The genes of the ancestors

When I had my DNA tested two years ago, I found out I have 330 distinctly Neanderthal markers in my genes.  This, apparently, is well above average for people of western European descent, and may explain why I like to run around half-naked and prefer my steaks medium-rare.

In all seriousness, most people of European descent have Neanderthal ancestry; it's less common in people of African and Asian ancestry, and in the indigenous peoples of Australia and North America.  It makes sense, once you know where they lived.  The Neanderthals were a predominantly European species (or sub-species; the experts differ, and honestly, the definition of species is so mushy anyhow that it's probably splitting hairs to argue about it).  They seem to have split off from the main population of hominins in the region something like five hundred thousand years ago.  The first unambiguously Neanderthal bones are 430,000 years old, and they persisted until 40,000 years ago -- and we still don't know why they died out.

What's certain is that it wasn't a lack of sophistication and intelligence by comparison with contemporaneous Homo sapiens, whatever you might have gleaned from Jean Auel's The Clan of the Cave Bear.  The Neanderthals were plenty smart.  They had culture, made paintings on cave walls, and created jewelry.  To judge by the Divje Babe flute they made music.  They ceremonially anointed their dead, and appear to have had some concept of an afterlife.  They had the same version of the FOX-P2 gene we do, suggesting they had spoken language.  So despite my earlier quip, Neanderthals were far from the slow, sluggish, stupid "cave men" we often picture when we hear the name.

[Image licensed under the Creative Commons Werner Ustorf, Neanderthal man reconstruction, Natural History Museum, London, CC BY-SA 2.0]

As my own ancestry indicates, there was a good bit of crossbreeding between Neanderthals and "modern" humans.  (I put modern in quotes not only because it's self-congratulatory, but because all organisms on Earth have exactly the same time duration of their ancestral lineages; words like primitive and modern really "less changed since the common ancestor" and "more changed since the common ancestor," but those are clunky.  So I'll continue to use primitive and modern, although with the caveat that they're not value judgments.)

What's interesting, though, is that the genetic input of the Neanderthals was asymmetrical.  Of the Neanderthal markers we carry around, none are on the Y chromosome, indicating that something blocked any contribution of Y-chromosomal genes from our Neanderthal forebears.  It's possible that the answer is simple -- that most inter-species matings were between "modern" human men and Neanderthal women.  But now a new study from The American Journal of Human Genetics, by Fernando Mendez, G. David Poznik, and Carlos Bustamante (of Stanford University), and Sergi Castellano (of the Max Planck Institute for Evolutionary Anthropology) has suggested another reason the Neanderthal Y chromosome didn't survive; mutations that caused male hybrid fetuses to spontaneously miscarry.

The authors write:

Sequencing the genomes of extinct hominids has reshaped our understanding of modern human origins.  Here, we analyze ∼120 kb of exome-captured Y-chromosome DNA from a Neandertal individual from El Sidrón, Spain.  We investigate its divergence from orthologous chimpanzee and modern human sequences and find strong support for a model that places the Neandertal lineage as an outgroup to modern human Y chromosomes—including A00, the highly divergent basal haplogroup.  We estimate that the time to the most recent common ancestor (TMRCA) of Neandertal and modern human Y chromosomes is ∼588 thousand years ago (kya)...  This is ∼2.1 times longer than the TMRCA of A00 and other extant modern human Y-chromosome lineages.  This estimate suggests that the Y-chromosome divergence mirrors the population divergence of Neandertals and modern human ancestors, and it refutes alternative scenarios of a relatively recent or super-archaic origin of Neandertal Y chromosomes.  The fact that the Neandertal Y we describe has never been observed in modern humans suggests that the lineage is most likely extinct.  We identify protein-coding differences between Neandertal and modern human Y chromosomes, including potentially damaging changes to PCDH11Y, TMSB4Y, USP9Y, and KDM5D.  Three of these changes are missense mutations in genes that produce male-specific minor histocompatibility (H-Y) antigens. Antigens derived from KDM5D, for example, are thought to elicit a maternal immune response during gestation.  It is possible that incompatibilities at one or more of these genes played a role in the reproductive isolation of the two groups.

Which is an interesting hypothesis.  It's possible, of course, that there was more than one thing going on, here; there may also have been a skewed distribution of genders in inter-species matings as well as a higher death rate in male children of male Neanderthals and female "modern" humans.   In fact, genetics and culture can sometimes create a feedback loop; the taboo in traditional Basque society against Basque women marrying non-Basque men is thought in part to have come from the high frequency amongst the Basques of the Rh negative blood group allele, resulting in children of Basque women (likely to be Rh negative) and non-Basque men (likely to be Rh positive) having a higher probability of dying of Rh incompatibility syndrome.

So sometimes cultural norms and genetics can intertwine in curious ways.

In any case, that's today's science story, tying together anthropology, genetics, and evolutionary biology, all particular fascinations of mine.  And the fact that it could well be talking about some of my own ancestry adds a nice twist.  Hopefully my forebears will forgive me for my jab about running around naked.  Maybe the most Neanderthal thing about me is that I play the flute.  Kind of turns the "cave man" trope upside down, doesn't it?

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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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Rehabilitating our cousins

The Neanderthals have gotten an undeservedly bad reputation.

"Neanderthal" has become an insult for someone perceived as dumb, crude, vulgar, lacking in any sort of refinement.  This perception wasn't helped any by Jean Auel's Clan of the Cave Bear and its sequels, where the "Clan" (the Neanderthals) are primitive, ugly, brutal people (personified by the violent and cruel Broud), contrasted to the beautiful, heroic, sophisticated Cro Magnons (such as virile, handsome, blue-eyed Jondalar, who is portrayed basically as a prehistoric Liam Hemsworth, only sexier).  The truth is way more complex than that; they certainly weren't unintelligent, and in fact, the most recent Neanderthals had an average brain size larger than a modern human's.  (I'm aware that brain size doesn't necessarily correlate with higher intelligence, but the depiction of them as tiny-brained primitives is almost certainly false.)

They had culture; the Mousterian tool complex, with its beautifully fluted stone arrowhead points, was Neanderthal in origin.  They were builders, weavers, jewelry-makers, and knew the use of medicinal plants.  There's evidence that they made music -- the Divje Babe flute, from 43,000 years ago, was made by Neanderthals from a bear femur, was probably made by Neanderthals.  The structure of the Neanderthal hyoid bone, and the presence of the FoxP2 gene, strongly suggests that they had the capacity for language, although cognitive scientist Philip Lieberman suggests that their mouth morphology would have made it difficult or impossible to articulate nasal sounds and the phonemes /a/, /i/, /u/, /ɔ/, /g/, and /k/, so any language they had probably wasn't as rich phonetically as ours are.  (Although that, too, is an overgeneralization; as I pointed out in a post only a month ago, the phonemic inventory of modern languages varies all over the place, with some only having a dozen or so distinct sounds.)

Another thing that people tend to get wrong is that the Neanderthals were displaced by modern Homo sapiens, and eventually driven to extinction, because we were smarter, faster, and more sophisticated.  Which is not only false, it carries that hint of self-congratulation that should be an immediate tipoff that there's more to it.  It's undeniable that our Neanderthal cousins did diminish and eventually disappear something on the order of forty thousand years ago, but what caused it is uncertain at best.  Other hypotheses regarding why they declined are climatic shifts, disease, and loss of food sources... and, most interestingly, that they interbred with, and were eventually subsumed by, modern humans.  Genetic analysis shows that a great many of us -- including most people of European ancestry -- contain genetic markers indicating Neanderthal ancestry.  Current estimates are that western Europeans have the highest percentage of Neanderthal DNA (at around four percent), while some groups, most notably sub-Saharan Africans, have almost none.

My own DNA apparently has 284 distinct Neanderthal markers, putting me in the sixtieth percentile.  So at least I'm above average in something.

[Image licensed under the Creative Commons Neanderthal-Museum, Mettmann, Homo sapiens neanderthalensis-Mr. N, CC BY-SA 4.0]

What brings this up is some new research indicating that the overlap between Neanderthals and anatomically modern humans may have lasted longer than we thought, and completely upends the picture of hordes of highly-advanced humans (led, of course, by Liam Hemsworth) sweeping over and destroying the primitive knuckle-dragging Neanderthal cave-dwellers.  Archaeologists working in the cave complex Grotte Mandrin, in the Rhône Valley of France, came upon a child's tooth and some stone tools (both of a distinctly modern sort), that date from 54,000 years ago -- a good twelve thousand years earlier than previous estimates.

"It wasn't an overnight takeover by modern humans," said Chris Stringer, of the Natural History Museum of London, who co-authored the paper.  "Sometimes Neanderthals had the advantage, sometimes modern humans had the advantage, so it was more finely balanced...  We have this ebb and flow.  The modern humans appear briefly, then there's a gap where maybe the climate just finished them off and then the Neanderthals come back again..  [W]e don't know the full story yet.  But with more data and with more DNA, more discoveries, we will get closer to the truth about what really happened at the end of the Neanderthal era."

Human history (and prehistory) are a lot more complex than you'd think on first glance, and it bears keeping in mind that usually when we build up a picture of something that happened in the past, we're working on (very) incomplete data filled in with guesses and surmises.  If a time machine is ever invented, and we can go back and look for ourselves, I think we'd be astonished at how much we missed -- or got flat wrong.

It reminds me of the famous quote by H. L. Mencken -- "For every problem, there is an answer that is clear, simple... and wrong."

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People made fun of Donald Rumsfeld for his statement that there are "known unknowns" -- things we know we don't know -- but a far larger number of "unknown unknowns," which are all the things we aren't even aware that we don't know.

While he certainly could have phrased it a little more clearly, and understand that I'm not in any way defending Donald Rumsfeld's other actions and statements, he certainly was right in this case.  It's profoundly humbling to find out how much we don't know, even about subjects about which we consider ourselves experts.  One of the most important things we need to do is to keep in mind not only that we might have things wrong, and that additional evidence may completely overturn what we thought we knew -- and more, that there are some things so far out of our ken that we may not even know they exist.

These ideas -- the perimeter of human knowledge, and the importance of being able to learn, relearn, change directions, and accept new information -- are the topic of psychologist Adam Grant's book Think Again: The Power of Knowing What You Don't Know.  In it, he explores not only how we are all riding around with blinders on, but how to take steps toward removing them, starting with not surrounding yourself with an echo chamber of like-minded people who might not even recognize that they have things wrong.  We should hold our own beliefs up to the light of scrutiny.  As Grant puts it, we should approach issues like scientists looking for the truth, not like a campaigning politician trying to convince an audience.

It's a book that challenges us to move past our stance of "clearly I'm right about this" to the more reasoned approach of "let me see if the evidence supports this."  In this era of media spin, fake news, and propaganda, it's a critical message -- and Think Again should be on everyone's to-read list.

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Art (pre)history

The human drive to produce beauty is a curious thing, and one that science has thus far been unable to explain fully.  No less a luminary than Albert Einstein highlighted this when he said, "It would be possible to describe everything scientifically, but it would make no sense; it would be without meaning, as if you described a Beethoven symphony as a variation of wave pressure."

Many of us -- most of us, I suspect -- feel at least some need to create.  I'm defining this in its broadest sense; I mean not only the most obvious examples of art and music, but abstract beauty in writing, the graceful fluidity of truly gifted dancers and athletes, and the simple, everyday enjoyment of gardening, crocheting, macramé, and all of the other dozens of creative hobbies we engage in.

I'm no stranger to this drive myself.  My primary outlets are writing and music, but I'm also an amateur potter.  I came to art rather late in the game, which is odd because both of my parents were talented artists -- my mother was an oil painter and porcelain sculptor, while my father made jewelry and stained glass windows.  I showed no aptitude for art while growing up, but on a lark (and mainly because my wife was doing it and encouraged me to give it a try) took a class in making wheel-thrown pottery about ten years ago.  I got hooked, and stuck with it despite the fact that such skills do not come naturally to me.  By this point I can turn out some pieces that are pretty decent even to my hypercritical and rather unforgiving eye.

A stoneware bottle from my most recent firing

The open question is why so many of us feel a compulsion to do these sorts of things.  That they serve no practical purpose has become something of a running joke between my wife and I; "I'm heading out to the studio, because heaven knows we need more pottery" is a phrase one of us utters on nearly a daily basis.

The facile answer ("'cuz it's fun") doesn't really explain very much, and although it's tempting to ascribe an evolutionary/selective rationale -- that art and music and so on foster social cohesion, perhaps, giving the group stronger bonds and a better chance of surviving through enhanced cooperation -- explanations like those rest on some pretty tenuous grounds.  The truth is we don't know, but given the ubiquity of creative endeavors, it's certainly a powerful driver whatever its origins and purpose.

And it has quite a significant history in our species.  Two recent papers have looked at different aspects of truly ancient art, and found that (1) the impulse to create art goes back at least fifty thousand years, and (2) our ancestors were motivated enough to create it that they were willing to undergo considerable hardships to do so.

In the first, which appeared in Nature this week, a team of archaeologists working at a site called Einhornhöhle in northern Germany found a deer bone engraved with what appear to be symbolic carvings (i.e. not just knife marks left by butchering).  The bone has been dated at 51,000 years old -- at which point that region of Europe was populated by Neanderthals.

So wherever this artistic impulse comes from, we apparently share it with our cousins.

The authors write:

While there is substantial evidence for art and symbolic behaviour in early Homo sapiens across Africa and Eurasia, similar evidence connected to Neanderthals is sparse and often contested in scientific debates.  Each new discovery is thus crucial for our understanding of Neanderthals’ cognitive capacity.  Here we report on the discovery of an at least 51,000-year-old engraved giant deer phalanx found at the former cave entrance of Einhornhöhle, northern Germany.  The find comes from an apparent Middle Palaeolithic context that is linked to Neanderthals.  The engraved bone demonstrates that conceptual imagination, as a prerequisite to compose individual lines into a coherent design, was present in Neanderthals.  Therefore, Neanderthal’s awareness of symbolic meaning is very likely.  Our findings show that Neanderthals were capable of creating symbolic expressions before H. sapiens arrived in Central Europe.

In the second, which appeared last week in PLOS-ONE, a team of researchers led by archaeologist Iñaki Intxaurbe of the University of the Basque Country (Leioa, Spain) decided to see what technical hurdles our distant kin had to overcome in order to create cave art.  Working barefoot while carrying torches made of juniper branches or carved stone lamps filled with animal fat -- a decent guess for the kinds of artificial lighting they might have used -- Intxaurbe and his team found that producing paintings in deep caves (like the ones at Lascaux, France and Armintxe, Spain) took some serious planning.  Torches give good lighting, but burn out quickly (an average of 41 minutes) and produce a lot of smoke.  Lamps are relatively smokeless but produce much lower illumination.  And each site presented different challenges because of issues like dampness, temperature, and airflow.

So whatever significance these paintings had -- whether they were some kind of representative ritual magic, or whether (like many of us) they simply felt driven to create -- we might never know.  But what seems certain is that we are the inheritors of a very, very powerful drive, and one that goes back at least fifty millennia.

Think about that next time you get out the knitting needles, paintbrushes, or clay.

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Most people define the word culture in human terms.  Language, music, laws, religion, and so on.

There is culture among other animals, however, perhaps less complex but just as fascinating.  Monkeys teach their young how to use tools.  Songbirds learn their songs from adults, they're not born knowing them -- and much like human language, if the song isn't learned during a critical window as they grow, then never become fluent.

Whales, parrots, crows, wolves... all have traditions handed down from previous generations and taught to the young.

All, therefore, have culture.

In Becoming Wild: How Animal Cultures Raise Families, Create Beauty, and Achieve Peace, ecologist and science writer Carl Safina will give you a lens into the cultures of non-human species that will leave you breathless -- and convinced that perhaps the divide between human and non-human isn't as deep and unbridgeable as it seems.  It's a beautiful, fascinating, and preconceived-notion-challenging book.  You'll never hear a coyote, see a crow fly past, or look at your pet dog the same way again.

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

Peering into the Neanderthal brain

Despite having taught genetics for 32 years, it still is astonishing to me that all of the genetic diversity of the 7.7-odd-billion humans on Earth is accounted for by differences amounting to only a tenth of a percent of the genome.

Put a different way, if you were to find the person who is the most genetically different from you, the two of you would still have a 99.9% overlap in your DNA.  A lot of that additional tenth of a percent is made up of genes for obvious appearance-related features -- eye color and shape, hair color and texture, skin color, body build, and so on.  But even these characteristics, which are usually considered to determine race, don't really tell you all that much.  A San man and his Tswana neighbor in Botswana were both called "black" by the white European colonists, but those same white Europeans were genetically closer to people in Japan than the San and Tswana were to each other.  There is, in fact, more human genetic diversity on the continent of Africa than there is in the entire rest of the world put together -- unsurprising, perhaps, given that our species originated there.

Race, then, is a social construct, not really a biological one.  There are some distinct genetic signatures in different ethnic groups, which is what allows the "percent composition" you get if you have your DNA analyzed by Ancestry or 23 & Me, and within their limitations, they don't have bad accuracy.  My own DNA test lined up almost perfectly with what I know of my family tree; something like two-thirds from western and northwestern France, a good chunk of the rest from Scotland and England, and an interesting (and spot-on) 6% of my DNA from my Ashkenazi Jewish great-great-grandfather.

Even more surprising, perhaps, is that the average difference between the human genome and that of our closest non-human relatives -- chimps and bonobos -- is still only 1.2%.  So all of the lineages that split off from our line of descent after the chimps and bonobos did, on the order of five million years ago, would be closer than that to us genetically.  This has been confirmed by analysis of DNA in those now-extinct groups of hominins -- Neanderthals, Denisovans, and so on.

Here, we're talking about way bigger physical differences than there are between any two races of modern humans you might pick.  Bone structure, brain size and structure, body proportions -- some pretty major stuff.  Still, the Neanderthals, Denisovans, and us are all the same species, by the rather mushy definition of a species as being a group of organisms capable of reproduction that results in fertile offspring; modern humans have a good chunk of Neanderthal and Denisovan DNA, also at least in part detectable by genetic testing.

[Image licensed under the Creative Commons Stefan Scheer, Neandertaler reconst, CC BY-SA 3.0]

Why all this comes up is a study in Science this week by a huge team led by Alysson Muotri of the University of California - San Diego in which geneticists tinkered with human stem cells, altering their DNA to reflect one of 61 genes that have been identified as differences between ourselves and our Neanderthal and Denisovan kin.  They then allowed those cells to proliferate and form organoids -- mini-brains that can form connections (synapses) just as a developing brain in an embryo would.

Well, my first thought was, "Haven't these people ever watched a science fiction movie?"  Because scientists always try shit like this in movies, and it always ends up with a giant brain-blob that goes rogue, escapes the lab, and proceeds to eat Tokyo.  But Dr. Muotri assures us that that's not possible in this case.  He explains that organoids are incapable of living all that long because they don't have all the support structures that real brains have -- a circulatory system for example -- so they'd never be capable of surviving outside the petri dish.

To which I say: of course, Dr. Muotri.  That's what you would say.  Just realize that in those same science fiction movies, it's always the scientist who says, "Wait, stand back!  Let me try to communicate with it!" and ends up being the first one to get devoured.

So don't say I didn't warn you.

In any case, what is kind of amazing is that these organoid brains with a single gene altered to what our Neanderthal cousins had developed in a way that was completely unlike our own.  As the press release in Science Daily explained it:

The Neanderthal-ized brain organoids looked very different than modern human brain organoids, even to the naked eye.  They had a distinctly different shape.  Peering deeper, the team found that modern and Neanderthal-ized brain organoids also differ in the way their cells proliferate and how their synapses -- the connections between neurons -- form.  Even the proteins involved in synapses differed.  And electrical impulses displayed higher activity at earlier stages, but didn't synchronize in networks in Neanderthal-ized brain organoids.

All of that, from a single gene.

"This study focused on only one gene that differed between modern humans and our extinct relatives. Next we want to take a look at the other sixty genes, and what happens when each, or a combination of two or more, are altered," Muotri said.  "We're looking forward to this new combination of stem cell biology, neuroscience and paleogenomics.  The ability to apply the comparative approach of modern humans to other extinct hominins, such as Neanderthals and Denisovans, using brain organoids carrying ancestral genetic variants is an entirely new field of study."

So that "less than a percent" label on the differences between ourselves and our nearest non-modern-human kin is a little misleading, because apparently some of that less-than-a-percent are really critical.

In any case, that's our view of the cutting edge of science for today.  One can't help but be impressed with studies like this, which accomplish feats of genetic messing-about that would have been themselves in the realm of science fiction twenty years ago.  I wonder what the next twenty years will bring?  Hopefully not brain blobs eating Tokyo.  I mean, I'm all for scientific advancement, but you have to draw the line somewhere.

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 Many of us were riveted to the screen last week watching the successful landing of the Mars Rover Perseverance, and it brought to mind the potential for sending a human team to investigate the Red Planet.  The obstacles to overcome are huge; the four-odd-year voyage there and back, requiring a means for producing food, and purifying air and water, that has to be damn near failsafe.

Consider what befell the unfortunate astronaut Mark Watney in the book and movie The Martian, and you'll get an idea of what the crew could face.

Physicist and writer Kate Greene was among a group of people who agreed to participate in a simulation of the experience, not of getting to Mars but of being there.  In a geodesic dome on the slopes of Mauna Loa in Hawaii, Greene and her crewmates stayed for four months in isolation -- dealing with all the problems Martian visitors would run into, not only the aforementioned problems with food, water, and air, but the isolation.  (Let's just say that over that time she got to know the other people in the simulation really well.)

In Once Upon a Time I Lived on Mars: Space, Exploration, and Life on Earth, Greene recounts her experience in the simulation, and tells us what the first manned mission to Mars might really be like.  It makes for wonderful reading -- especially for people like me, who are just fine staying here in comfort on Earth, but are really curious about the experience of living on another world.

If you're an astronomy buff, or just like a great book about someone's real and extraordinary experiences, pick up a copy of Once Upon a Time I Lived on Mars.  You won't regret it.

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

Back to Africa

I was kind of tickled, when I got my "23 & Me" results back a couple of years ago, to find out that I had 284 identified Neanderthal markers, identifying me as having more Neanderthal ancestry than 60% of the samples tested.

The reason I was happy about this is not because it gave me an explanation for why I like my steaks rare and have a general aversion to wearing clothes.  It was more because I find the Neanderthals a fascinating bunch.  Far from the low-intelligence cave trolls a lot of us picture them as -- witness the use of their name as an insult -- by the end they actually had larger brains than your average modern Homo sapiens.  They had culture; they anointed and buried their dead, seem to have had music (if the archaeologists are correct about the origin of the Divje Babe flute), and might even have had language -- they had the same variant of the FOX-P2 gene that we do, which is instrumental to our ability to understand and produce spoken language.

[Image licensed under the Creative Commons Clemens Vasters, Neanderthal in a business suit, CC BY 2.0]

It also wasn't terribly surprising in my own case, as Europeans generally have more Neanderthal ancestry than any other group, and my test results showed me to be -- also unsurprising, given what I know of my family tree -- nearly 100% of European origin, mainly French, Scottish, Dutch, German, and English.  The Neanderthals themselves are named after the Neander Valley of Germany, where archaeologists found the first fossils of the species (or subspecies, depending on who you believe).  So once it was determined that they had interbred with early modern Homo sapiens, their geographical distribution led to a (correct) surmise that Europeans would have more Neanderthal ancestry than other ethnic groups, for the same reason that southeast Asians and Native Australians have more Denisovan ancestry than the rest of us.

That's why a paper in Cell two weeks ago came as such a shock.  In it, a team led by Lu Chen of Princeton University found that a number of African ethnic groups, especially those in northern and western Africa, have a lot more Neanderthal ancestry than anyone realized.

Because it's still not as much as the Europeans have, and the African Neanderthal genes identified are variants usually found in Europe, the guess is that some of the European Homo sapiens/Neanderthal hybrids made their way across (or around) the Mediterranean in a "back-to-Africa" migration, injecting Neanderthal genes into groups that previously had little to no Neanderthal ancestry.

It also means that geneticists may be underestimating the number of Neanderthal markers in the rest of us.  Because those estimates were made using comparison between sample DNA and that of people thought to have no Neanderthal ancestry at all -- such as the Yoruba of Nigeria -- if those African groups did have ancestry that was the result of a back-to-Africa migration by European hybrids, then that revises the baseline upward.  The former estimates of 1.7-1.8% Neanderthal DNA for your average person of European descent might be on the low side.

"Our work highlights how humans and Neanderthals interacted for hundreds of thousands of years, with populations dispersing out of and back into Africa," said study co-author Joshua Akey in an interview with Science News.  "Remnants of Neanderthal DNA survive in every modern human population studied to date."

I find it fascinating how DNA is now being used to track relationships and migratory patterns not only of other animal species, but of humans.  And it's gotten pretty accurate.  It picked up my Ashkenazic ancestry, identifying it at 6% -- just about right based on my one great-great-grandfather, Solomon Meyer-Lévy of Dauendorf, Alsace, who emigrated from his birthplace and joined a small community of French-speaking Jews in Donaldsonville, Louisiana in around 1850.  The other interesting result in my own DNA that made sense was a smattering of Italian ancestry, undoubtedly because my father's paternal line ancestor, Jacques-Esprit Ariey-Bonnet, was born in a little town in the French Alps, quite close to the border of Italy.

So the amount we can learn about our own past from our genes is staggering, and I'm sure there are other surprises in store for us.  It informs us not only of our physical makeup but our history, a millions-of-years-long trail leading back to our most distant hominid ancestors on the savannas of Kenya and Tanzania.

Although it still doesn't explain the rare steaks and nudity thing.

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This week's book recommendation is a fascinating journey into a topic we've visited often here at Skeptophilia -- the question of how science advances.

In The Second Kind of Impossible, Princeton University physicist Paul Steinhardt describes his thirty-year-long quest to prove the existence of a radically new form of matter, something he terms quasicrystals, materials that are ordered but non-periodic.  Faced for years with scoffing from other scientists, who pronounced the whole concept impossible, Steinhardt persisted, ultimately demonstrating that an aluminum-manganese alloy he and fellow physicists Luca Bindi created had all the characteristics of a quasicrystal -- a discovery that earned them the 2018 Aspen Institute Prize for Collaboration and Scientific Research.

Steinhardt's book, however, doesn't bog down in technical details.  It reads like a detective story -- a scientist's search for evidence to support his explanation for a piece of how the world works.  It's a fascinating tale of persistence, creativity, and ingenuity -- one that ultimately led to a reshaping of our understanding of matter itself.

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

A window into the distant past

I love a good mystery, and mysteries abound regarding human prehistory.

Of course, that's kind of self-evident, given that it's pre-history.  Anything we know is based on inference, from looking at artifacts and other traces left behind for us to find.  And like fossils, we have to keep in mind that what we're seeing is a small percentage -- no one knows how small -- of what was originally out there.  (One of my biology professors said that trying to reconstruct the Tree of Life from the existing fossil record is analogous to reconstructing the entire History of Art from a dozen paintings or sculptures chosen at random from the tens of thousands that have been created by humanity.  This was before the use of genetic evidence for determining phylogeny, so the situation has improved -- but we're still working from inference and very incomplete evidence.)

So that's pretty much where we are with our knowledge of human prehistory.  Which is why when there are eye-opening new discoveries in that field, it always makes me sit up and take notice.

Today we're going to look at three new archeological finds that have given us a new lens into our distant ancestors' lives, and all of which were published in the last week.

First, some new artifacts from Scotland have provided information about one of the least-known European cultures -- the Picts.

The Picts were a collection of (probably) Celtic-speaking tribes that inhabited Scotland prior to its invasion first by the Irish Dál Riata and then by the Vikings.  We know next to nothing about them or their culture.  Even the name of the group isn't native to them -- it comes from the Latin pictus ("painted"), from their habit of going into battle naked, covered with paint.

Which, I have to admit, is pretty damn badass.

But we don't know much else about them, because they left no written records at all.  We assume they spoke a Celtic language, but don't really know for sure; and any suggestion of root words in Gaelic that may have come from Pictish are guesses (such as the claim that place names starting with Pit-, Lhan-, and Aber- come from Pictish words).

So any artifacts that are unequivocally Pictish in origin are pretty amazing.  Like the ones discovered earlier this year by Anne MacInnes of the North of Scotland Archaeological Society.

The face of the stone in the photograph not only has designs and a pretty cool-looking mythical beast, it has an inscription -- in Latin letters -- that may well be a Latin transliteration of the Pictish language.  Which makes it a rarity indeed.

"The two massive beasts that flank and surmount the cross are quite unlike anything found on any other Pictish stone," said John Borland, of Historic Environment Scotland and the Pictish Arts Society.  "These two unique creatures serve to remind us that Pictish sculptors had a remarkable capacity for creativity and individuality.  Careful assessment of this remarkable monument will be able to tell us much about the production of Pictish sculpture that we could never have guessed at."


Then, there's the discovery that was made near the Tollense River, on the Baltic coast of Germany, that indicates the existence of mercenary soldiers -- three thousand years ago.

On a historic -- well, prehistoric -- battleground, a team from the Lower Saxony State Agency for Cultural Heritage discovered, alongside skeletal remains showing war-related injuries, a toolkit brought in by one of the soldiers.  It contains a chisel, a knife, an awl, and a small sword, along with fasteners that seem to indicate its origin in southern Germany -- a distance of about five hundred miles.

"It was a surprise to find a battlefield site.  It was a second surprise to see a battlefield site of this dimension with so many warriors involved, and now it's a big surprise that we are dealing with a conflict of a European scale," says Thomas Terberger, co-author of the study.  "We had before speculated that some of these people might have come from the south.  Now we have, from our point of view, a quite convincing indication that people from southern Central Europe were involved in this conflict."

Suggesting that the man who carried the bag may have been a mercenary, although that is (of course) an inference.  So right around the time King David ruled the Israelites, there were professional soldiers waging war upon either other in northern Europe.

Last, we have a study showing that the Greek islands have been occupied for longer than we'd realized...

... a lot longer.

When most people in North America and Western Europe think of an "old civilization," they come up with Greece, Rome, Egypt, Sumer, China, India, the Inca, the Mayans...  but all of those (venerable and fascinating though they are) only date back a few thousand years.  The Great Pyramid at Giza, for example, was built around 3,500 years ago -- which seems like a lot.

But this new discovery shows that the island of Naxos was inhabited by our ancestors (and/or near relatives) two hundred thousand years ago.

At that point, they weren't exactly human, or at least not what we usually consider to be modern humanity.  These inhabitants of Naxos were Neanderthals, and had crossed into what is now an island during a time when the sea level was considerably lower because a lot of the water was locked up in glacial ice.

"Until now, the earliest known location on Naxos was the Cave of Zas, dated to 7,000 years ago," said project director Tristan Carter, an anthropologist at Ontario’s McMaster University.  "We have extended the history of the island by 193,000 years...  It was believed widely that hominin dispersals were restricted to terrestrial routes until the later Pleistocene, but recent discoveries are requiring scholars to revisit these hypotheses."

The word "Neanderthal" has, in common parlance, become synonymous with "uncultured cave man," and that characterization misses the mark by a mile.  They had culture -- they buried their dead, apparently made music, and may have even had spoken language (DNA studies show that they had the FOX-P2 gene, which is one of the genetic underpinnings of language in humans).  They made artifacts not only of utility but of great beauty:

A Neanderthal Acheulean hand-axe from about 50,000 years ago

Some of the archaeologists associated with the Naxos study even think the Neanderthal inhabitants of the island may not have walked there when the sea level was low -- they may actually have arrived there by boat.

Pretty smart folks, the Neanderthals.

It's also uncertain that they actually represent a different species from us.  Most of us carry Neanderthal genetic markers -- apparently I have three-hundred-odd of them, making me in the sixtieth percentile, cave-man-wise -- so there was definitely interbreeding between them and modern humans.  So they might be more correctly considered a subspecies -- although, as I've mentioned before, the concept of species is one of the wonkiest definitions in biology, and all attempts to refine it have resulted in more exceptions and contradictions than ever.

So probably best just to say that they're part of the family.

In any case, we've got three papers in one week that give us some very impressive new data on prehistory.  Until we invent time travel, this kind of evidence is about all we can rely on to create a picture of what life was like back then.  Which, even with the new information, leaves lots of room for refinement -- and imagination.

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In keeping with Monday's post, this week's Skeptophilia book recommendation is about one of the most enigmatic figures in mathematics; the Indian prodigy Srinivasa Ramanujan.  Ramanujan was remarkable not only for his adeptness in handling numbers, but for his insight; one of his most famous moments was the discovery of "taxicab numbers" (I'll leave you to read the book to find out why they're called that), which are numbers that are expressible as the sum of two cubes, two different ways.

For example, 1,729 is the sum of 1 cubed and 12 cubed; it's also the sum of 9 cubed and 10 cubed.

What's fascinating about Ramanujan is that when he discovered this, it just leapt out at him.  He looked at 1,729 and immediately recognized that it had this odd property.  When he shared it with a friend, he was kind of amazed that the friend didn't jump to the same realization.

"How did you know that?" the friend asked.

Ramanujan shrugged.  "It was obvious."

The Man Who Knew Infinity by Robert Kanigel is the story of Ramanujan, whose life ended from tuberculosis at the young age of 32.  It's a brilliant, intriguing, and deeply perplexing book, looking at the mind of a savant -- someone who is so much better than most of us at a particular subject that it's hard even to conceive.  But Kanigel doesn't just hold up Ramanujan as some kind of odd specimen; he looks at the human side of a man whose phenomenal abilities put him in a class by himself.

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

Neanderthal family reunion

Last year, I did a 23 and Me DNA test.

Besides the not-particularly-earthshattering conclusion that I'm mostly French, Scottish, German, and Dutch, I was amused to find that the test showed I have 284 Neanderthal markers.  This puts me in the 60th percentile as compared to the population overall, which probably explains why I like my steaks rare and run around half naked when the weather is warm.

What's fascinating is that some research released last week, a paper in Cell by David Enard of the University of Arizona and Dmitri A. Petrov of Stanford University called, "Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans," has shown that some of these genes didn't get passed along the usual way, but by a process called transduction -- when viruses transmitted from one host to another carry novel genes with them.

The authors write:

After their divergence 500,000 to 800,000 years ago, modern humans and Neanderthals interbred at least twice: the first time ∼100,000 years ago and the second ∼50,000 years ago.  The first interbreeding episode left introgressed segments (IS) of modern human ancestry within Neanderthal genomes, as revealed by the analysis of ancient DNA from a single Altai Neanderthal individual sequenced by Prüfer et al. (2014).  This first interbreeding event appears not to have left any detectable segments of Neanderthal ancestry in extant modern human genomes.  In contrast, the second interbreeding episode left detectable IS of Neanderthal ancestry within the genomes of non-African modern humans. 

Recent advances in the detection of introgression have led to the discovery that the majority of genomic segments initially introgressed from Neanderthals to modern humans were rapidly removed by purifying selection.  Harris and Nielsen (2016) estimated that the proportion of Neanderthal ancestry in modern human genomes rapidly fell from ∼10% to the current levels of 2%–3% in modern Asians and Europeans.
This history of interbreeding and purifying selection against IS raises several important questions. First, among the introgressed sequences that were ultimately retained, can we detect which sequences persisted by chance because they were not as deleterious or not deleterious at all to the recipient species, and which persisted not despite natural selection but because of it—that is, which IS increased in frequency due to positive selection?  If any of the introgressed sequences were indeed driven into the recipient species due to positive selection, can we determine which pressures in the environment drove this adaptation? 

Recently we found that proteins that interact with viruses (virus-interacting proteins [VIPs]) evolve under both stronger purifying selection and tend to adapt at much higher rates compared to similar proteins that do not interact with viruses.  We estimated that interactions with viruses accounted for ∼30% of protein adaptation in the human lineage.   Because viruses appear to have driven so much adaptation in the human lineage, and because it is plausible that when Neanderthals and modern humans interbred they also exchanged viruses either directly by contact or via their shared environment, we hypothesized that some introgressed sequences might have provided a measure of protection against the exchanged viruses and were driven into the recipient species by positive directional selection.  Consistent with this model, several cases of likely adaptive introgression from Neanderthals to modern humans involve immune genes that are specialized to deal with pathogens including viruses.

Which is amazingly cool.  Viruses are parasites, and as such usually wreak havoc with our systems, but here we have viruses acting as carriers not only for genes that generate diversity, but that protect our cells from the damage viruses can cause.

Great-great grandpa Ugg [Image licensed under the Creative Commons Stefan Scheer, Neandertaler reconst, CC BY-SA 3.0]

"It's not a stretch to imagine that when modern humans met up with Neanderthals, they infected each other with pathogens that came from their respective environments," lead author David Enard said.  "By interbreeding with each other, they also passed along genetic adaptations to cope with some of those pathogens."

"Many Neanderthal sequences have been lost in modern humans, but some stayed and appear to have quickly increased to high frequencies at the time of contact, suggestive of their selective benefits at that time," Petrov said.  "Our research aims to understand why that was the case.  We believe that resistance to specific RNA viruses provided by these Neanderthal sequences was likely a big part of the reason for their selective benefits."

"One of the things that population geneticists have wondered about is why we have maintained these stretches of Neanderthal DNA in our own genomes," Enard added.  "This study suggests that one of the roles of those genes was to provide us with some protection against pathogens as we moved into new environments."

So having Neanderthal DNA isn't something to be ashamed of.  All of this highlights how incredibly cool the evolutionary model is, and the depth of its explanatory power.  Now, y'all'll have to excuse me.  I'm going to go get a snack.  I wonder if I have any roast mammoth left in the fridge?  Probably not.  I guess grilled cheese will have to do.

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This week's Skeptophilia book recommendation is from the brilliant essayist and polymath John McPhee, frequent contributor to the New Yorker.  I swear, he can make anything interesting; he did a book on citrus growers in Florida that's absolutely fascinating.  But even by his standards, his book The Control of Nature is fantastic.  He looks at times that humans have attempted to hold back the forces of nature -- the attempts to keep the Mississippi River from changing its path to what is now the Atchafalaya River, efforts in California to stop wildfires and mudslides, and a crazy -- and ultimately successful -- plan to save a harbor in Iceland from a volcanic eruption using ice-cold seawater to freeze the lava.

Anyone who has interest in the natural world should read this book -- but it's not just about the events themselves, it's about the people who participated in them.  McPhee is phenomenal at presenting the human side of his investigations, and their stories will stick with you a long time after you close the last page.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

Mechanical brain transplant

New from the "Well, I can't see any way that could go wrong, do you?" department, we have: scientists growing Neanderthal brain fragments in petri dishes and then connecting them to crab-like robots.

My first thought was, "Haven't you people ever watched a science fiction movie?"  This feeling may have been enhanced by the fact that just a couple of days ago I watched the Dr. Who episode "The End of the World," wherein the Doctor and his companion are damn near killed (along with everyone else on a space station) when a saboteur makes the shields malfunction using little scuttling metallic bugs.

The creator of the Neanderthal brain bits is Alysson Muotri, geneticist at the University of California - San Diego's School of Medicine.  He and his team isolated genes that belonged to our closest cousins, Homo sapiens neanderthalensis, and transferred them into stem cells.  Then, they allowed the cells to grow into proto-brains to see what sorts of connections would form.

Muotri says, "We're trying to recreate Neanderthal minds."  So far, they've noticed an abnormally low number of synapses (as compared to modern humans), and have speculated that this may indicate a lower capacity for sophisticated social behavior.

But Muotri and his team are going one step further.  They are taking proto-brains (he calls them "organoids") with no Neanderthal genes, and wiring them and his "neanderthalized" versions into robots, to make comparisons about how they learn.  Simon Fisher, a geneticist for the Department of Psycholinguistics at the Max Planck Institute, said, "It's kind of wild.  It's creative science."

That it is.

I have to admit there's a cool aspect to this.  I've always wondered about the Neanderthals.  During the peak of their population, they actually had a brain capacity larger than modern humans.  They clearly had culture -- they ceremonially buried their dead, probably had language (as they had the same variant of the "linguistic gene" FOXP2 that we do), and may have even made music, to judge by what appears to be a piece of a 43,000 bone flute that was found in Slovenia.

All that said, I'm not sure how smart it would be to stick a Neanderthal brain inside a metallic crab.  If this was a science fiction movie, the next thing that happened would be that Muotri would be in his lab late at night working with his Crab Cavemen, and he'd turn his back and they'd swarm him, and the next morning all that would be found is his skeleton, minus his femur, which would have been turned into a clarinet.

Okay, I know I'm probably overreacting here.  But it must be admitted that our track record of thinking through our decisions is not exactly unblemished.  Muotri assures us that these little "organoids" have no blood supply and therefore no potential for developing into an actual brain, but still.  I hope he knows what he's doing.  As for me, I'm going to go watch Dr. Who.

Let's see, what's the next episode?  "Dalek."  *reads description*  "A superpowerful mutant intelligence controlling a mechanical killing device goes on a rampage and attempts to destroy humanity."

Um, never mind.  *switches channel to Looney Tunes*

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This week's book recommendation is from one of my favorite writers and documentary producers, Irish science historian James Burke.  Burke became famous for his series Connections, in which he explored the one-thing-leads-to-another phenomenon which led to so many pivotal discoveries -- if you've seen any of the episodes of Connections, you'll know what I mean when I say that it is just tremendous fun to watch how this man's brain works.  In his book The Pinball Effect, Burke investigates the role of serendipity -- resulting in another tremendously entertaining and illuminating read.