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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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!]

An early walker

A recent discovery of a proto-hominid has been raising eyebrows in the paleoanthropology circles, for a variety of reasons.

Called Rudapithecus, it dates from the late Miocene Epoch, around ten million years ago.  It was small, at least compared to some of our other cousins, weighing in at between twenty and forty kilograms, roughly the size of your average golden lab.  Exactly where it fits in our family tree isn't certain yet, although most likely it's a collateral line, not one that is directly ancestral to Homo sapiens.

So far, nothing that surprising.  But there are a few things about Rudapithecus that are causing some serious head-scratching.  Among them:

• Rudapithecus was bipedal.  This is pretty certain from the shape of the pelvis, which has a morphology much more like ours than it is like the largely-quadrupedal chimps and gorillas.
• This bipedalism evolved way earlier than we'd thought.  The first unequivocal evidence we have of bipedalism -- or, that we had before this discovery -- was the African species Ardipithecus from a bit over four million years ago.  So if the inferences are correct, this more than doubles the antiquity of bipedalism in our relatives.
• Weirdest of all -- Rudapithecus didn't live in Africa.  This discovery was made in a quarry in Rudabánya, Hungary.

So this will require some serious reworking of our understanding of primate evolution.

Lineage of hominins. That's us, way up near the top left. The left-hand scale is a time axis, in millions of years before present. [Image licensed under the Creative Commons Dbachmann, Hominini lineage, CC BY-SA 4.0]

"Rudapithecus was pretty ape-like and probably moved among branches like apes do now—holding its body upright and climbing with its arms," said Carol Ward, a Curators Distinguished Professor of Pathology and Anatomical Sciences in the University of Missouri School of Medicine, and lead author of the study.  "However, it would have differed from modern great apes by having a more flexible lower back, which would mean when Rudapithecus came down to the ground, it might have had the ability to stand upright more like humans do.  This evidence supports the idea that rather than asking why human ancestors stood up from all fours, perhaps we should be asking why our ancestors never dropped down on all fours in the first place...  We were able to determine that Rudapithecus would have had a more flexible torso than today's African apes because it was much smaller...  This is significant because our finding supports the idea suggested by other evidence that human ancestors might not have been built quite like modern African apes."

So -- contrary to our usual picture of our ancestry -- it may be that the most recent common ancestor of humans, chimps, and gorillas (somewhere in the red slice on the graph) might have been more like us than they were like the other great apes, at least in terms of locomotion.  Kind of punches another hole in our self-importance, doesn't it?  We tend to have the attitude, "Of course we're the most highly evolved primate.  The further back you go, the more primitive and ape-like they get."  Now, it's looking like we may need to reconsider that.  It may be that the mostly-quadrupedalism of chimps and gorillas may have been the more recent innovation.

In any case, I'm sure this won't be the last you hear on the subject.  As with everything in science, it's subject to revision if new data comes to light.  And given the discovery of this fossil in a most unlikely location, I'm not even putting any money on where the next bit of evidence will come from.

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This week's Skeptophilia book recommendation is especially for those of you who enjoy having their minds blown.  Niels Bohr famously said, "Anyone who is not shocked by quantum theory has not understood it."  Physicist Philip Ball does his best to explain the basics of quantum theory -- and to shock the reader thereby -- in layman's terms in Beyond Weird: Why Everything You Thought You Knew About Quantum Physics is Different, which was the winner of the 2018 Physics Book of the Year.

It's lucid, fun, and fascinating, and will turn your view of how things work upside down.  So if you'd like to know more about the behavior of the universe on the smallest scales -- and how this affects us, up here on the macro-scale -- pick up a copy of Beyond Weird and fasten your seatbelt.

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

A fight over teeth

It may seem like a trivial thing to gripe about, but I am absolutely sick unto death of people taking some completely ordinary scientific discovery, and shrieking, "This will completely rewrite every textbook on the subject!", or worse, "This invalidates everything we thought we knew about X!"

I know a bit about the history of scientific inquiry.  I'm no expert, but I'm definitely Better Than The Average Bear.  And when it comes to real, honest-to-Galileo scientific revolutions, I can only think of a few:

• The Copernican idea of the planets (including the Earth) going around the Sun, further modified by Kepler, who found out they weren't moving in perfect circles
• Isaac Newton's theories of force, motion, and gravitation
• Charles Darwin's explanation of the mechanism of evolution
• The elucidation of electricity and magnetism by James Clerk Maxwell and others
• The discovery of the gene as the fundamental unit of heredity, followed by a century and a half of refinement of our understanding of how DNA produces traits
• The discovery of radioactivity, which directly led to our understanding of atomic structure and quantum mechanics -- a discovery, it must be said, that immediately followed the eminent physicist Lord Kelvin stating, "There is nothing new to be discovered in physics now.  All that remains is more and more precise measurement."
• The discovery of plate tectonics as a driver for geological processes, by Alfred Wegener, Harry Hess, J. Tuzo Wilson, and others

And that's about it.  Oh, there were other big developments.  The invention of the computer, for example, has changed our experience about as much as anything I can think of.  But it really wasn't an overturning of our understanding of how the world works; it was more a new and clever application of known physical laws to the problem of computation and information storage.

So what stands out about real scientific revolutions is how uncommon they are.  And given the precision of our tools, and the level of our inquiry in the past century, the chances of our having missed something fundamental is pretty slim.

Which is why I rolled my eyes and said a very bad word when I saw an article over at Inverse entitled, "9.7 Million-Year-Old Teeth Found In Germany Could Recast Human History."  The discovery, which is actually fairly cool, is that a team led by Herbert Lutz, director of the Natural History Museum of Mainz, Germany discovered some hominin teeth in a dig near the Rhine River.  It is an unusual find; most of the hominin fossils of that age have been confined to Africa.  But it certainly doesn't "rewrite human history."  The fact that there might have been a branch of hominins that made it to Europe ten-odd million years ago is interesting, but doesn't really overturn anything.  It just adds a branch to our family tree (and one that almost certainly isn't our director ancestor, anyhow).

One of the Eppelsheim teeth [image courtesy of the Mainz Natural History Museum]

Lutz himself didn't help matters any by his statement to the press.  "It’s something completely new, something previously unknown to science," Lutz said.  "It’s a complete mystery where this individual came from, and why nobody’s ever found a tooth like this somewhere before."

I can put this reaction down to a scientist being understandably excited about his own work.  But when the media hears the words "unknown to science" and "mystery," they picture scientists sitting around with befuddled looks on their faces, then standing up and throwing away all of the textbooks and journals on the subject in question.

Which is a far sight from the truth, as Michael Greshko of National Geographic states.  "Do these teeth, as many news outlets have proclaimed, 'rewrite human history?'" Greshko writes.  "In a word, no."

In fact, there's still a lot of argument amongst paleontologists over whether the teeth are actually from a hominin, as Lutz believes.  Bence Viola of the University of Toronto, a world-renowned expert on the structure of hominin and hominoid teeth, is doubtful.  "I think this is much ado about nothing," Viola said.  "The second tooth (the molar), which they say clearly comes from the same individual, is absolutely not a hominin, [and] I would say also not a hominoid."

Viola suspects that the teeth are from some kind of pliopithecoid, a branch of primates only distantly related to humans, and which are known to have lived in Europe and Asia between seven and seventeen million years ago.

Viola's colleague, paleoanthropologist David Begun, is even more dismissive.  "The 'canine' looks to me like a piece of a ruminant tooth," Begun said.  "It has a funny break that makes it look a bit like a canine, but it is definitely not a canine, nor is it [from] a primate."

So not only do the teeth not "rewrite human history," there isn't even agreement about what animal the teeth were from.  So if you were thinking we were going to add an eighth scientific revolution to the seven I mentioned above based on Lutz's discovery, I fear you are destined for disappointment.

And the problem only gets worse when you're talking about a field in which people have a vested interest to disbelieve.  I can't tell you the number of times I've seen headlines like, "Paleontologist Finds Bone in a Dig Site -- Evolutionists Baffled!" or "Blizzard On the Way -- Climate Change Supporters Fumble for Explanation."  Trust me on this: no one's baffled or fumbling, and they're not rewriting the textbooks.  What the scientists are doing is adding another bit to our understanding of the universe.

Because that's how science works.

Bigfoot exists!... or, how science is not done

Well, the cryptozoological world has been buzzing the last few days about a press release from (in)famous Dr. Melba Ketchum, who has announced that her team has proven that DNA from a hair sample is from a non-human hominin species:

Our study has sequenced 20 whole mitochondrial genomes and utilized next generation sequencing to obtain 3 whole nuclear genomes from purported Sasquatch samples. The genome sequencing shows that Sasquatch mtDNA is identical to modern Homo sapiens, but Sasquatch nuDNA is a novel, unknown hominin related to Homo sapiens and other primate species. Our data indicate that the North American Sasquatch is a hybrid species, the result of males of an unknown hominin species crossing with female Homo sapiens.

Hominins are members of the taxonomic grouping Hominini, which includes all members of the genus Homo. Genetic testing has already ruled out Homo neanderthalis and the Denisova hominin as contributors to Sasquatch mtDNA or nuDNA. The male progenitor that contributed the unknown sequence to this hybrid is unique as its DNA is more distantly removed from humans than other recently discovered hominins like the Denisovan individual.

Sasquatch nuclear DNA is incredibly novel and not at all what we had expected. While it has human nuclear DNA within its genome, there are also distinctly non-human, non-archaic hominin, and non-ape sequences. We describe it as a mosaic of human and novel non-human sequence. Further study is needed and is ongoing to better characterize and understand Sasquatch nuclear DNA.

Well, that's just fine and dandy, but it's not really going to convince anyone who wasn't already convinced.  Because this, unfortunately, is not how good science is published.

This is, perhaps, the biggest misunderstanding about science on the part of the general public.  People have this sense that scientists go out and make discoveries, write them up, and the next thing you know, it's all over the "Science" section of Time magazine.  In fact, the first thing that should happen is peer review -- the data, methodology, and conclusions should be spread out for others in the field to take their best shots at.  Were the techniques used appropriate to the study?  Does the data unambiguously support the conclusion, or is there another conclusion (or more than one) that could be drawn?  Were reasonable controls in place to guard against bias, false positives, or sample contamination?

At that point, assuming that all went well with the peer review process, you trumpet your results to the public.  But not before.  In fact, that's been the problem all along with this study; hints and allegations were being made almost a year ago that the team had found something amazing, but the hard facts -- the actual data -- were shrouded in secrecy.  Months went by, and all we got were further teasers.  The whole thing was handled so as to maximize public hype -- rather like the whole kerfuffle over the "Baltic Sea Anomaly" (and notice how we haven't heard anything more about this non-story?).

Now, I'm not saying they haven't discovered anything; Melba Ketchum is a geneticist of excellent credentials, apparently, and it's hard to fathom why a reputable scientist would risk her career if there wasn't something real here.  (Although I am, reluctantly, reminded of the debacle over "cold fusion" that was handled in much the same way -- and the resultant irreparable damage done to the reputations of the two physicists responsible, Stanley Pons and Martin Fleischmann.)  What I am saying is that what has been released thus far isn't going to convince anyone who holds support of scientific discoveries to any usual standard of rigor.  So, predictably, the main ones who are greeting this press release with joyous shouts of acclamation are the ones who already believed Bigfoot was real before the study was even done.  Most of the rest of us are still sitting here, saying, "Okay, Dr. Ketchum, that's nice.  Now show us the goods."

This will, of course, earn more criticism for scientists and skeptics as being "closed-minded."  Actually, closed-minded is exactly what we're not; we haven't made our minds up at all, not until we've seen how the conclusions were reached, and whether the data support them.  It is to be hoped that Dr. Ketchum et al. will release more of their results into the peer-review system soon -- because until then, I'm afraid the response on the part of the rest of the scientific world will be lukewarm at best.