, and therefore god and the bible and the flood and all the rest of it.

Pardon me for a moment while I recover from the headdesk I just did.

I always expect, somehow, that logic and science and rationality will reach people.  Science remains our best tool for understanding the universe, and has a proven track record of uncovering the deepest, subtlest mechanisms of the world around us.

And what's odd is that the creationists pretty much buy all of it except evolution and cosmology.  Anything else is awesome -- chemistry, medical science, atmospheric science, most of physics, much of geology, and damn near all of the technological manifestations of scientific research.  Science and the scientific method, apparently, work just fine in all of those realms.

But not in biology and paleogeology, apparently.  The same scientific method that gives right answers in chemistry gives answers in biology and paleogeology that are off by three to four orders of magnitude (six orders of magnitude if you're talking about cosmology and the Big Bang).

So I'm probably engaging in a forlorn hope to think that the recent work on the Denisovans will have any effect on that.  Call me foolish, but I keep believing that one day, this will change, that the habit of teaching Bronze-Age creation myths to children as if they were fact will be over for good.

But to quote Aragorn, that day is not today.  As I said earlier, if you assume your conclusion, magic happens.  It's just that in this case, the magic has to do with insulating you from reality.