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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Walkabout

A couple of days ago, a long-time reader of (and frequent contributor of topics for) Skeptophilia sent me an email saying "Time to get your Archaeo-Geek excited!", with a link to a study about archaeological finds in Australia.  I was really confused at first because I read "Geek" as "Greek" and was puzzled about how there could be an ancient Greek settlement in Australia. 

I need new glasses.

Anyhow, once I got that sorted, I found that the actual research was pretty amazing.  A team of archaeologists led by Kasih Norman of Griffith University has discovered artifacts dating back to the Late Pleistocene Epoch -- on the order of twenty thousand years ago -- indicating a large human population living in a thriving ecosystem, with rolling hills and a large freshwater lake, all of which are now at the bottom of the Gulf of Carpentaria.

The authors write:

The submerged Northwest Shelf of Sahul (the combined landmass of Australia and New Guinea at times of lower sea level) was a vast area of land in the Late Pleistocene that connected the Australian regions of the Kimberley and western Arnhem Land during times of lower sea level than today.  The shelf extends >500 km northwest from the modern-day shoreline with a now-submerged landmass of ∼400,000 km2, an area more than 1.6 times larger than the United Kingdom.  The region might have been an area of initial entry for the peopling of Sahul.  Irrespective of the precise locations people used to disperse into Sahul, the Northwest Shelf is adjacent to the oldest known archaeological sites in Australia , and might have been one of the first inhabited landscapes on the continent.  Archaeological evidence for Late Pleistocene use of the continental shelves of Sahul by the First Australians is demonstrated on multiple large islands that are remnant portions of the continental margin, including Barrow Island, Kangaroo Island, Hunter Island, and Minjiwarra (Stradbroke Island).

The distribution of artifacts, which include stone axes, flint tools, and arrowheads, indicate at east two major pulses of settlement, which is cool because it lines up with what we know about the linguistics of the region.  The majority of the indigenous languages of northern and central Australia -- 306 of the 400 recorded native languages -- belong to the Pama-Nyungan family, which is (as a group) a linguistic isolate, related to no other known language group.  The rest are scattered clusters of unrelated languages, indicative of arrivals at different times or from different places, apparently when the Gulf of Carpentaria was mostly dry land and you could walk from New Guinea to Australia without getting your feet wet.

Eventually, of course, as we were coming out of the last ice age, the sea level rose and gradually that block of lowlands filled in from both sides, isolating Australia from the islands to the north and halting the walkabout that allowed for easy settlement.  But at its height, the archaeologists believe the now-submerged region could have been home to between fifty and five hundred thousand people.

"[Sea level rise] likely caused a retreat of human populations, registering as peaks in occupational intensity at archaeological sites," the authors write.  "Those who funneled into an archipelago on the shelf would go on to become the first maritime explorers from Wallacea [what is now the islands of eastern Indonesia], creating a familiar environment for their maritime economies to adapt to the vast terrestrial continent of Sahul."

Further research into the archaeology, topography, and paleoecology of the region is sure to turn up more information about a landscape that has altered dramatically in the last fifteen-thousand-odd years.  It also spurs researchers to look at other regions flooded by sea level rise -- like Doggerland, now beneath the turbulent waters of the North Sea -- perhaps to recover more clues about where and how our distant ancestors lived.

"Now submerged continental margins clearly played an important role in early human expansions across the world," the researchers write.  "The rise in undersea archaeology in Australia will contribute to a growing worldwide picture of early human migration and the impact of climate change on Late Pleistocene human populations."

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The bottleneck

When I was young, I was very much attracted to stories where things worked out because they were fated to happen that way.

It explains why so many of my favorite books and movies back then were Hero's Journey stories -- The Lord of the Rings, The Chronicles of Prydain, A Wrinkle in Time, Star Wars.  The idea that there's a reason things happen -- that life isn't just chaotic -- is seductive.  (And, of course, it's a major theme in most religions; so many of them have some version of "God has a plan.")

Appealing as this is, my view now is more like the conclusion Brother Juniper comes to by the end of Thornton Wilder's brilliant and devastating novel The Bridge of San Luis Rey -- that either God's plan is so subtle the human mind can't fathom it, or else there is no plan.  In my sixty-two years on this planet, most of what I've seen is much less like some orderly pattern than it is like a giant pinball game.

This seems to be true not only in the realm of human affairs, but in the natural world as well.  There are overall guiding principles (such as evolution by natural selection), but much of what happens isn't destined, it's contingent.  Even such basic things as our bilaterally symmetric body plans with paired organs, and our having five digits on each appendage, seem to be the result of what amount to evolutionary accidents.  (Which is why, if we're ever lucky enough to contact alien life, it is extremely unlikely to be humanoid.)

Another chaotic factor is introduced by random geological and astronomical occurrences -- the eruption of the Siberian Traps, for example, that kicked off the cataclysmic Permian-Triassic Extinction, and the Chicxulub Meteorite collision that took out (amongst many other groups) the non-avian dinosaurs.  Each of those events radically altered the trajectory of life on Earth; what things would look like now, had either or both of these not occurred, can only be vaguely guessed at.

It's a little humbling to think of all of the different ways things could have happened.  Most of which, it must be said, would result in Homo sapiens never evolving.  And researchers have just identified one more near miss on nonexistence our species had -- a colossal genetic bottleneck around nine hundred thousand years ago, during which our entire ancestral population appears to have dwindled to around thirteen hundred breeding individuals.

[Image licensed under the Creative Commons Jerónimo Roure Pérez, Homo heidelbergensis. Museo de Prehistoria de Valencia, CC BY-SA 4.0]

Species like ourselves, that are slow to reach maturity, which have few offspring at a time and require lots of parental care -- ones that, in the parlance of ecological science, are called K-selected -- tend not to recover from events like this.  The precariousness of the situation is highlighted by evidence that the population didn't really bounce back for over a hundred thousand years.

We were teetering on the edge of oblivion for a long time.

Evidence for this bottleneck comes from two sources -- a drastic decrease in human remains in the fossil record, and strong genetic evidence that all modern humans today descend from an extremely restricted gene pool, a little less than a million years ago.  This event coincided with the onset of a period of glaciation, during which sea level dropped, ice coverage expanded from the polar regions, and there were widespread droughts.  These conditions destroyed all but a tiny remnant of the human population -- and those few survivors are the ancestors of all seven billion of us modern humans.

Populations this tiny are extremely vulnerable, and that they survived long enough to recover is downright astonishing.  "It’s an extraordinary length of time," said Chris Stringer, of the Natural History Museum of London, who was not involved in the study.  "It’s remarkable that we did get through at all.  For a population of that size, you just need one bad climate event, an epidemic, a volcanic eruption and you’re gone."

We made it through, though.  Somehow.  And I guess near-catastrophes like this don't really settle the issue of whether it was all Meant To Be.  You can just as well interpret our winding path from the origins of life four billion years ago, with all of the close calls and almost-wipeouts we survived, as coming from our being part of some Master Plan.  But to me, it seems more like the vagaries of a chaotic universe -- one where all of us, humans and non-human species alike, are walking a tightrope.  If you went back sixty-seven million years and looked around, you'd have seen no reason to believe that the dinosaurs would ever be anything but the dominant group on Earth, but in the blink of the eye geologically, they would all be gone.  It's a cautionary tale about our own fragility -- something we should take to heart, as we're the only species on Earth that has evolved the intelligence to see the long-term consequences of our own actions, and potentially, to forestall our own being toppled from our position of dominance.

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A refuge from the cold

I've always wondered how our distant ancestors survived during the various ice ages.

After all, we're mostly-hairless primates evolved on the warm, comfy African savanna, and it's hard to imagine how we coped with conditions like you often see depicted in books on early humans:

Le Moustier Neanderthals by Charles Knight (1920) [Image is in the Public Domain]

Despite the bear pelts around their nether regions, I've always wondered how they didn't all freeze to death.  When the weather's nice, bare skin is fine; I only wear a shirt during the summer under duress, and can't remember the last time I wore swim trunks when I went swimming in my pond.  But when the weather's cold -- which, here in upstate New York, is more often than not -- I'm usually wearing layers, and that's even indoors with our nice modern heating system.  Okay, admittedly I'm a wuss about the cold, but the fact remains that we're evolved to dwell in temperate regions.  Which, for a significant part of the Pleistocene Epoch, most of the world was not.

In particular, during the Last Glacial Maximum, between twenty-six and twenty thousand years ago, much of the Northern Hemisphere was experiencing a climate that the word "unpleasant" doesn't even begin to describe.  The average temperature was 6 C (11 F) colder than it is today, which was enough to cause ice sheets to spread across much of North America and northern Europe (where I currently sit, in fact, was underneath about thirty meters of ice).  Much of the non-glaciated land experienced not only dreadful cold, but long periods of drought.  The combined result is that the sea level was an estimated 130 meters lower than it is today, and broad dry valleys lay across what are now the bottoms of the Bering Sea, the North Sea and English Channel, and the Gulf of Carpentaria.

These conditions opened up passageways for some people, and closed off living space for others.  This was the time that the various pulses of immigrants crossed from Siberia through Beringia and into North America, where they became the ancestors of today's Indigenous Peoples of North and South America.  (If you want to read a brilliant account of how this happened, and some of the science behind how we know, you must read Jennifer Raff's wonderful book Origin: A Genetic History of the Americas.)  The same sort of thing happened from southeast Asia into what is now Australia.

In Europe, though, things got dicey to the point that it's a wonder anyone survived at all.  In fact, what brings this up is a study that appeared in Nature last week by a humongous team led by paleogeneticist Cosimo Posth of the Max Planck Institute of Evolutionary Anthropology.  The team did a complete genomic analysis of 356 individuals whose remains range from thirty-five thousand to five thousand years of age -- so right across that awful Last Glacial Maximum period -- to try to figure out how groups moved when the ice started coming in, and afterwards, once it retreated.

What they found was that only one part of Europe showed a consistent human genetic signature throughout the time period: the Iberian Peninsula.  What this indicates is that modern Spain and Portugal were a "climate refugium" during the worst of the glaciation, where people came to stay when the climate turned very cold, and pretty much stayed put.  Other areas that you might think were possible candidates for comparatively warm hideouts, such as what are now Italy and Greece, show a significant genomic shift across the Last Glacial Maximum, indicating that the people there before the cold set in either migrated or else died out, and were replaced by immigrants who moved in after things warmed and the area once again became more hospitable for humans.

"At that time, the climate warmed up quickly and considerably and forests spread across the European continent," said Johannes Krause, senior author of the study, in an interview with Science Daily.  "This may have prompted people from the south to expand their habitat.  The previous inhabitants may have migrated to the north as their habitat, the 'mammoth' steppe, dwindled,.  It is possible that the migration of early farmers into Europe triggered the retreat of hunter-gatherer populations to the northern edge of Europe.  At the same time, these two groups started mixing with each other, and continued to do so for around three thousand years."

Me, I'm curious what happened to these people afterward.  As a linguist, not to mention a white guy of western European descent, I've wondered if we're talking about my forebears, here -- and what languages they spoke.  My suspicion is that we're looking at the ancestors of today's Basques, who still live in northern Spain; they speak a non-Indo-European language that is usually considered a relic of the earliest languages spoken in Europe.  The Indo-European-speaking peoples (therefore the ancestors of the majority of today's Europeans) didn't reach Europe until about four thousand years ago, so long after the heyday of the people who were the subjects of the Posth et al. paper.

So you have to wonder who the descendants of these very early Europeans are.  "Not me" is my general assessment, considering my general cold-hardiness.  Drop me into an ice age where I had to live in a cave, hike on glaciers, hunt mammoth, and fend off cave bears, and I'd last maybe three days, tops.  I'm highly impressed by the ability of these ancient humans to survive, but given a choice I'll stick with my warm house, indoor plumbing, electric stove, and coffee maker.

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Dire straits

During my junior year as an undergraduate, I had to take a humanities elective as part of my degree requirements and settled upon a class in archaeology, a subject which had always been an interest of mine.  The course description sounded pretty cool, and I thought it would be a fun challenge to take on.

However, I had not reckoned with the fact that the professor, one Dr. Servello, seemed to have a screw loose.  I found this out early on when one day he caught a glimpse of some genealogical charts in my binder (part of a family tree project I was doing as an anniversary gift for my parents), and added that to the fact that I wore a St. Christopher medal, and concluded from this that I was a member of a cult.

He kept me after class that day to ask me what my cult believed.  When I protested that in fact, I did not belong to a cult, he became genuinely concerned and said, "No, no, you don't need to be afraid to tell me!  I'm fascinated by alternative belief systems!"

But the most striking thing about Dr. Servello was that he never admitted to being wrong.  About anything.  He had a nearly Trumpian ability to continue arguing his point even after having hard evidence that he'd misspoken thrown into his face.  One time he argued for a half-hour over the correct pronunciation of a Chinese archaeological site -- with a student from China.  In very short order we learned not to bother contradicting him about any of the wacky things he said, because it never accomplished anything but wasting inordinate amounts of class time.

But as in any group, in the class there was That Guy.  He felt duty-bound to challenge Dr. Servello every time he made shit up, which was usually several times per class.  But the one that stands out in my memory was the epic argument that ensued when Dr. Servello was telling us about dire wolves.

"It's one of the largest predatory mammals ever," he said, with great conviction.  "They were fourteen feet tall at the shoulder."

Simultaneously all of the two-dozen-odd students in the class gave Dr. Servello the human equivalent of the Canine Head Tilt of Confusion.  Even so, most of us just added it to our growing list of bizarre Servello-isms, and were prepared to let it go.

But not That Guy.

"That's impossible," he said flatly.

"No, no, they were huge!" Dr. Servello insisted.  "Biggest predatory mammal ever!"

"That's impossible," That Guy said through clenched teeth.  "A wolf that big could look into a second-story window."

There followed a good forty-five minute-long argument, ending with That Guy grabbing his binder and storming out of class.

I related the story to some friends later.  These friends always waited with bated breath for me to come out of archaeology class, to see what lunatic pronouncements Dr. Servello had made that day.  This one, however, was impressive even by comparison to his previous efforts.

"That," one of my friends said reverently, "is one big bow-wow."

The topic comes up because while dire wolves are not fourteen feet high at the shoulder (which, for the record, would make them taller than a full-grown male African elephant) they are a fascinating species.  They were pretty impressive animals -- adults averaged a meter high at the shoulder and a little over two meters from tip to tail -- but their skeletal morphology led taxonomists to believe they were simply larger cousins of the North American gray wolf, descended from a parental species that had crossed the Bering Land Bridge into Eurasia.  But that idea is being challenged by some new analysis of DNA from dire wolves who were trapped in the La Brea Tar Seeps forty-some-odd thousand years ago, and a comparison with gray wolf DNA supports a conclusion that the last common ancestry of the two species was around 5.7 million years ago, before the ancestors of today's gray wolves had crossed into North America.

Dire wolf skeleton in the Sternberg Museum, Hays, Kansas [Image licensed under the Creative Commons James St. John, Canis dirus Sternberg Museum, CC BY 2.0]

The research, which was the subject of a paper in Nature this week, suggests that the morphological similarities between gray wolves and dire wolves are due to convergent evolution -- the evolution of superficially similar traits in distantly-related species that are under the same selective pressures.  And of course, these two were starting out closer in structure anyhow; no one is doubting that dire wolves are canids.  But the DNA difference is striking enough that the researchers are proposing to take the dire wolf out of the genus Canis and place it in its own new genus -- Aenocyon, meaning "terrible wolf."

"These results totally shake up the idea that dire wolves were just bigger cousins of gray wolves," said paleontologist Grant Zazula, who was not involved in the new study, in an interview with Scientific American.  "The study of ancient DNA and proteins from fossil bones is rapidly rewriting the ice age and more recent history of North America’s mammals."

It is not, for the record, rewriting how big they were.  As terrible as Aenocyon was, it wouldn't have towered over an elephant.  However, it is thought to have had the greatest bite force of any canid ever, and as it seems to have been a pack hunter, could take down some of the megaherbivores of its time -- giant ground sloths, North American camels and horses, bison... and even mastodons.

But like most of the Ice Age megafauna, the changing climate at the end of the Pleistocene put the dire wolf in dire straits.  They're thought to have persisted in areas of the northern Rockies as little as 9,500 years ago, but when the big prey animals began to disappear, selection favored their smaller (now thought to be distant) cousins, gray wolves.

Which is kind of a shame.  They were impressive beasts, even if they weren't the big bow-wows Dr. Servello claimed they were.  And it's nice to clarify at least a little more of their genetics and history, turning a lens on a species we thought we understood.

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As a biologist, I've usually thought of myself as immune to being grossed out.  But I have to admit I was a little shocked to find out that the human microbiome -- the collection of bacteria and fungi that live in and on us -- outnumber actual human cells by a factor of ten.

You read that right: if you counted up all the cells in and on the surface of your body, for every one human cell with human DNA, there'd be ten cells of microorganisms, coming from over a thousand different species.

And that's in healthy humans.  This idea that "bacteria = bad" is profoundly wrong; not only do a lot of bacteria perform useful functions, producing products like yogurt, cheese, and the familiar flavor and aroma of chocolate, they directly contribute to good health.  Anyone who has been on an antibiotic long-term knows that wiping out the beneficial bacteria in your gut can lead to some pretty unpleasant side effects; most current treatments for bacterial infections kill the good guys along with the bad, leading to an imbalance in your microbiome that can persist for months afterward.

In The Human Superorganism: How the Microbiome is Revolutionizing the Pursuit of a Healthy Life, microbiologist Rodney Dietert shows how a lot of debilitating diseases, from asthma to allergies to irritable bowel syndrome to the inflammation that is at the root of heart disease, might be attributable to disturbances in the body's microbiome.  His contention is that restoring the normal microbiome should be the first line of treatment for these diseases, not the medications that often throw the microbiome further out of whack.

His book is fascinating and controversial, but his reasoning (and the experimental research he draws upon) is stellar.  If you're interested in health-related topics, you should read The Human Superorganism.  You'll never look at your own body the same way again.

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