The bottleneck

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

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

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

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

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

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

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

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

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

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

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

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

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A refuge from the cold

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

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

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

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

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

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

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

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

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

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

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

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Letters from the home world

In choosing topics for this blog, I try not to have it simply devolve into taking random pot shots at crazies.  Loony ideas are a dime a dozen, and given the widespread access to computers that is now available, just about anyone who wants one can have a website.  Given these two facts, it's inevitable that wacky webpages grow like wildflowers on the fields of the internet.

When an alert reader brought this one to my attention, however, I just couldn't help myself.  Entitled "Did Humans Come From Another Planet?", it represents one of the best examples I've ever seen of adding up a bunch of facts and obtaining a wildly wrong answer.  The only ones who, in my experience, do this even better are the people who write for the Institute for Creation Research, and to be fair, they've had a lot longer to practice being completely batshit crazy, so it's only to be expected.

Anyhow, the contention of the "Did Humans Come From Another Planet?" people can be summed up by, "Yes. Duh."  We are clearly aliens, and I'm not just talking about such dubiously human individuals as Mitch McConnell.  All of us, the article claims, descend from an extraterrestrial race.  But how can we prove it?

Well, here's the argument, if I can dignify it with that term.

1. Human babies are born completely unable to take care of themselves, and remain that way for a long time.  By comparison, other primate babies, despite similar gestation periods, develop much more rapidly.
2. In a lower gravitational pull, humans could fall down without hurting themselves, "just like a cat or a dog."
3. Humans have biological clocks, and in the absence of exposure to the external day/night cycle, they come unlocked from "real time" and become free-running.  So, clearly we came from a planet that had a different rotational period.
4. Humans don't have much body hair.  At least most of us don't, although I do recall once going swimming and seeing a guy who had so much back hair that he could have singlehandedly given rise to 80% of the Bigfoot sightings in the eastern United States.
5. Geneticists have found that all of humanity descends from a common ancestor approximately 350,000 years ago; but the first modern humans didn't exist until 100,000 years ago.  So... and this is a direct quote, that I swear I am not making up: "In what part of the universe was he [Homo sapiens] wandering for the remaining 250 thousand years?"

Now, take all of this, and add:

1. Some nonsense about Sirius B and the Dogon tribe, including a bizarre contention that the Sun and Sirius once formed a double-star system, because this "doesn't contradict the laws of celestial mechanics;"
2. The tired old "we only use 3% of our brains" contention;
3. Adam and Eve; and
4. the ancient Egyptians.

Mix well, and bake for one hour at 350 degrees.

The result, of course, is a lovely hash contending that we must come from a planet with a mild climate where we could run around naked all the time, not to mention a lower gravitational pull so we could just sort of bounce when we fall down, plenty of natural food to eat, and "no geomagnetic storms."  I'm not sure why the last one is important, but it did remind me of all of the "cosmic storms" that the folks in Lost in Space used to run into.  And they also came across lots of weird, quasi-human aliens, while they were out there wandering around.  So there you are.

In any case, that's today's example of adding 2 + 2 and getting 439.  All of this just goes to show that even if you have access to a lot of factual information, not to mention the internet, you still need to know how to put that factual information together in order to get the right answer.  For that, you need science, not just a bunch of nutty beliefs, assumptions, and guesses.  So, as usual, science FTW.

Which, of course, applies to a good many more situations than just this one, but as I've already given a nod to the Institute for Creation Research, I'll just end here.

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Author and biochemist Camilla Pang was diagnosed with autism spectrum disorder at age eight, and spent most of her childhood baffled by the complexities and subtleties of human interactions.  She once asked her mother if there was an instruction manual on being human that she could read to make it easier.

Her mom said no, there was no instruction manual.

So years later, Pang recalled the incident and decided to write one.

The result, Explaining Humans: What Science Can Teach Us About Life, Love, and Relationships, is the best analysis of human behavior from a biological perspective since Desmond Morris's classic The Naked Ape.  If you're like me, you'll read Pang's book with a stunned smile on your face -- as she navigates through common, everyday behaviors we all engage in, but few of us stop to think about.

If you're interested in behavior or biology or simply agree with the Greek maxim "gnothi seauton" ("know yourself"), you need to put this book on your reading list.  It's absolutely outstanding.

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

When the volcano blows

Nobel Prize-winning physicist Richard Feynman once said, "I would rather have questions that cannot be answered than answers that cannot be questioned."

The strength of science is in its ability to self-correct, but this does engender a problem; it may well be that some of the questions we're asking will never be satisfactorily answered.  There are sometimes when we must admit ignorance, and hold our determination to have everything figured out in abeyance -- possibly indefinitely.

That may be the situation we're in with regards to an interesting question surrounding the largest volcanic eruption in modern times, the eruption of Toba in the Indonesian archipelago.  This eruption dwarfed Mount Saint Helens, the 1883 eruption of Krakatoa, and even the catastrophic eruption of Tambora (also in Indonesia) in 1815, that threw so much in the way of debris up into the atmosphere that it caused the "Year Without a Summer," in which Quebec City got a foot of snow -- in mid-July.

The Toba eruption, 74,000 years ago, was bigger than all of the above; by some estimates, it threw a hundred times more in the way of pulverized rock into the air than Tambora did.  It is certain that it caused not only localized devastation, but worldwide climate change.  And the conventional wisdom is that it nearly wiped out the human species -- that we were driven into a genetic bottleneck, in which only a few survivors became the ancestors of everyone currently alive today.

The Toba caldera [image courtesy of the Wikimedia Commons]

Michael Rampino and Stanley Ambrose, of New York University, were amongst the first proponents of the Toba bottleneck theory.  In their paper "Volcanic Winter in the Garden of Eden: The Toba Supereruption and the Late Pleistocene Human Population Crash," published in 2000 in the Papers of the Geological Society of America, they write:

Genetic studies indicate that sometime prior to ca. 60,000 yr ago humans suffered a severe population bottleneck (possibly only 3,000-10,000 individuals), followed eventually by rapid population increase, technological innovations, and migrations.  The climatic effects of the paroxysmal Toba eruption could have caused the bottleneck, and the event might have been a catalyst for the technological innovations and migrations that followed.  The present results as to the predicted environmental and ecological effects of the eruption lend support to a possible connection between the Toba event and the human population bottleneck, and suggest that similar bottlenecks among other organisms might be expected at about the same time. 

However, it appears that the question is far from settled.  A paper by Eugene Smith et al. that came out last week in Nature, "Humans Thrived in South Africa Through the Toba Eruption about 74,000 Years Ago," completely counters the conventional wisdom -- and suggests that if the bottleneck did occur, it may not have been the fault of the volcano:

Approximately 74 thousand years ago (ka), the Toba caldera erupted in Sumatra.  Since the magnitude of this eruption was first established, its effects on climate, environment and humans have been debated.  Here we describe the discovery of microscopic glass shards characteristic of the Youngest Toba Tuff—ashfall from the Toba eruption—in two archaeological sites on the south coast of South Africa, a region in which there is evidence for early human behavioural complexity.  An independently derived dating model supports a date of approximately 74 ka for the sediments containing the Youngest Toba Tuff glass shards.  By defining the input of shards at both sites, which are located nine kilometres apart, we are able to establish a close temporal correlation between them.  Our high-resolution excavation and sampling technique enable exact comparisons between the input of Youngest Toba Tuff glass shards and the evidence for human occupation.  Humans in this region thrived through the Toba event and the ensuing full glacial conditions, perhaps as a combined result of the uniquely rich resource base of the region and fully evolved modern human adaptation.

The reason I bring this up -- besides the fact that I'm interested in human population genetics, and it's cool -- is that this may be a question that we simply don't have the data to answer.  It's possible that the "thriving" population that Smith et al. found was a localized group of lucky people, and elsewhere, humanity got clobbered.  On the other hand, it could be that the Rampino and Ambrose paper was simply wrong -- that the population genetics studies, which are not without their a priori assumptions, overestimated the extent of the Toba bottleneck (or the whatever-caused-it bottleneck).

But -- and this is the most critical point -- you keep looking.  If there's no definitive solution, you are forced to admit it, but the research doesn't stop there.  Ignorance is the beginning, not the end, of the scientific process.

So we may never know exactly how close humanity came to extinction 74,000 years ago.  The important thing is that we've asked the question -- and that science gives us a means to evaluate the evidence, and determine if a particular answer is supported.  And what we learn along the way will open up further avenues for exploration, enough to keep the scientific world occupied for a long, long time.

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Grandpa the pig

It bears mention that having a Ph.D. (or other advanced credentials) is no guarantee against being a complete wingnut.  This topic comes up because of a website link sent to me by a regular reader of Skeptophilia that was authored by Eugene McCarthy, Ph.D. in genetics, and author of Handbook of Avian Hybrids of the World.

It starts off reasonably enough; McCarthy describes the fact that, contrary to our perception of species as being little watertight compartments, hybridization (and thus gene flow between species) is rather common.  Not all hybrids are sterile, like the familiar example of the mule; a lot of them are back-fertile to either parental species (an example is the "Brewster's Warbler," which was once thought to be a separate species and is now known to be a hybrid between the Golden-winged and Blue-winged Warblers).

So McCarthy asks an interesting question: are humans a hybrid?  The answer, apparently, is yes; recent studies have shown that most human populations show the genetic signature of three ancestral populations -- modern humans, Neanderthals, and Denisovans.  (Biologists disagree, however, as to whether these three represent different species -- a distinction that, in reality, probably doesn't mean very much.  The concept of species is one of the hardest-to-pin-down terms in all of biological science.)

But, unfortunately, it isn't this intermixing between three proto-hominins that McCarthy is talking about.  He thinks we're a much more interesting hybrid than that.  He gives his evidence first: humans have low fertility, and males produce a great many abnormal sperm (kind of a surprise given our reproductive success -- you have to wonder, if this is true, how there can be seven billion of us).

What?  You want more evidence than that?  Sorry, that's it.  Guys produce lots of abnormal sperm, and allegedly we have low fertility.  So we're hybrids.  That's enough, right?

Of course right.  So now, if we're hybrids, we have to figure out which two species gave rise to humans.  One of them, McCarthy says, was clearly something like a chimp.  But he states, in all apparent seriousness, "Many characteristics that clearly distinguish humans from chimps have been noted by various authorities over the years."  Can't argue with that.  But then he goes right off the edge of the cliff:

One fact, however, suggests the need for an open mind: as it turns out, many features that distinguish humans from chimpanzees also distinguish them from all other primates. Features found in human beings, but not in other primates, cannot be accounted for by hybridization of a primate with some other primate. If hybridization is to explain such features, the cross will have to be between a chimpanzee and a nonprimate — an unusual, distant cross to create an unusual creature.

If this sets alarm bells off, good -- because this would require a fertile hybrid being produced from a mating of animals not just from two different genera, or two different families, but two different orders.  Entirely possible, McCarthy says, despite the fact that there is not a single example -- not one -- of an interordinal hybrid known from nature.  Anywhere.  That includes animals, plants, fungi, and so on.

Nevertheless, that doesn't stop McCarthy:

Looking at a subset of the listed traits [unique features of humans are listed in the sidebar on page two of his website; there are too many to list here], however, it's clear that the other parent in this hypothetical cross that produced the first human would be an intelligent animal with a protrusive, cartilaginous nose, a thick layer of subcutaneous fat, short digits, and a naked skin. It would be terrestrial, not arboreal, and adaptable to a wide range of foods and environments. 

So, let's not dillydally any more; if a chimp is one of our parental species, what's the other?

What is this other animal that has all these traits? The answer is Sus scrofa, the ordinary pig. What are we to think of this fact? If we conclude that pigs did in fact cross with apes to produce the human race, then an avalanche of old ideas must crash to the earth. But, of course, the usual response to any new perspective is "That can't be right, because I don't already believe it." This is the very response that many people had when Darwin first proposed that humans might be descended from apes, an idea that was perceived as ridiculous, or even as subversive and dangerous. And yet, today this exact viewpoint is widely entertained. Its wide acceptance can be attributed primarily to the established fact that humans hold many traits in common with primates. That's what made it convincing... Let us take it as our hypothesis, then, that humans are the product of ancient hybridization between pig and chimpanzee.

So, basically, the logic is, "people laughed at Darwin, and he turned out to be right, so if people laugh at me, I must be right?"

But I don't want to be accused of jumping to conclusions ("That can't be right, because I don't already believe it"), so I took what I think is a critical look at the list of allegedly unique features of humans -- ones that, in McCarthy's view, must have come from our other, non-primate parental species.  And most of them have to do with quantities and sizes -- "sparse" hair, "large amounts" of elastic fiber in the skin, "richly" vascularized dermis, "narrow" eye opening, "heavy" eyelashes, and so on.  Traits involving quantities and sizes are highly responsive to selective pressures, the idea being once you have genes for the production of a feature, it is relatively straightforward to evolve to produce more or less of it.

Of the features he claims are found only in humans and pigs, it appears that in several cases, he is simply wrong.  Take multipyramidal kidneys -- he is correct that only humans have this feature amongst primates, but it is hardly unique in the mammalian world.  Besides humans and pigs, elephants have multipyramidal kidneys, as do bears, rhinoceroses, bison, and "nearly all marine mammals," according to a paper by M. F. Williams (available here).  Williams' contention is that multipyramidal kidneys evolved in animals that lived in coastal or marine environments in order to deal with high levels of salt -- and that each of these lineages evolved it independently, as it represents a unique feature on separate, distantly related branches of the phylogenetic tree (evolutionary biologists call these features "apomorphies").

Then, of course, he has some things on the list of allegedly unique human characteristics that are simply weird.  "Particular about place of defecation?"  (Has he ever owned a cat?)  "Snuggling?"  "Extended male copulation time?"  "Good swimmer?"

I'm sorry, Dr. McCarthy, but I'm calling bullshit on this.

Now, please understand; it's not like I have any particular problem with our having a checkered ancestry.  I'm an evolutionary biologist by training, for cryin' in the sink, I know we're animals.  But the idea that Homo sapiens arose when a chimp had sex with a pig... that stretches credulity too far.

Even if you do have a Ph.D.