The oasis

I've always thought it was astonishing that anything short of extremely cold-adapted species could make it through an ice age.

During the last major glacial period, which peaked about twenty-one thousand years ago, the spot where I'm sitting right now was under a thirty-meter-thick layer of ice.  In fact, the hills about fifty kilometers south of us -- the Elmira Moraine -- marks the terminus of the glacier, where rocks, gravel, and soil that had been pushed forward by the advancing ice sheet got left behind as it melted.  During this period, the average global temperature was 6 C colder than it is now, and so much water was locked up as ice that the sea level was over a hundred meters lower than it is today.

My picture of how species survived (excluding the aforementioned cold-lovers) was that everything shifted range toward lower latitudes as the temperature cooled and the ice advanced, then reversed the process as the glacial period ended and the ice receded.  Species that couldn't shift quickly enough, or for which the climatic changes happened too fast to adapt, became extinct.  But according to a paper last week in Science Advances, the picture may not have been quite so simple.

One clue that our understanding was incomplete had to do with genetic diversity.  For a lot of species, we have a pretty good understanding of how quickly genetic mutations accrue, so looking at the genetic makeup of various populations within a species gives you an estimate of how long ago they had a common ancestor.  (And also tells you how closely each of those populations are related to the others.)  And in Europe, the populations of warmth-loving tree species like oaks suggested strongly that modern individuals weren't all descended from southern survivors which gradually expanded their ranges back northward as the glacial period ended twenty-odd-thousand years ago.  Their genetic diversity was too high for that to be plausible -- and some of the northern populations of modern oaks seemed to be a genetic cluster only distantly related to their southern cousins.

Fossils from the Czech Republic strongly suggest that what happened was that patches of the original forest were able to survive, clustered around hot springs that even at the height of the glacial period never froze over.  Geologist Jan Hošek of the Czech Geological Survey, who was lead author of the paper, found fossils of warmth-loving tree species preserved in geyserite -- a sedimentary rock produces by hot water dissolving and then depositing layers of opaline silica on exposed surfaces.  The hot springs created an oasis covering an estimated fifty square kilometers.  Not huge, but enough that a population of oaks and other temperate woodland plants (and presumably the animals they hosted) were able to survive the worst of the cold.

Artist's conception of the hot spring refugium [Image credit: artist Jiří Svoboda]

Being a warmth-lover myself, I always find it astonishing that species made it through some of these climatic extremes.  Not only the cold ones, of course; episodes like the Paleocene-Eocene Thermal Maximum, when the global temperature was 8 C above what it is now, can't have been pleasant, either.  But the recent discoveries show that given even a small refuge, living things will hang on despite all odds.

As Ian Malcolm famously put it, "Life, uh, finds a way."

****************************************

The global melting pot

One of the shakiest concepts in biological anthropology is race.

Pretty much all biologists agree that race, as usually defined, has very little genetic basis.  Note that I'm not saying race doesn't exist; just that it's primarily a cultural, not a biological, phenomenon.  Given the fact that race has been used as the basis for systematic oppression for millennia, it would be somewhere beyond disingenuous to claim that it isn't real.

The problem is, determination of race has usually been based upon a handful of physical characteristics, most often skin, eye, and hair pigmentation and the presence or absence of an epicanthal fold across the inner corner of the eye.  These traits are not only superficial and not necessarily indicative of an underlying relationship, the pigment-related ones are highly subject to natural selection.  Back in the nineteenth and early twentieth century, however, this highly oversimplified and drastically inaccurate criterion was used to develop maps like this one:

The "three great races" according to the 1885 Meyers Konversations-Lexikon 

This subdivides all humanity into three groups -- "Caucasoid" (shown in various shades of blue), "Negroid" (shown in brown), and "Mongoloid" (shown in yellow and orange).  (The people of India and Sri Lanka, shown in green, are said to be "of uncertain affinities.")  If you're jumping up and down saying, "Wait, but... but..." -- well, you should be.  The lumping together of people like Indigenous Australians and all sub-Saharan Africans (based mainly on skin color) is only the most glaring error.  (Another is that any classification putting the Finns, Polynesians, Koreans, and Mayans into a single group has something seriously amiss.)

The worst part of all of this is that this sort of map was used to justify colonialism.  If you believed that there really was a qualitative difference (for that, read genetic) between the "three great races," it was only one step away from deciding which one was the best and shrugging your shoulders at the subjugation by that one of the other two. 

The truth is way more complicated, and way more interesting.  By far the highest amount of genetic diversity in the world is in sub-Saharan Africa; a 2009 study by Jeffrey Long found more genetic differences between individuals from two different ethnic groups in central Africa than between a typical White American and a typical person from Japan.  To quote a paper by Long, Keith Hunley, and Graciela Cabana that appeared in The American Journal of Physical Anthropology in 2015: "Western-based racial classifications have no taxonomic significance."

The reason all this comes up -- besides, of course, the continuing relevance of this discussion to the aforementioned systematic oppression based on race that is still happening in many parts of the world, including the United States -- is a paper that appeared last week in Nature looking at the genetics of the Swahili people of east Africa, a large ethnic group extending from southern Somalia down to northern Mozambique.  While usually thought to be a quintessentially sub-Saharan African population, the Swahili were found to have only around half of their genetic ancestry from known African roots; the other half came from southwestern Asia, primarily Persia, India, and Arabia.

The authors write:

[We analyzed] ancient DNA data for 80 individuals from 6 medieval and early modern (AD 1250–1800) coastal towns and an inland town after AD 1650.  More than half of the DNA of many of the individuals from coastal towns originates from primarily female ancestors from Africa, with a large proportion—and occasionally more than half—of the DNA coming from Asian ancestors.  The Asian ancestry includes components associated with Persia and India, with 80–90% of the Asian DNA originating from Persian men.  Peoples of African and Asian origins began to mix by about AD 1000, coinciding with the large-scale adoption of Islam.  Before about AD 1500, the Southwest Asian ancestry was mainly Persian-related, consistent with the narrative of the Kilwa Chronicle, the oldest history told by people of the Swahili coast.  After this time, the sources of DNA became increasingly Arabian, consistent with evidence of growing interactions with southern Arabia.  Subsequent interactions with Asian and African people further changed the ancestry of present-day people of the Swahili coast in relation to the medieval individuals whose DNA we sequenced.

Note that on the Meyers Konversations-Lexikon map, the Arabians and Persians are considered "Caucasoid," the Indians are "uncertain," while the Swahili are definitely "Negroid."

A bit awkward, that.

It's appalling that we still use an outmoded and scientifically-unsound concept to justify bigotry, prejudice, and discrimination, despite the mountains of evidence showing that there's no biological basis whatsoever to the way race is usually defined.  Easy, I suppose, to hang on to your biases like grim death rather than questioning them when new data comes along.  Not even all that new; the Long study I referenced above was from fourteen years ago.  And hell, the Italian geneticist Luigi Luca Cavalli-Sforza was researching all this back in the 1960s.  Okay, it takes time for people's minds to catch up with scientific discovery, but how much damn time do you need?

The truth is that (1) ultimately, we all come from Africa, (2) since then, we've continued to move around all over the place, and therefore (3) the world is just a huge single melting pot.  Oh, and (4), the result is that we're all of (very) mixed ancestry.  I'm sorry if that makes some people feel squinky, but as I've pointed out before, the universe is under no obligation to align with your preconceived notions about how the world should work.

Time to accept the beauty and complexity of our shared humanity, and stop looking for further ways to divide us.

****************************************

Dog days

My wife and I share our living space with two canine companions.

First, we have Grendel, a (very) mixed breed, who looks like the result of blenderizing DNA from a pug, a German shepherd, a pit bull, a husky, and a fireplug.  He's cute, in a melancholy, "what are you so sad about, boy?" kind of way, and uses his wide range of pathetic expressions to get attention and food scraps.

Then we have Lena, whose ancestry includes redbone, blue-tick coonhound, and beagle.  She's eternally cheerful, has a tail that never stops wagging, lives for chasing squirrels, and has the intelligence of a loaf of bread.

They get along pretty well, although I kind of get the impression they don't really understand each other.  Grendel sometimes tries to play with Lena, in his ponderous sort of way, but it never lasts very long.  Lena usually ends up capering around, trying to fit all of the toys in her mouth at the same time, and Grendel gives up, sighs heavily, and plods over to us hoping we'll give him a dog cookie for at least giving it a shot.

I've always had dogs.  There's something about having a dog in my house that just seems necessary.  It always comes along with bushels of pet hair, muddy pawprints, and a variety of carpet stains, but I can't imagine that part of my life being missing.

I bring all of this up because I've always wondered about how dogs were domesticated.  Some people think they started out as utilitarian hunting animals, and after selection for responsiveness to human interaction, gradually morphed into what we have today.  Others think that the companionship aspect was there from the beginning, perhaps from as long ago as our cave-dwelling days.

The question, of course, will probably never have much going for it other than speculation, given that we don't have much in the way of evidence on which to base an answer.  However, a study by Laurent Frantz of Oxford University et al., published this week in Science, has at least given us a little more information about when and where this pivotal event took place.

According to Frantz's team, a study of DNA from the remains of 59 ancient dogs, including one from the late Neolithic Period (this particular mutt lived in Newgrange, Ireland about 4,800 years ago), dogs were domesticated at least twice -- once in Western Europe, and once in East Asia.  The East Asian dogs came with their human friends during migrations, and interbred with preexisting European Paleolithic dogs to produce most of the breeds familiar in Europe and America.  Says Tina Hesman Saey, who wrote about the study in Science News:

Using the Newgrange dog as a calibrator and the modern dogs to determine how much dogs have changed genetically in the past 4,800 years, Frantz and colleagues determined that dogs’ mutation rate is slower than researchers have previously calculated.  Then, using the slower mutation rate to calculate when dogs became distinct from wolves, the researchers found that separate branches of the canine family tree formed between 20,000 and 60,000 years ago.  Many previous calculations put the split between about 13,000 and about 30,000 years ago, but the new dates are consistent with figures from a study of an ancient wolf’s DNA.

Which is a long time ago, considering that most of the distinct modern dog breeds trace back to a common ancestor only a few centuries ago.  (Exceptions include some of the old Chinese breeds, such as the Pekingese, Shih-Tzu and Sharpei, which seem to be a good bit older than that.)  But despite the recent diversification of shapes, sizes, colors, and behaviors, what seems pretty certain is that dogs in some form have been our friends for a long, long time.

Compare this to cats.  A recent study done in Japan found that cats recognize their own names and their owners' voices, but apparently evolved not to give a damn.  Their ears turn and whiskers twitch when their owners speak, but it doesn't make a lot of difference to their behavior otherwise.  I find this result unsurprising.  I can say from personal experience that my 18-year-old cat Geronimo considers me to be warm-blooded furniture, and his expression usually says, "I am only refraining from clawing your eyes out because you feed me expensive canned food every day."  Contrast this to Lena, whose body language communicates "I LOVE YOU SOOOO MUCH" if I give her a muddy stick to chew on.

Not that I'm biased, or anything.  I'm sure that a lot of this is my projecting my own emotions, thoughts, and feelings onto my pets, but when Grendel looks up at me with those big sad eyes, it's hard not to sense a bond.  Maybe we've evolved into the relationship, too, because there's something primal and comforting about having a dog around.

Despite the hair, muddy pawprints, and carpet stains.

Skin deep

We were talking in my AP Biology class yesterday about the potential for skin damage from exposure to ultraviolet light.  Later in the day,  a student sent me a YouTube video called "How the Sun Sees You" that uses a UV-sensitive camera to see the sun damage on people's skin (and also illustrates that sunscreen does work, given that it looks an opaque black when filmed in the ultraviolet region of the spectrum).

All of which is well and good, but then I scrolled down to the comments section, which I know I should never do, and I found the following.  Spelling and grammar are as written, so I don't use up my "sic" allotment all in one go:

First off everyone has to stop believing that Melanin a.k.a. Carbon protects us from u.v. rays.  Carbon in the skin actually absorbs ultraviolet rays in a process that is now being called Ultrafast Internal Conversion.  Not one person has mentioned this..  The Elemental Compound for C Carbon is 666.  6 Electrons 6 Neutrons 6 Protons.  The origins of the 666.  The Catholics call It "the mark of beast" which is code for "mark of the our destroyers"  We all know that Carbon is the building blocks of life.  Carbon defines life therefore us Moors who are incorrectly referred to as "Black People" are the building blocks for Human life and biology.  This is true because no one else on the planet possesses the levels of Carbon in the body and brain quite like The Moors. (remember a moor is a black man or women)  In other words, us "Black people" are and forever will be The genetic template for the Human being.  Black ppl we are Human In it's truest form.  Of course there are plenty lies circulating the damn truth.  All non black people are merely human hybrids.  All races were genetically engineered from the supreme Human.  Clones much?  DARK POWER!!

So naturally I thought, "Well, that's a viewpoint I've never run into before."  (I also thought, "I hope this person is on medication" and "this is what it looks like when someone fails high school biology.")  But I did some research, and I found out that this is not the claim of a lone wacko.  This is the claim of a large number of wackos.  There's a whole school of thought (although I hesitate to use either word in this context) that revolves around the contention that people of African descent are superior because they have lots more carbon in them.

Take, for example, the page "Carbon & Melanin Secret of Secrets" over at the amazingly wacky site Godlike Productions.  In it, we find a wall of text that can be summarized as follows:

• Carbon is some seriously mystical stuff.  Besides the 6-6-6 thing mentioned above, it has four bonds that are shaped like a swastika.
• It also has something to do with the Buddhist "om," the Christian cross, and the Greek letters alpha and omega.
• Melanin is dark.  So is carbon.  Therefore melanin is carbon.
• Melanin is the "key to life" and is the "organizing molecule for living systems."
• Melanin is an ordinary conductor, a semiconductor, and a superconductor.  Don't ask me how it can be all three at the same time.
• Satan and Saturn are the same thing.
• Because the symbol for carbon is C, and the symbol for cytosine (one of the nitrogenous bases in DNA) is C, they're the same thing.  It couldn't be because in English, both of them have names that start with "c."
• Some other weird stuff about DMT and alchemy and prophecies that frankly I couldn't read because my eyes were spinning.

I read this whole thing with an expression like this:

What bothers me most about all of this is not that crazy people are making shit up.  That's what crazy people do, after all.  What bothers me is that apparently this claim has gotten some traction amongst people who want justification for believing that dark-skinned humans are intrinsically better than light-skinned humans, and who cannot even be bothered to take a look at the Wikipedia page for melanin, wherein we find that melanin isn't carbon.  It contains carbon, but after all, so does chalk, which last I looked was white.

The ironic thing is that when you talk to actual anthropologists and geneticists, most of 'em will tell you that the biological basis for race is tenuous at best.  Race is a cultural phenomenon, not a genetic one.  If you want your mind blown on this topic, consider the following quote from Alan Goodman:

Richard Lewontin did an amazing piece of work which he published in 1972, in a famous article called "The Apportionment of Human Variation." Literally what he tried to do was see how much genetic variation showed up at three different levels. 

One level was the variation that showed up among or between purported races. And the conventional idea is that quite a bit of variation would show up at that level. And then he also explored two other levels at the same time. How much variation occurred within a race, but between or among sub-groups within that purported race. 

So, for instance, in Europe, how much variation would there be between the Germans, the Finns and the Spanish? Or how much variation could we call local variation, occurring within an ethnicity such as the Navaho or Hopi or the Chatua? 

And the amazing result was that, on average, about 85% of the variation occurred within any given group. The vast majority of that variation was found at a local level. In fact, groups like the Finns are not homogeneous - they actually contain, I guess one could literally say, 85% of the genetic diversity of the world. 

Secondly, of that remaining 15%, about half of that, seven and a half percent or so, was found to be still within the continent, but just between local populations; between the Germans and the Finns and the Spanish. So, now we're over 90%, something like 93% of variation actually occurs within any given continental group. And only about 6-7% of that variation occurs between "races," leaving one to say that race actually explains very little of human variation...

But, for the most part, you know that the basic human plan is really the basic human plan, and is found almost anywhere in the world. Most variation is found locally within any group. Why don't we believe that? Because we happen to ascribe great significance to skin color, and a few other physical cues... And, in fact, though, these may happen to be a few of the things that do widely vary from place to place. But, that's not true under the skin. Rather, quite another story is told by looking at genes under the skin.

Which should really inform us about how we treat people who don't look like us, shouldn't it?  We're all human.  We have a vast overlap in our genetics, even if you choose two people who look very different from each other.  And at our cores, most of us want the same things -- food, shelter, love, security, compassion.  When we start claiming that people of different ethnicities deserve different levels of privilege, we're engaging in a mindset that is not only destructive, it's counterfactual.

And that applies to all racists equally, whether they're neo-nazis or cranks who claim that anyone without much melanin in their skin is an evil hybrid clone.