The man in the well

Some time around 1150 C.E. in the Faroe Islands, a comb-maker named Unås and his wife Gunnhild had a baby boy, whom they named Sverre.  Unås's brother Roe was the bishop of Streymoy, and once the boy was old enough Roe saw to it that Sverre was educated, intending that he would eventually be ordained as a priest.

However, Sverre had other ideas.  He had dreams that he was destined for greatness.  Then in 1175, when Sverre was about twenty-five, Gunnhild threw gasoline on the fire by telling him that his father wasn't actually the humble comb-maker Unås, but King Sigurd Munn of Norway, who had been killed by his brother Inge Haraldsson twenty years earlier, precipitating what would end up being a fifty-year civil war.

After finding out about his paternity, Sverre decided to head over to Norway and see what he could do to rectify the situation.

Historians differ on whether they accept the claim that Sverre was actually Sigurd's son.  The main source for this claim, Sverris Saga (thought to have been written by Karl Jónsson, Abbot of Þingeyraklaustur Monastery in Iceland), was certainly biased -- no aspersions meant toward the good abbot, but it was written under the direction and supervision of Sverre himself, so it's no surprise that in the saga the claim is treated as rock-solid fact.  And certainly, kings fathering children with mistresses isn't unusual.  But the whole thing definitely has overtones of mythology -- "the king's lost heir coming back to claim the throne" is a tale old as the hills.  (Interesting that most of the fictional ones, like Aragorn son of Arathorn and Taran the Wanderer, succeeded brilliantly, while the real-life ones, like Perkin Warbeck, Lambert Simnel, and Kaspar Hauser, almost always came to bad ends.)

Whether or not his claim was legitimate, Sverre certainly acted like he deserved the throne.  He landed in Norway in 1176, and predictably meeting with little support, allied himself with a rebel group called the Birkbeiners ("Birchlegs," so called because they were so poor they made themselves leggings out of birch bark).  And initially, that didn't go so well, either.  Sverre and the Birkbeiners were defeated in a series of battles, eventually whittling their numbers down to about seventy.  But in a turn of fate that is astonishing by any measure, in 1179 they beat the much larger forces of King Magnus V Erlingsson, seizing control of the entire district of Trøndelag.  

Magnus wouldn't give up, however, and certainly wouldn't accept Sverre as a co-regent. Sverre had to fight for another five years before fate once again intervened on his behalf.  After yet another battle between the Birkbeiners and the Heklungs (Magnus's supporters) led to an unexpected rout, the surviving Heklungs -- including Mangus himself -- attempted to flee on ships down the long, narrow Sognefjord.  The overloaded ships sank, drowning Magnus and the majority of his supporters, leaving Sverre the uncontested king of Norway.

A marble sculpture of Sverre Sigurdsson from Nidaros Cathedral (ca. 1200)  [Image is in the Public Domain]

Sverre's reign, however, was never to see real peace.  There were conflicts with landholding nobles, conflicts with the church, uprisings from rival parties, and even (ironically) a pretender to the throne who claimed to be Magnus's long-lost son.  (The pretender, unsurprisingly, didn't last very long.)  It was during one of these fights, however, that an event occurred that is why the whole topic comes up today.

In 1197, Sverre's forces were trapped in Sverresborg Castle outside the city of Trondheim, and it wasn't looking good.  In a desperate attempt to end the siege and wipe out Sverre and the Birkbeiners once and for all, the besieging forces threw the dead body of one of the men killed in a skirmish into a well -- the main water source for the castle -- in the hopes that it would poison the water and either kill them outright or force them to give up.  In the end it did neither -- Sverre would live to fight on for another five years -- and the story would have seemed to be one of those odd historical filigrees that could as easily be fabricated as true.

Except that researchers at the Norwegian University of Science and Technology believe they found the body.

The skeleton of a blond, blue-eyed man, approximately thirty years old at death, was found in a well near Sverresborg Castle that had been clogged with stones.  There were two deep cuts in his skull that are thought to be what caused his death.  From DNA extracted from a tooth, the scientists determined not only the bits about his appearance, but a surmise that he came from the province of Vest-Agder, in the very southernmost tip of Norway.

"This is the first time that a person described in these historical texts has actually been found," said Michael D. Martin, who co-authored the study.  "There are a lot of these medieval and ancient remains all around Europe, and they're increasingly being studied using genomic methods...  The important Norwegian Saint Olaf is thought to be buried somewhere in Trondheim Cathedral, so I think that if eventually his remains are uncovered, there could be some effort to describe him physically and trace his ancestry using genetic sequencing."

It's amazing that techniques of cutting-edge genetic analysis are being brought to bear on questions from history.  And in this case have corroborated a peculiar story from a saga long thought to be of questionable veracity -- giving us a lens into a turbulent, violent, and chaotic period of Scandinavian history.

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Big apple

On August 14, 2003, my wife and I were returning from a trip to Hawaii.  It was a lovely vacation, but the return home was, to put it mildly, fraught with mishaps.  The most spectacular one occurred as we were descending into LaGuardia Airport in New York City.  It was late afternoon and I was watching the lights of the city zooming along below us, when, all of a sudden...

... the entire skyline went dark.

I nudged Carol and asked her to confirm that I was, in fact, seeing what I thought I was seeing.  The pilot landed the plane, but the jet bridges weren't working so we deplaned via a rolling ladder.  The entire airport was dark except for a few lights that were kept on by a generator.  Remember that this is a little less than two years after 9/11, so our immediate (and terrifying) thought was that it was a terrorist attack, but it turned out we'd gotten caught up in the Great Northeastern Blackout, which knocked out the electricity to a huge chunk of the northeastern United States and eastern Canada, and which apparently had been triggered by a software bug.

The upshot was we got stuck in the airport overnight with a bunch of other people who were also trying to get back to the Ithaca area, and one of these was a very nice woman who worked for the Apple Genomics Project at Cornell Orchards.  That evening she and I had a real Nerd-O-Rama about the ins and outs of plant genetics, which was a very peculiar way to make the best of a bad situation.

She and her team had a fascinating job -- going all over Europe, the Caucasus, Anatolia, and Central Asia looking for apple germ line -- basically, anything that can be used to reproduce an entire tree (seeds and cuttings being two of the most obvious examples).  They hired translators to accompany them, who asked locals to point out the best apple trees for various uses -- cooking, cider, making wine or vinegar, drying/preserving, or eating fresh -- and they took samples of germ line (along with copious notes) to bring home to the Orchards for growing and hybridizing.  Besides just looking for good fruit quality, they were also interested in finding strains that are resistant to pests and diseases.

The most diversity they discovered was in Kazakhstan and Uzbekistan, which is where apples originate.  ("American as apple pie" is about as inaccurate as you can get; apples not only aren't native to the United States, they were brought into North America in the mid-1600s by a Frenchman, Pierre Martin -- who settled in Nova Scotia.)  And some research out of the Max Planck Institute for the Science of Human History that appeared last week in Frontiers in Plant Science found that the spread of apples from their homeland, thousands of miles across Europe, was due to two factors; megafauna and the Silk Road.

[Image licensed under the Creative Commons Sandstein, Civni-Rubens apple, CC BY 3.0]

The modern apple is the result of hybridization between at least four wild species, followed by centuries of backcrossing and artificial selection.  Let apples cross-pollinate and plant the seeds, and you'll end up with something like a wild crabapple.  Originally, the bright fruits of apples were eaten by large herbivores like horses and wild cattle, and the seeds dispersed long distances, but with the disappearance of the huge herds that used to exist in central Asia, apple seeds were poorly dispersed.  (Apples aren't the only plants that got into trouble when their seed-disperser disappeared, something about which I wrote in more detail a couple of years ago.)  Fortunately for apples, though, their many uses were noted by humans, and when people moved -- especially along the Silk Road -- they took apple germ line with them, just as my Cornell researcher friend did a thousand years later.

The author, Robert Nicholas Spengler, writes:

Large fruits in Rosaceae [the family apples belong to] evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene.  Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers.  Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning.  Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Current archaeobotanical evidence seems to suggest that apple domestication took place over a period of less than 100 generations, much less for the earliest morphological changes.  It seems feasible that rapid domestication through hybridization occurred in as little as one or a few generations, and most of the modern diversity in landraces is probably a recent phenomenon, through directed breeding.  Not only do protracted models of domestication fall short when discussing apples, the concept of a “center” of domestication is misleading. Genetic studies illustrate that wild apple populations across Europe and West Asia collectively contributed to the modern domesticated apple in a hybrid complex of species distributed across a continent and a half.

So that's something to think about next time you bite into a crisp apple -- you're enjoying a fruit that has roots reaching back millions of years, the current shape, color, and taste of which were created by megafaunal seed dispersers and the travel of human populations down the Silk Road.

Oh, and we eventually did get back home.  Carol and I, our geneticist friend, and four other people finally decided to hire a limousine when it became obvious that (1) the power, and therefore the airport, was going to be out of commission for a long time, and (2) there wasn't a rental car to be had anywhere in the New York City area.  We figured that splitting the cost of a limousine all the way to Ithaca seven ways wasn't going to be much more than each of us separately hiring a rental car anyhow.  All was going well until the limousine overheated and died in the middle of nowhere in the Poconos, leaving us stranded by the side of the highway with all our luggage.

By then, even my new friend and I didn't feel much like talking about genetics.

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Escapees from Siberia

As you might expect from someone who is passionately interested in genealogy, linguistics, and evolutionary genetics, when there's a study that combines all three, it's a source of great joy to me.

This was my reaction to a study in Nature on the evolutionary history of humans in northern Europe, specifically the Finns.  Entitled, "Ancient Fennoscandian Genomes Reveal Origin and Spread of Siberian Ancestry in Europe," it was authored by no less than seventeen researchers (including Svante Pääbo, the Nobel Prize-winning Swedish biologist who is widely credited as founding the entire science of paleogenetics) from the Max Planck Institute, the University of Helsinki, the Russian Academy of Sciences, the Vavilov Institute for General Genetics, and the University of Turku.

Quite a collaborative effort.

It's been known for a while that Europe was populated in three broad waves of settlement.  First, there were hunter-gatherers who came in as early as forty thousand years ago, and proceeded not only to hunt and gather but to have lots of hot caveperson-on-caveperson sex with the pre-existing Neanderthals, whose genetic traces can be discerned in their descendants unto this very day.  Then, there was an agricultural society that came into Europe from what is now Turkey starting around eight thousand years ago.  Finally, some nomadic groups -- believed to be the ancestors of both the Scythians and the Celts -- swept across Europe around 4,500 years ago.

Anyone with European ancestry has all three.  Despite the genetic distinctness of different ethnic groups -- without which 23 & Me genetic analysis wouldn't work at all -- there's been enough time, mixture, and cross-breeding between the groups that no one has ancestry purely from one population or another.

Which, as an aside, is one of the many reasons that the whole "racial purity" crowd is so ridiculous.  We're all mixtures, however uniform you think your ethnic heritage is.  Besides, racial purity wouldn't a good thing even if it were possible.  That's called inbreeding, and causes a high rate of homozygosity (put simply, you're likely to inherit the same alleles from both your mother and father).  This causes lethal recessives to rear their ugly heads; heterozygous individuals are protected from these because the presence of the recessive allele is masked by the other, dominant (working) copy.  It's why genetic disorders can be localized to different groups -- cystic fibrosis in northern Europeans, Huntington's disease in people whose ancestry comes from eastern England, sickle-cell anemia from sub-Saharan Africa, Tay-Sachs disease in Ashkenazic Jews, and so on.

So mixed-ethnic relationships are more likely to produce genetically healthy children.  Take that, neo-Nazis.

Map of ethnic groups in Europe, ca. 1899  [Image is in the Public Domain]

In any case, the current paper looks at the subset of Europeans who have a fourth ancestral population -- people in northeastern Europe, including Finns, the Saami, Russians, the Chuvash, Estonians, and Hungarians.  And they found that the origin of this additional group of ancestors is all the way from Siberia!

The authors write:

[T]he genetic makeup of northern Europe was shaped by migrations from Siberia that began at least 3500 years ago.  This Siberian ancestry was subsequently admixed into many modern populations in the region, particularly into populations speaking Uralic languages today.  Additionally... [the] ancestors of modern Saami inhabited a larger territory during the Iron Age.

The coolest part is that this lines up brilliantly with what we know about languages spoken in the area:

The Finno-Ugric branch of the Uralic language family, to which both Saami and Finnish languages belong, has diverged from other Uralic languages no earlier than 4000–5000 years ago, when Finland was already inhabited by speakers of a language today unknown.  Linguistic evidence shows that Saami languages were spoken in Finland prior to the arrival of the early Finnish language and have dominated the whole of the Finnish region before 1000 CE. Particularly, southern Ostrobothnia, where Levänluhta is located, has been suggested through place names to harbour a southern Saami dialect until the late first millennium, when early Finnish took over as the dominant language.  Historical sources note Lapps living in the parishes of central Finland still in the 1500s.  It is, however, unclear whether all of them spoke Saami, or if some of them were Finns who had changed their subsistence strategy from agriculture to hunting and fishing.  There are also documents of intermarriage, although many of the indigenous people retreated to the north...  Ancestors of present-day Finnish speakers possibly migrated from northern Estonia, to which Finns still remain linguistically close, and displaced but also admixed with the local population of Finland, the likely ancestors of today’s Saami speakers.

Which I think is pretty damn cool.  The idea that we can use the genetics and linguistics of people today, and use it to infer migratory patterns back forty thousand years, is nothing short of stunning.

Unfortunately, however, I have zero ancestry in Finland or any of the other areas the researchers were studying.  According to 23 & Me, my presumed French, Scottish, Dutch, German, and English ancestry was shown to be... French, Scottish, Dutch, German, and English.  No surprise admixtures of genetic information from some infidelity by my great-great-grandmother with a guy from Japan, or anything.

On the other hand, I did have 284 markers associated with Neanderthal ancestry.  Probably explaining why I like my steaks medium-rare and run around more or less naked when the weather's warm.  Which I suppose makes up for my lack of unexpected ethnic heritage.

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Inner space

Donald Rumsfeld famously said, "There are known knowns.  These are things we know that we know.  There are known unknowns.  That is to say, there are things that we know we don't know.  But there are also unknown unknowns.  There are things we don't know we don't know."

At the time, much fun was made of his choice of words.  But although I wouldn't choose this as an exemplar of clarity, I have to admit the point he was making is valid enough.  Sometimes discovery starts with determining exactly what it is we don't yet know, with sketching out what astrophysicist Neil deGrasse Tyson (more eloquently) called "the perimeter of our ignorance."

This is the point of the Unknome Project, which is an effort to take our own genome and figure out what parts of it are, at present, unstudied and unexplained.  Cellular biologist Seth Munro and his colleagues at the Medical Research Council Laboratory of Molecular Biology in Cambridge, England, have developed a catalogue of thirteen thousand gene families found in humans (or other mammals that have been sequenced), coding for over two million proteins, and assigned each a "knownness score" -- a number describing to what extent the function of each is understood.  And three thousand of the families -- a little less than a quarter of them -- have a knownness score of zero.

That's a lot of genes that were (at least before Munro et al.) unknown unknowns.

[Image licensed under the Creative Commons Christoph Bock, Max Planck Institute for Informatics, DNA methylation, CC BY-SA 3.0]

What's even cooler is that the group is working to chip away at this bit of the perimeter of our ignorance, and to learn something about the mysteries of our own genetic inner space.  They found 260 genes with low knownness scores that are also present in fruit flies -- a much easier species to study -- and used a technique to suppress the expression of those genes.

Astonishingly, reducing the expression of sixty of these hitherto-unknown genes killed the flies outright.  Dampening others inhibited such important functions as reproduction, growth, mobility, and resistance to stress.

If these poorly-studied genes have analogous effects in humans -- and it's suspected that they do, given that they were evolutionarily conserved since the last common ancestor of humans and fruit flies, something like a half a billion years ago -- that's a lot of critical parts of our genome we don't yet understand.

What it got me wondering is how many of these are involved in diseases for which we haven't yet determined the causes.  There are so many disorders -- like, unfortunately, most mental illnesses -- for which the treatments are erratic at best, in part because we don't know for sure what the underlying origin of the condition is.  In my own case, I know for sure that depression and anxiety run in both sides of my family -- my mother and maternal grandmother both suffered from major depression, and a paternal great-grandmother committed suicide after (according to the newspaper article that reported it) "becoming mentally unbalanced by the illness of her husband."  Part of the problem with these sorts of things is, of course, that it's hard to tease apart the genetic from the environmental factors.  Growing up with mental illness in the family certainly doesn't make for an easy childhood; as my wise grandmother once said, "Hurt people hurt people" -- something that was certainly true enough within her own family.

It's fantastic that Munro and his colleagues are working to try and elucidate the functions of these mysterious genes, and I hope that perhaps some of them might turn out to be good targets for medications to alleviate conditions that have heretofore been resistant to treatment.  Certainly, anything we can do to reduce the perimeter of our own ignorance -- to eliminate some of those unknown unknowns -- is a good thing.

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In vino veritas

One of the best explanations of how modern evolutionary genomics is done is in the fourth chapter of Richard Dawkins's fantastic The Ancestor's Tale.  The book starts with humans (although he makes the point that he could have started with any other species on Earth), and tracks backwards in time to each of the points where the human lineage intersects with other lineages.  So it starts out with chapters about our nearest relatives -- bonobos and chimps -- and gradually progresses to more and more distantly-related groups, until by the last chapter we've united our lineage with every other life form on the planet.

In chapter four ("Gibbons"), he describes something of the methodology of how this is done, using as an analogy how linguists have traced the "ancestry" (so to speak) of the surviving copies of Chaucer's The Canterbury Tales, each of which have slight variations from the others.  The question he asks is how we could tell what the original version looked like; put another way, which of those variations represent alterations, and which were present in the first edition.

The whole thing is incredibly well done, in the lucid style for which Dawkins has rightly become famous, and I won't steal his thunder by trying to recap it here (in fact, you should simply read the book, which is wonderful from beginning to end).  But a highly oversimplified capsule explanation is that the method relies on the law of parsimony -- that the model which requires the fewest ad hoc assumptions is the most likely to be correct.  When comparing pieces of DNA from groups of related species, the differences come from mutations; but if two species have different base pairs at a particular position, which was the original and which the mutated version -- or are both mutations from a third, different, base pair at that position?

The process takes the sequences and puts together various possible "family trees" for the DNA; the law of parsimony states that the likeliest one is the arrangement that requires the fewest de novo mutations.  To take a deliberately facile example, suppose that within a group of twelve related species, in a particular stretch of DNA, eleven of them have an A/T pair at the third position, and the twelfth has a C/G pair.  Which is more likely -- that the A/T was the base pair in the ancestral species and species #12 had a mutation to C/G, or that C/G was the base pair in the ancestral species and species #1-11 all independently had mutations to A/T?

Clearly the former is (hugely) more likely.  Most situations, of course, aren't that clear-cut, and there are complications I won't go into here, but that's the general idea.  Using software -- none of this is done by hand any more -- the most parsimonious arrangement is identified, and in the absence of any evidence to the contrary, is assumed to be the lineage of the species in question.

This is pretty much how all cladistics is done.  Except in cases where we don't have DNA evidence -- such as with prehistoric animals known only from fossils -- evolutionary biologists don't rely much on structure any longer.  As Dawkins himself put it, "Even if we were to erase every fossil from the Earth, the evidence for evolution from genetics alone would be overwhelming."

The reason this comes up is a wonderful study that came out this week in Science that uses these same techniques to put together the ancestry of all the modern varieties of grapes.  A huge team at the Karlsruher Institut für Technologie and the Chinese Yunnan Agricultural University analyzed the genomes of 3,500 different grapevines, including both wild and cultivated varieties, and was able to track their ancestry back to the southern Caucasus in around 11,000 B.C.E. (meaning that grapes seem to have been cultivated before wheat was).  From there, the vine rootstocks were carried both ways along the Silk Road, spreading all the way from China to western Europe in the process.

[Image licensed under the Creative Commons Ian L, Malbec grapes, CC BY 2.0]

There are a lot of things about this study that are fascinating.  First, of course, is that we can use the current assortment of wild and cultivated grape vines to reconstruct a family tree that goes back thirteen thousand years -- and come up with a good guess about where the common ancestor of all of them lived.  Second, though, is the more general astonishment at how sophisticated our ability to analyze genomes has become.  Modern genomic analysis has allowed us to create family trees of all living things that boggle the mind -- like this one:

[Image licensed under the Creative Commons Laura A. Hug et al., A Novel Representation Of The Tree Of Life, CC BY 4.0]

These sorts of analyses have overturned a lot of our preconceived notions about our place in the world.  It upset a good many people, for some reason, when it was found we have a 98.7% overlap in our DNA with our nearest relatives (bonobos) -- that remaining 1.3% accounts for the entire genetic difference between yourself and a bonobo.  People were so used to believing there was a qualitative biological difference between humans and everything other living thing that to find out we're so closely related to apes was a significant shock.  (It still hasn't sunk in for some people; you'll still hear the phrase "human and animal" used, as if we weren't ourselves animals.)

Anyhow, an elegant piece of research on the ancestry of grapes is what got all this started, and after all of my circumlocution you probably feel like you need a glass of wine.  Enjoy -- in vino veritas, as the Romans put it, even if they may not have known as much about where their vino originated as we do.

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Psychic genomics

Before I start today's post, allow me to begin with a disclaimer: I am not claiming psychic abilities are impossible.  I am not hostile to any attempts to demonstrate their existence scientifically.  In fact, I would love it if all of the claims were true, because it would be wonderful fun to telekinetically control Tucker Carlson while he's on the air and make him unable to do anything but sing the theme song to SpongeBob SquarePants over and over, or put a deadly and horrific curse on Mitch McConnell so that he suddenly develops a soul or something.

But as my grandma was fond of saying, wishin' don't make it so.  In science the usual progression of things is (1) produce unequivocal evidence that the phenomenon you've observed actually exists, (2) find correlations between that phenomenon and whatever you believe is causing it, and (3) show that those correlations actually do represent causation.

Polish "psychic" Stanisława Tomczyk levitating a pair of scissors, which totally wasn't connected to her fingers by a piece of thread or anything (ca. 1909) [Image is in the Public Domain]

Unfortunately, a lot of psychic researchers get the whole thing backwards, which is a little maddening.  Take the story I read yesterday in Mystery Wire about some research by the rather notorious Dean Radin, who has been for decades trying to put psychic stuff unequivocally on a scientific footing.  While, like I said, I have no problem with this as a general goal, much about what Radin does sounds an awful lot like assuming your conclusion and then casting about for incidental evidence to support what you already believed was true.

Turns out Radin was the co-author of a paper in Elsevier called "Genetics of Psychic Ability: A Pilot Case-Control Exome Sequencing Study," that basically looked at genome sequencing people who self-reported a family history of psychic abilities and compared those sequences to people who self-reported no psychic abilities in their family heritage.  And they found differences.

That, unfortunately, constitutes about the sum total of their findings, but Radin et al. proceeded to crow that they'd found a genetic basis for psychic ability.  But amongst the (many) problems, here are a few that jump out right away:

• Out of a sample size of 1,000, only thirteen people reported a family history of psychic stuff.  They then had to actively look for thirteen people who didn't, to use as a control.  This seems like an awfully small sample size from which to draw such a profound conclusion.
• There was no indication that they ruled out other reasons for the similarities.  Given that claims of psychic abilities have at least some tendency to be culture-dependent, isn't it at least possible that the common gene sequences they found were due to similar ethnic background?
• More reputable crowd-based human genomic studies -- such as the one being conducted by 23 & Me -- are still hesitant to assume the commonalities and differences they find in the DNA are causative of phenotype.  Due to the phenomenon of pleiotropy (one gene, many effects) and complicating factors like epigenetics, the most I've seen them say is that (after hundreds of thousands of sequences analyzed) "you have a higher than average likelihood of having trait X."  (Such as when I was told that I am likely to have hair that photo-bleaches in the sun -- which turns out to be true.)
• From their study, they concluded that being genetically psychic is the "wild type" and that we non-psychics are the mutants.  Why, with a grand total of 26 people to compare, they decided this I can't tell, and that's even after reading the actual paper.  Seems to me it's more along the lines of "the modern scientific approach has blunted our perception of the mystical oneness of reality that we once had in the past" stuff that you hear so often from these types.
• As I mentioned earlier, there has yet to be any sort of scientifically admissible evidence that psychic abilities exist, so looking for an underlying cause seems to be a tad premature.

Then, unfortunately, Radin launches off into the ionosphere during an interview with Mystery Wire's writer George Knapp.  He describes another "experiment" (I hesitate even to dignify it by that name) in which a supposed double-blind experiment showed that people who drank tea that had been blessed felt happier than ones who had drunk unblessed tea.  As if this weren't enough, Radin comes up with an inadvertently hilarious explanation:

So we used a little plant called Arabidopsis thaliana, which is in the mustard family.  So it’s got [sic] a little weed.  And a little weed is interesting because its genome was sequenced before the human genome.  And it turns out that like most living creatures around the world have very similar DNA.  [sic again]  So if this plant has a disease that’s genetically based it has an analogue in humans.  [Nota bene: This is where I started laughing.]  So the plants are used for studying genetic diseases without using humans for it.  [NB:  No, they're not.]  So, it also turns out that there are various mutations that are understood about this plant.  And in particular, all living systems on earth have a protein called cryptochrome.  So cryptochrome is interesting because it is a protein that is thought to have quantum properties.  [NB: All molecules have quantum properties.  That's kind of what "quantum property" means -- the behavior of matter and energy on extremely small scales.]  So we thought, okay, let’s get an Arabidopsis plant, that is a particular mutation where it overexpresses cryptochrome, so when there’s blue light on it, the cryptochrome is activated, it overexpresses, it grows more.  So we thought, well, maybe that would be an interesting target, to use for intention, because we think there may be a relationship between observing quantum systems, in this case of protein, and the response to that system.  So again, under double blind conditions, the Buddhist monks have treated water, they have the same water that is not treated, the seeds are grown into two water mediums.  And then there’s a variety of different measures you can take.  One of which is called a hypocotyl.  So the hypocotyl is the point where the stem begins from the seed up to the beginning of the leaves.  So if it’s short and fat, it means that it’s a healthy plant, because it’s not using all of its energy to try to reach the surface or turn upside down or something.  So short fat hypocotyl, we did nine repetitions of the experiment and got extremely significant differences, terms of magnitude is only a matter of a couple of millimeters. [sic]  But so many experiments in such precise results, we can tell there was a really significant difference in growth, better growth with the treated water or the blessed water.

Yeesh.  A hypocotyl a "couple of millimeters" longer constitutes "extremely significant results"?  That rule out all other possible factors, including natural variability and the difficulty of measuring the stem of a small plant to millimeter accuracy?

And as an aside, beginning every other sentence with the word "So" is almost as annoying as the people who use "like" as, like, a punctuation in, like, every, like, thing they say.  What it does not do is make you come across as an articulate intellectual.

Anyhow, I encourage you to read the Mystery Wire article, and (especially) the original paper, which is helpfully included therein.  See if you think I'm being unwarrantedly harsh.  And it's not that I expect scientists -- or anyone, really -- to be completely unbiased; they obviously can't start out from the standpoint that all possible explanations are on equal footing, and they understandably have at least some intellectual and emotional investment in showing their own hypotheses to be correct.

But to say this study lacks dispassionate objectivity is a colossal understatement.  I do have respect for people who investigate fringe phenomena from a scientific standpoint -- the work of the Society for Psychical Research in the UK comes to mind -- but unfortunately, this one ain't it.

So back to the drawing board.  I guess I'll have to keep waiting for McConnell's soul to appear and for Carlson to humiliate himself completely in front of millions of viewers.  Pity, that.

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Author Michael Pollan became famous for two books in the early 2000s, The Botany of Desire and The Omnivore's Dilemma, which looked at the complex relationships between humans and the various species that we have domesticated over the past few millennia.

More recently, Pollan has become interested in one particular facet of this relationship -- our use of psychotropic substances, most of which come from plants, to alter our moods and perceptions.  In How to Change Your Mind, he considered the promise of psychedelic drugs (such as ketamine and psilocybin) to treat medication-resistant depression; in this week's Skeptophilia book recommendation of the week, This is Your Mind on Plants, he looks at another aspect, which is our strange attitude toward three different plant-produced chemicals: opium, caffeine, and mescaline.

Pollan writes about the long history of our use of these three chemicals, the plants that produce them (poppies, tea and coffee, and the peyote cactus, respectively), and -- most interestingly -- the disparate attitudes of the law toward them.  Why, for example, is a brew containing caffeine available for sale with no restrictions, but a brew containing opium a federal crime?  (I know the physiological effects differ; but the answer is more complex than that, and has a fascinating and convoluted history.)

Pollan's lucid, engaging writing style places a lens on this long relationship, and considers not only its backstory but how our attitudes have little to do with the reality of what the use of the plants do.  It's another chapter in his ongoing study of our relationship to what we put in our bodies -- and how those things change how we think, act, and feel.

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

The horse warriors

I'm always drawn to a historical mystery.

The difficulty, of course, is given that a huge amount of our history has either highly unreliable records or else no records at all, a lot of mysteries will never get resolved satisfactorily.  Two examples I read about recently which are as fascinating as they are frustrating are the true identity of Jack the Ripper, and the fate of the "Princes in the Tower" -- the two young sons of English King Edward IV, who disappeared in around 1483 and were probably murdered.  

As a quick aside, it bears mention that in the latter case the alleged culprit, King Richard III, was not the horrific, amoral villain you might think, if your only source is the play by Shakespeare.  He was actually competent and not a selfish monster, nor was he a hunchback; the Shakespearean smear job makes for great theater, and appeased the anti-Yorkist monarchy of the time, but has unfairly tarred a man who -- if Henry Tudor hadn't decided to swipe the throne -- probably would have been considered a pretty good leader.  He may still have had the princes killed, though; such behavior by a king anxious to eliminate rivals and put his own claim to the throne beyond question was not at all uncommon at the time.  But Shakespeare having Queen Margaret call him a "deformed, bunch-backed toad" seems a little excessive.

Sometimes there's an entire ethnic group that is mysterious, again usually because we have mostly archaeological evidence to go by, supplemented by dubiously accurate accounts written down by other (often hostile) cultures.  In fact, the whole reason why the subject of historical mysteries comes up is because of a paper I read a couple of days ago about the Scythians, the central Asian "horse warriors" who bumped up against the cultures their territory bordered -- principally Greece, Rome, China, and Persia -- and whose accounts form the basis of our knowledge of who they were.

The Golden Stag of Kostromskaya, one of the most famous Scythian artifacts (ca. 7th century B.C.E.) [Image licensed under the Creative Commons Joanbanjo, Placa en forma de cérvol tombat, trobada al túmul de Kostromskoy a Kuban, segle VII aC, CC BY-SA 3.0]

In "Ancient Genomic Time Transect from the Central Asian Steppe Unravels the History of the Scythians," which appeared last week in Science Advances and was authored by a huge team led by Guido Alberto Gnecchi-Ruscone of the Max Planck Institute for the Science of Human History, we read about a genomic study of the remains of over a hundred individuals from Scythian burial sites, and find out that they were hardly a single unified ethnic group -- their genomes show a significant diversity and represent multiple origins.  So the Scythians seem more like a loose confederation of relatively unrelated people than the single unified, monolithic culture of fierce nomads depicted in the writings of their rivals.

The authors write:

The Scythians were a multitude of horse-warrior nomad cultures dwelling in the Eurasian steppe during the first millennium BCE.  Because of the lack of first-hand written records, little is known about the origins and relations among the different cultures.  To address these questions, we produced genome-wide data for 111 ancient individuals retrieved from 39 archaeological sites from the first millennia BCE and CE across the Central Asian Steppe.  We uncovered major admixture events in the Late Bronze Age forming the genetic substratum for two main Iron Age gene-pools emerging around the Altai and the Urals respectively.  Their demise was mirrored by new genetic turnovers, linked to the spread of the eastern nomad empires in the first centuries CE.

 If that's not intriguing enough, last week there was also new information uncovered about an artifact from the same place but a lot earlier, the "Shigir idol," which was uncovered from a peat bog in the Ural Mountains in 1890.  Its age is apparently greater than scientists have thought -- the new study suggests it's about 12,500 years old, making it the oldest wooden representation of a human figure known.

The Shigir idol [Image licensed under the Creative Commons Владислав Фальшивомонетчик, Большой шигирский идол, CC BY-SA 3.0]

"The idol was carved during an era of great climate change, when early forests were spreading across a warmer late glacial to postglacial Eurasia," said study lead author Thomas Terberger, of the University of Göttingen, in an interview in the New York Times.  "The landscape changed, and the art—figurative designs and naturalistic animals painted in caves and carved in rock—did, too, perhaps as a way to help people come to grips with the challenging environments they encountered."

What it brings home to me is the humbling thought of how little we actually know of our own history.  For every mystery we know about -- like Jack the Ripper and the Princes in the Tower we began with -- there are probably thousands of other equally fascinating events we don't have any way of knowing about.  The vast majority of humans died without leaving any extant traces, and since human remains and biodegradable artifacts (like the Shigir idol) only survive under specific (and uncommon) conditions, the vast majority of those are gone beyond recall, too.  When we luck out and find tangible evidence, like the Scythian burials, we can sometimes glean further information about a culture we knew little about.  The unfortunate but tantalizing truth, though, is that most of our own history is both unknown and unknowable.

Which for me makes it even more appealing, although inevitably, as frustrating as it is fascinating.

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The sad truth of our history is that science and scientific research has until very recently been considered the exclusive province of men.  The exclusion of women committed the double injury of preventing curious, talented, brilliant women from pursuing their deepest interests, and robbing society of half of the gains of knowledge we might otherwise have seen.

To be sure, a small number of women made it past the obstacles men set in their way, and braved the scorn generated by their infiltration into what was then a masculine world.  A rare few -- Marie Curie, Barbara McClintock, Mary Anning, and Jocelyn Bell Burnell come to mind -- actually succeeded so well that they became widely known even outside of their fields.  But hundreds of others remained in obscurity, or were so discouraged by the difficulties that they gave up entirely.

It's both heartening and profoundly infuriating to read about the women scientists who worked against the bigoted, white-male-only mentality; heartening because it's always cheering to see someone achieve well-deserved success, and infuriating because the reason their accomplishments stand out is because of impediments put in their way by pure chauvinistic bigotry.  So if you want to experience both of these, and read a story of a group of women who in the early twentieth century revolutionized the field of astronomy despite having to fight for every opportunity they got, read Dava Sobel's amazing book The Glass Universe: How the Ladies of the Harvard Observatory Took the Measure of the Stars.

In it, we get to know such brilliant scientists as Willamina Fleming -- a Scottish woman originally hired as a maid, but who after watching the male astronomers at work commented that she could do what they did better and faster, and so... she did.  Cecilia Payne, the first ever female professor of astronomy at Harvard University.  Annie Jump Cannon, who not only had her gender as an unfair obstacle to her dreams, but had to overcome the difficulties of being profoundly deaf.

Their success story is a tribute to their perseverance, brainpower, and -- most importantly -- their loving support of each other in fighting a monolithic male edifice that back then was even more firmly entrenched than it is now.  Their names should be more widely known, as should their stories.  In Sobel's able hands, their characters leap off the page -- and tell you a tale you'll never forget.

[Note: if you purchase this book using 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!]

Bird trees

I'm a birdwatcher, which in my specific case kind of crosses the line into a mild mental illness.  I've traveled all over the world to see new birds, which is kind of cool, but it's also led me to do stuff like standing calf-deep in the snow, in far-below-freezing temperatures and gale-force winds, to see a rare species of duck that happened to end up for some reason in nearby Cayuga Lake in midwinter.  From the standpoint of seeing a bird species I'd never seen before, it was a great day.

It was a somewhat less-than-great day with respect to frostbite, hypothermia, and people in passing (heated) cars rolling down their windows to yell "What the hell is wrong with you?"

The reason this all comes up because of how excited I am about a recent release of new information by the Bird 10,000 Genomes Project, which has as its fairly lofty goal the sequencing of the genomes for all ten-thousand-plus species of birds currently living on the Earth.

The cool thing about genetic information to determine relationships is that it's much more accurate than relying on such obvious characteristics as external appearance or behavior.  Through genetic analysis, the B10K Genomes Project, as it's affectionately known, has found the following surprises:

• Flamingos are fairly closely related to grebes, a family of small diving water birds, and both as a group are more closely related to pigeons than to any other species of aquatic bird.
• Likewise, the bizarre flightless dodos, now extinct but once common on two remote islands in the Indian Ocean, are most closely related to pigeons.
• The three main groups of birds that regularly prey on mammals -- hawks and eagles, owls, and falcons -- aren't closely related at all, and their similarities seem to have developed through convergent evolution.
• Despite superficial similarities in appearance and behavior, vultures in North and South America are only very distantly related to vultures in Africa and Europe.
• Hummingbirds, swifts, and nightjars (such as the more-often-seen-than-heard whippoorwill) are all on the same branch of the bird family tree.  A different branch includes such disparate groups as loons, pelicans, albatrosses... and penguins.
• Emus, ostriches, and kiwis -- flightless species that are on the same basic branch, a group called ratites -- all descend from a common ancestor that could fly, and apparently evolved flightlessness independently.

Here's a circular representation of what we know so far, with illustrations of a few selected species:

Clockwise from the top: golden eagle, thick-billed murre, ruddy turnstone, white-bellied storm petrel, western bronze ground dove, squirrel cuckoo, Anna’s hummingbird, marbled wood quail, little spotted kiwi, redwing blackbird, akiapolaau, black sunbird, wall creeper, Cape rockjumper, chestnut wattle-eye, chowchilla, Amazonian royal flycatcher, rosy-faced lovebird and keel-billed toucan.  [Image courtesy of S. Feng et al./Nature, 2020; Illustrations by Jon Fjeldså]

So the study is pretty cool, expanding greatly what we know about the feathered dinosaurs we see flitting about every day.  As the B10K Genome Project site puts it:

The B10K project will allow the completion of a genomic level tree of life of the entire living avian class, decode the link between genetic variation and phenotypic variation, uncover the correlation of genetic evolutionary and biogeographical and biodiversity patterns across a wide-range of species, evaluate the impact of various ecological factors and human influence on species evolution, and unveil the demographic history of an entire class of organisms...  We envision this project will have significant scientific and public impact that will change our understanding of avian biology and evolution, which in turn will affect our understanding of other organisms and open doors to new areas of research.

I'm really looking forward to seeing what else they uncover.  It might not explain my obsession with trying to see every bird there is -- something a friend of mine calls "Pokémon for Adults" -- but it certainly will give me something new to think about when I'm shivering in the snow looking for rare ducks.

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This week's Skeptophilia book-of-the-week is one that has raised a controversy in the scientific world: Ancient Bones: Unearthing the Astonishing New Story of How We Became Human, by Madeleine Böhme, Rüdiger Braun, and Florian Breier.

It tells the story of a stupendous discovery -- twelve-million-year-old hominin fossils, of a new species christened Danuvius guggenmosi.  The astonishing thing about these fossils is where they were found.  Not in Africa, where previous models had confined all early hominins, but in Germany.

The discovery of Danuvius complicated our own ancestry, and raised a deep and difficult-to-answer question; when and how did we become human?  It's clear that the answer isn't as simple as we thought when the first hominin fossils were uncovered in Olduvai Gorge, and it was believed that if you took all of our millennia of migrations all over the globe and ran them backwards, they all converged on the East African Rift Valley.  That neat solution has come into serious question, and the truth seems to be that like most evolutionary lineages, hominins included multiple branches that moved around, interbred for a while, then went their separate ways, either to thrive or to die out.  The real story is considerably more complicated and fascinating than we'd thought at first, and Danuvius has added another layer to that complexity, bringing up as many questions as it answers.

Ancient Bones is a fascinating read for anyone interested in anthropology, paleontology, or evolutionary biology.  It is sure to be the basis of scientific discussion for the foreseeable future, and to spur more searches for our relatives -- including in places where we didn't think they'd gone.

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