Talking to the animals

An Introduction to Language (by Victoria Fromkin and Robert Rodman, Third Edition, 1974) defines language as "rule-governed arbitrary symbolic communication."

The "rule-governed" and "arbitrary" parts might seem contradictory, but they're not.  That language has rules is self-evident whether you are a prescriptivist (someone who believes there are correct and incorrect ways to use language) or a descriptivist (someone who believes that as long as communication is occurring, it's language; so the primary role of the linguist is not to enforce rules but to document them).  Being that my master's degree is in historical linguistics, I'm strongly of a descriptivist bent; if I thought there were an inflexible lexicon and set of grammatical rules that never ever changed, I'd kind of be out of a job.

The arbitrary part is less obvious.  It has to do with the sound-to-meaning correspondence.  Dog in English is inu in Japanese, chien in French, kare in Hausa, and hundur in Icelandic; none of those words are, in fact, especially doggy in nature.  Other than a handful of onomatopoeic words like bang, oink, meow, and hiccup, the connection between a word and its meaning is essentially accidental.

Curiously, humans are the only species on Earth that we are certain have true language, by the Fromkin and Rodman definition.  There's long been a suspicion that dolphin and whale vocalizations might be language, but as of this writing, that remains conjecture.  Recently, there have been some interesting studies of other primates indicating that certain features of language might exist outside of Homo sapiens -- a paper out of the University of Warwick last week suggests that orangutan vocalizations might exhibit recursion, the nesting structure you see in the children's rhyme "This is the House That Jack Built."  The researchers found that the sounds orangutans make are grouped into clusters, and those clusters put together in at least two additional tiers of structure, hinting that their vocalizations might have a much richer information-carrying capacity than we'd thought.

Another recent study, this one out of the University of Vienna, found that chimps might use drumming as a means of long-distance communication -- that the spacing of beats when they drum on tree roots varies but is non-random.  Like the recursion found in orangutans, the fact that the rhythm of drumming in chimps isn't just random noise opens up the possibility that it might be meaningful.  The researchers found that different chimps have different rhythmic styles, and that groups also developed their own unique patterns of drumming -- suggestive that drumming in chimps could be a cultural phenomenon.

How we developed language, and (likely) no other extant species did, is still open to question.  There are some interesting genetic pieces to the puzzle; the forkhead box protein 2 (FOX-P2) gene seems to be an important one, as the human variant of FOX-P2 isn't found in any known living species other than ourselves, and mutations in that sequence result in significant problems with learning and utilizing language.  (Genetic studies of Neanderthal remains found that Neanderthals had an identical FOX-P2 gene to that of modern humans; obviously we can't be sure that they had language, but it seems likely.)

[Image licensed under the Creative Commons Emw, Protein FOX-P2 PDB 2a07, CC BY-SA 3.0]

Actually, it was genetics that got me thinking about this topic today; yet another study, this one out of Rockefeller University and Cold Springs Harbor Laboratory, did a gene insertion on mice, replacing the murine version of the NOVA-1 gene with the human variant.  The human NOVA-1 has only a single base pair substitution as compared with that of other mammals, but -- like FOX-P2, damage to this gene is known to impair language learning and production.

And when you replace a mouse embryo's NOVA-1 gene with a human's, the resulting adult mouse is capable of making strikingly more complex vocalizations than your ordinary mouse can do.

"When adult male mice were genetically altered with the human NOVA-1 variant, their squeaks during courtship didn't become higher pitched like the pups," said Robert Darnell, who was lead author on the paper.  "Instead, their vocalizations included more complex syllables.  They 'talked' differently to the female mice.  One can imagine how such changes in vocalization could have a profound impact on evolution....  NOVA-1 encodes a protein that can cut out and rearrange sections of messenger RNA when it binds to neurons.  This changes how brain cells synthesize proteins, probably creating molecular diversity in the central nervous system...  The 'humanized' mice with the NOVA-1 variant had molecular changes in the RNA splicing seen in brain cells, especially in regions associated with vocal behavior."

So we're one step closer to figuring out a uniquely human phenomenon.  That communication in the animal world exists on a spectrum of complexity is certain, but by the Fromkin/Rodman definition, we're kind of it for true language, as far as we know.  How we gained that ability is still not entirely clear, but its advantages are obvious -- and it may be that mutations in two regulatory genes are what kickstarted a capacity for chatter that in large part is responsible for our dominance of the entire biosphere.

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Copy-and-paste

I'm really interested in research on aging, and I'd like to think that it's not solely because I'm Of A Certain Age myself.  The whole fact of our undergoing age-related system degradation is fascinating -- more so when you realize that other vertebrates age at dramatically different rates.  Mice and rats age out after about a year and a half to two years; dogs (sadly) rarely make it past fifteen (much less in some breeds); and the Galapagos Tortoise can still be hale and hearty at two hundred years of age.

A lot of research has gone into why different organisms age at such different speeds, and (more importantly) how to control it.  The ultimate goal, selfish though it may sound, is extending the healthy human life span.  Imagine if we reached our healthy adult physiology at (say) age twenty-five or so, and then went into stasis with respect to aging for two hundred or three hundred years -- or more?

Heady stuff.  For me, the attraction is not so much avoiding death (although that's nice, too).  I was just chatting with a friend yesterday about the fact that one of my biggest fears is being dependent on others for my care.  The idea of my body and/or mind degrading to the point that I can no longer care for my own needs is profoundly terrifying to me.  And when you add to the normal age-related degradation the specter of diseases such as Alzheimer's and ALS -- well, all I can say is that I agree with my dad, who said that compared with that fate, "I'd rather get run over by a truck."

Leaving that aside, though, a particularly interesting piece of research that has bearing on this field was published last week in the journal Science Advances.  But to understand it, you have to know a little bit about a peculiarity of genetics first.

Several decades ago, a geneticist named Barbara McClintock was working with patterns of seed color inheritance in "Indian corn."  In this variety, one cob can bear seeds with dozens of different colors and patterns.  After much study, she concluded that her data could only be explained by there being "transposable elements" -- genetic sequences that were either clipped out and moved, or else copied and moved -- functions similar to the "cut-and-paste" and "copy-and-paste" commands on your computer. McClintock wrote a paper about it...

... and was immediately ignored.  For one thing, she was a woman in science, and back when she was doing her research -- in the 1960s and 1970s -- that was sufficient reason to discount it.  Her colleagues derisively nicknamed her theory "jumping genes" and laughed it into oblivion.

Except that McClintock wouldn't let it go.  She was convinced she was right, and kept doggedly pursuing more data, data that would render her conclusion incontrovertible.  She found it -- and won the Nobel Prize in Physiology and Medicine in 1983, at the age of 81.

Barbara McClintock in her laboratory at Cold Spring Harbor [Image licensed under the Creative Commons Smithsonian Institution/Science Service; Restored by Adam Cuerden, Barbara McClintock (1902-1992) shown in her laboratory in 1947]

McClintock's "transposable elements" (now called "transposons") have since been found in every vertebrate studied.  They are used to provide additional copies of essential genes, so that if one copy succumbs to a mutation, there's an extra working copy that can take over.  They're also used in gene switching.  Move a gene near an on-switch called a promoter, and it turns on; move it away, and it turns off.

The problem is, like any natural process, it can go awry.  The copy-and-paste function especially seems to have that tendency.  When it malfunctions, it acts like a runaway copy-and-paste would in your word processing software.  Imagine the havoc that would ensue if you had an important document, and the computer went haywire and inserted one phrase over and over again in random points in the text.

This should give you an idea of why it's so important to keep this process under control.

You have a way of taking care of these "rogue transposons" (as they're called).  One such mechanism is methylation, which is a chemical means of tangling up and permanently shutting down genes.  But the paper just released suggests that aging is (at least in part) due to the rogue transposition of one particular sequence getting ahead of methylation, leaving a particular chunk of DNA scattered again and again across the genome.

The current research, out of New York University, looked at a transposon called Long Interspersed Nuclear Element 1 (LINE-1) that has become especially good at this copy-and-paste trick, to the extent that the human genome contains five hundred thousand copies of it -- a full twenty percent of our genetic material.  The researchers found that LINE-1 can only accomplish this self-insertion when a molecule called ORF1p is present in sufficient quantities to assemble into clumps called condensates.  Find a way to block ORF1p, and LINE-1 is effectively disabled -- potentially slowing down age-related genetic malfunction.

Of course, even in the best-case scenario, it's unlikely that tweaking one molecule will affect overall aging in any kind of dramatic way.  Even so, the whole thing is tremendously interesting.  On the other hand, I have to say that the idea that we are getting to the point that we can tinker around with fundamental processes like aging is a little frightening.  It opens up practical and ethical issues we've never had to consider before.  How this would affect human population growth?  Who would have access to such genetic modifications if they proved effective and safe?  You can bet the rich would have first dibs (and the last thing we need is Rupert Murdoch living to two hundred years old.)  

Even such things as how we approach the idea of careers and retirement would require significant rethinking.  Imagine if you reached the age of sixty and could expect another fifty or more years of active health.  More staggering still is if the effect on humans was greater -- and the upper bound of human life span was increased to two hundred or three hundred years.  It seems like science fiction, but with the research that is currently happening, it's not outside of the realm of possibility.

Who would want to retire at sixty if you still had the physiology and mental acuity of a twenty-five year old?  At the same point, who would want to stay in the same job for another hundred years or more? 

The whole thing would require a drastic reorganization of our society, a far more pervasive set of changes than any scientific discovery has yet caused.  And lest you think that I'm exaggerating the likelihood of such an eventuality; remember how much progress has happened in biological science in the last century.  Only a hundred years ago, children in industrialized countries were still dying by the thousands of diphtheria and measles.  There were dozens of structures in cells, and a good many organs in humans, about whose function we knew essentially nothing.  We knew that DNA existed, but had no idea that it was the genetic material, much less how it worked.

Makes you wonder what our understanding will be in another hundred years, doesn't it?

And maybe some of the people reading this right now will be around to see it.

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Genetic walkabouts

Today's topic comes to us from the One Thing Leads To Another department.

I got launched into this particular rabbit hole by a notice from 23 & Me that they'd refined their analysis of their test subjects' DNA, and now had a bigger database to extract from, allowing them to make a better guess at "percent composition" not only by general region, but by specific sub-region.

So I took a look at my results.  My DNA came out 63.5% French, 25.3% Scottish and English, 6.4% Ashkenazi, and the remaining 4.8% a miscellany.  This works out to be pretty much what I'd expect from what I know of my family tree.  My mom was close to 100% French, but a great-grandfather of hers, one Solomon Meyer-Lévy, was a French Jew from Alsace and is the origin of the Ashkenazic DNA.  My dad was a bit of a hodgepodge in which French, Scottish, and English predominate.

So like I said, no surprises.  I'm a white guy of western European descent, which if you look at my profile photo, is probably not going to come as any sort of shock.

What I thought was more interesting was the regional breakdown.  The Scottish and English bits were especially interesting because I only have a handful of records documenting where exactly my British Isles forebears were from.  Apparently I have a cluster of genetic relatives around Glasgow, the London area, and Yorkshire.  Other than my dad's paternal family (which was from the French Alps, near Mont Blanc and the border of Italy) and my Alsatian great-great-grandfather, my French ancestry is all in western France; this lines up with what I know of my mom's family, which came from Bordeaux, Poitou, the Loire Valley, and Brittany.

So all of this shores up their claims to accuracy, because this was ascertained purely by my DNA -- I didn't send them my family tree, or anything.  But then this got combined with another random thing, which is that I've been reading a book called The Ancient Celts by anthropologist Barry Cunliffe, and I was kind of surprised at how much of Europe the Celts once ruled -- not only the British Isles and all of France (then called Gaul), but what is now Switzerland, southern Germany, Austria, the northern half of Italy, the eastern half of Spain, and down into a big chunk of the Balkans.  They seem to have been nothing if not inveterate wanderers, and their walkabouts took them just about everywhere in Europe but Scandinavia.  They were there for a long while, too; it was only when the Romans got their act together and started to push back that the Celts retreated; they were shoved farther west when first the Germanic tribes, and then the Slavs, moved in from the east and kind of kept moving.

[Image is in the Public Domain]

This all got me thinking, "Okay, when I say my ancestry is on the order of 2/3 French, what exactly am I saying?"  So I started doing some research into "the ethnic origin of the French," and I found out that it's not simple.  The western parts of France (whence my mom's family originated) are mostly of Celtic (Gaulish) ancestry.  People in the southeast, especially the lowlands near Marseilles, have a lot of Roman and Etruscan forebears.  When you get over into Languedoc -- the southwestern part of France, near the border of Spain -- there's an admixture not only from the Moors of North Africa, but from the Basques, who seem to be the remnants of the earliest settlers of Europe, and are the only ones in western Europe who don't speak an Indo-European language.  In Normandy there's a good admixture of Scandinavian blood, from Vikings who settled there a thousand years ago -- in fact, "Normandy" means "North-man-land."  Despite the fact that the name of the country and its people comes from a Germanic tribe (the Franks), the only place there's a significant amount of Germanic ancestry in France is in the east -- from Burgundy north into Alsace, Lorraine, and Picardy.

Apparently the only reason the French are Frankish is because the Franks ruled the place for a few hundred years, a bit the way the Normans did in England.  The common people, your average seventeenth-century peasants in Bordeaux, probably were nearly 100% Gaulish Celt.

So when I say my mom's family is French, and a guy from Lille and a woman from Marseilles say the same thing, what exactly do we mean?

And there's nothing unusual about the French in that regard; I just use them as an example because I happen to know more about them.  The same is true pretty much anywhere you look except for truly insular cultures like Japan, which have had very little migration in or out for millennia.  We're almost all composites, and ultimately, all cousins.  I remember when I first ran into this idea; that the further back you go, the more our family trees all coalesce, and at some point in the past every human on Earth could be sorted into one of two categories -- people who were the ancestors of every one of us, and people who left no living descendants.

That point, most anthropologists believe, is way more recent than most of us would suspect.  I've heard -- to be fair, I've never seen it rigorously proven, but it sounds about right -- that the two-category split for those of us with western European ancestry happened in around 1,200 C.E.  So pick out anyone from thirteenth century western Europe, and (s)he's either my ancestor, or (s)he has no descendants at all.

This brings up a couple of things.  First, "royal blood" is an idiotic concept from just about whichever angle you choose.  Not only does royal ancestry not confer fitness for leading a country -- let's face it, a lot of those kings were absolute loonies -- I can pretty much guarantee that I descend from Charlemagne, and if you have European ancestry, so do you.  My wife actually descends from an illegitimate child of King Edward IV of England (something she likes to remind me about whenever I get uppity), but the truth is, all of us have royal blood and peasant blood pretty well mixed indiscriminately.

Second, racism, ethnicism, and xenophobia are all equally ridiculous, since (1) we're virtually all genetic mixtures, (2) regardless of our ethnicity, our genetic similarities far outweigh our differences, and (3) we're all cousins anyhow.  I find that rather cool, honestly -- that a Zulu woman living in Botswana and I have common ancestry if you go back far enough.  Race is a cultural construct, not a genetic one, which you can see with extraordinary vividness if you take a DNA test, or if you read anything about the migration patterns humanity has taken since first leaving the East African savanna something like 250,000 years ago.

Anyhow, those are my musings about ethnicity, DNA, ancestry, and so on.  It all goes to show that we're wonderfully complex creatures, and the determination of some of us to see the world as if it was straightforward black-and-white is not only inaccurate, it misses a great deal of the most interesting parts of it.  As the brilliant science fiction writer Ursula LeGuin put it, "I never knew anybody who found life simple.  I think a life or a time looks simple only if you leave out the details."

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The viral accelerator

It's virus season, which thus far I've been able to avoid participating in, but seems like half the people I see are hacking and snorting and coughing so even with caution and mask-wearing I figure it's only a matter of time.  Viruses are odd beasts; they're obligate intracellular parasites, doing their evil work by hijacking your cellular machinery and using it to make more viruses.  Furthermore, they lack virtually all of the structures that cells have, including cell membranes, cytoplasm, and organelles.  They really are more like self-replicating chemicals than they are like living things.

Simian Polyoma Virus 40 [Image licensed under the Creative Commons Phoebus87 at English Wikipedia, Symian virus, CC BY-SA 3.0]

What is even stranger about viruses is that while some of the more familiar ones, such as colds, flu, measles, invade the host, make him/her sick, and eventually (with luck) are cleared from the body -- some of them leave behind remnants that can make their presence known later.  This behavior is what makes the herpes family of viruses so insidious.  If you've been infected once, you are infected for life, and the latent viruses hidden in your cells can cause another eruption of symptoms, sometimes decades later.

Even weirder is when those latent viral remnants cause havoc in a completely different way than the original infection did.  There's a piece of a virus left in the DNA of many of us called HERV-W (human endogenous retrovirus W) which, if activated, can trigger multiple sclerosis or schizophrenia.  Another one, Coxsackie virus, has an apparent connection to type-1 diabetes and Sjögren's syndrome.  The usual sense is that all viral infections, whether or not they're latent, are damaging to the host.  So it was quite a shock to me to read a piece of recent research that there's a viral remnant that not only is beneficial, but is critical for creating myelin -- the coating of our nerve cells that is essential for speeding up nerve transmission!

The paper -- which appeared last week in the journal Cell -- is by a team led by Tanay Ghosh of the Cambridge Institute of Science, and looked at a gene called RetroMyelin.  This gene is one of an estimated forty (!) percent of our genome that is made up of retrotransposons, DNA that was inserted by viruses during evolutionary history.  Or, looking at it another way, genes that made their way to us using a virus as a carrier.  Once inside our genome, transposons begin to do what they do best -- making copies of themselves and moving around.  Most retrovirus-introduced elements are deleterious; HIV and feline leukemia, after all, are caused by retroviruses.  But sometimes, the product of a retroviral gene turns out to be pretty critical, and that's what happened with RetroMyelin.

Myelin is a phosopholipid/protein mixture that surrounds a great many of the nerves in vertebrates.  It not only acts as an insulator, preventing the ion distribution changes that allow for nerve conduction to "short-circuit" into adjacent neurons, it is also the key to saltatory conduction -- the jumping of neural signals down the axon, which can increase transmission speed by a factor of fifty.  So this viral gene acted a bit like a neural accelerator, and gave the animals that had it a serious selective advantage.

"Retroviruses were required for vertebrate evolution to take off," said senior author and neuroscientist Robin Franklin, in an interview in Science Daily.  "There's been an evolutionary drive to make impulse conduction of our axons quicker because having quicker impulse conduction means you can catch things or flee from things more rapidly.  If we didn't have retroviruses sticking their sequences into the vertebrate genome, then myelination wouldn't have happened, and without myelination, the whole diversity of vertebrates as we know it would never have happened."

The only vertebrates that don't have myelin are the jawless fish, such as lampreys and hagfish -- so it's thought that the retroviral infection that gave us the myelin gene occurred around the same time that jaws evolved on our branch of the vertebrate family tree, on the order of four hundred million years ago.

So even some fundamental (and critical) traits shared by virtually all vertebrates, like the myelin sheaths that surround our neurons, are the result of viral infections.  Just proving that not all of 'em are bad.  Something to think about the next time you feel a sore throat coming on.

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Going to the dogs

I understand dogs a great deal better than I understand my fellow humans.

Dogs are straightforward.  They interact with their world in a direct way, whether it be motivated by love, anger, curiosity, hunger, enthusiasm, or fear.  There's nothing feigned about a dog's emotions or the way they express them.  I've sometimes misinterpreted one of my dogs' signals, but that's on me; the signals were there, even if I only recognized them in retrospect.  Once you grok dog behavior, it's much less fraught than the complex, confusing morass of human interaction.

This is why when I'm invited to social events, I'm always hoping the host will have a dog so there'll be someone for me to have a conversation with.

The dogs we've had have nearly all been rescues, and came with all the baggage and bad backstories that rescue dogs have, but one and all were and are wonderful companions, and enriched our lives tremendously.  This latter part is the only possible explanation for why during the holidays, my wife and I were looking around and thinking, "Wow, our house sure has a lot of clutter and dirt and chaos.  We never seem to be able to keep up with the housekeeping.  Hey, I know... let's get a puppy!"

So, without further ado, allow me to introduce to the Skeptophilia readership...

... Jethro.

Jethro is -- and I say this with all modesty and restraint -- the cutest puppy in the whole entire world.  He's five months old, has the sweetest, happiest disposition ever, and soft, silky hair that gathers burs, mud, and debris like some sort of bizarre magnet.  Like many puppies, he has two settings -- "Full Throttle" and "Off."

He's currently set at "Off" and is sleeping at my feet, which is the only way I'm able to write this.  Otherwise I would be engaged in the essential task of Playing With Jethro.

We got him from the amazing Stay Wild Rescue and Wildlife Rehabilitation Center on New Year's Eve.  If you are looking for a wonderful and deserving place to make a donation, please consider Stay Wild.  They do fantastic work on a shoestring budget, and the owners -- Jane George and Dan Soboleski -- work tirelessly to help find rescue pets forever homes, and to rehabilitate wild animals for re-release.  Please check out their website and consider supporting them.

In the few days we've had Jethro, he's already bonded with our other two dogs, Guinness and Rosie.  Rosie is an Australian Cattle Dog mix who pretty much loves everyone, so she was easy.

Guinness is a big galumphing American Staffordshire Terrier/Husky/Chow cross who can be cranky and gets jealous easily, especially when it comes to sharing Carol's attention with anyone, because he's a big ol' Mama's Boy.  He is, however, a very natty dresser. 

But yesterday, all three of them were romping around together in the back yard, and Guinness was letting Jethro chase him like they'd been best friends forever instead of just three days.  Guinness even responded with the doggie "play-bow" before they took off running again.

Like with most rescues, we're not sure what kind of a mix Jethro is.  Jane at Stay Wild said she thought he had some Golden Retriever in him, which makes sense given his silky coat and general head shape, but his striking and beautiful black face and brindle coloration have to come from somewhere else.  He's got huge paws, indicating he's got some serious growing to do, but whether he'll turn out to be long and lanky or barrel-chested and stocky is anyone's guess.  Dog-loving friends of mine have speculated a lot of possible contributions to his ancestry -- suggestions have included various spaniels and setters, Border Collie, Boxer, German Shepherd, even Saint Bernard -- but we won't be sure until we have him DNA-tested.  (The kit has already been ordered.)

A photo of Jethro from five minutes ago, because why not

It's tempting to say his lovable, playful temperament is indicative of his Golden Retriever genes, but a surprising study at the University of Massachusetts just last year found the contribution of breed to behavior is way smaller than most people think.  We often associate particular behavioral traits with certain types of dog -- labs are friendly and loyal, hounds laid-back but stubborn, Dalmatians nervous and prone to biting, and so on -- but the researchers found exceptions to the rule are so common that the rule isn't really a rule.  And while we've had dogs who seemed to conform to the breed expectations, all of them have their own unique characteristics and quirks.

Dogs are as varied in personality as people are, I suppose.

In any case, now we've got three dogs.  I commented yesterday that this means we're outnumbered, and that it's a good thing this is a benevolent dictatorship and not a democracy.  Although a friend of mine responded, "I'm sure your dogs would vote for you anyway."

Given the fact that Jethro is snoozing happily right next to me, I suspect my friend is right.

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The biochemical zoo

The human/alien hybrid is a common trope in science fiction.  From the angst-ridden half-Vulcan Mr. Spock, to the ultra-competent and powerful half-Klingon B'Elanna Torres, to the half-Betazoid empath Deanna Troi, the idea of having two intelligent humanoid species produce children together is responsible for dozens of plot twists in Star Trek alone.

Much as I love the idea (and the show), the likelihood of a human being able to engage in any hot bow-chicka-bow-wow with an alien, and have that union produce an offspring, is damn near zero.  Even if the two in question had all the various protrusions and indentations more or less lined up, the main issue is the compatibility of the genetic material.  I mean, consider it; it's usually impossible for two ordinary terrestrial species to hybridize -- even related ones (say, a Red-tailed Hawk and a Peregrine Falcon) are far enough apart genetically that any chance mating would produce an unviable embryo.

Now consider how likely it is to have genetic compatibility between a terrestrial species and one from the fourth planet orbiting Alpha Centauri.

Any hope you might have had for a steamy tryst with an alien was smashed even further by a study that came out of a study from the Tokyo Institute of Technology, Emory University, and the German Aerospace Center.  Entitled, "One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules," by Henderson James Cleaves II, Christopher Butch, Pieter Buys Burger, Jay Goodwin, and Markus Meringer, the study shows that the DNA and RNA that underlies the genetics of all life on Earth is only one of millions of possible information-encoding molecules that could be out there in the universe.

It was amazing how diverse these molecules were, even given some pretty rigid parameters.  Restricting the selection to linear polymers (so the building blocks have to have attachment points that allow for the formation of chains), and three constituent atoms -- carbon, hydrogen, and oxygen, like our own carbohydrates -- the researchers found 706,568 possible combinations (counting configurations and their mirror images, pairs of molecules that are called stereoisomers).  Adding nitrogen (so, hooking in chemicals like proteins and the DNA and RNA nitrogenous bases, the letters of the DNA and RNA alphabets) complicated matters some -- but they still got 454,442 possible configurations.

The results were a surprise even to the researchers.  "There are two kinds of nucleic acids in biology, and maybe twenty or thirty effective nucleic acid-binding nucleic acid analogs," said Henderson James Cleaves, who led the study, in an interview in SciTechDaily.  "We wanted to know if there is one more to be found...  The answer is, there seem to be many, many more than was expected."

Co-author Pieter Burger of Emory University is excited about the possible medical applications of this study.  "It is absolutely fascinating to think that by using modern computational techniques we might stumble upon new drugs when searching for alternative molecules to DNA and RNA that can store hereditary information," Burger said.  "It is cross-disciplinary studies such as this that make science challenging and fun yet impactful."

While I certainly can appreciate the implications of this research from an Earth-based standpoint, I was immediately struck by its application to the search for extraterrestrial life.  As I mentioned earlier, it was already nearly impossible that humans and aliens would have cross-compatible DNA, but now it appears that alien life might well not be constrained to a DNA-based genetic code at all.  I always thought that DNA, or something very close to it, would be found in any life form we run across, whether on this planet or another; but the Cleaves et al. study suggests that there are a million or more other ways that organisms might spell out their genetic code.

So this drastically increases the likelihood of life on other planets. The tighter the parameters for life, the less likely it is -- so the discovery of a vast diversity of biochemistry opens up the field in a manner that is breathtaking.

... but the chance that the aliens will look like this is, sadly, pretty low.

This raises the problem of whether we'll recognize alien life when we see it.  The typical things you look for if you're trying to figure out if something's alive -- such as a metabolism involving the familiar organic compounds all our cells contain -- might cause us to overlook something that is alive but is being carried along by a completely different chemistry.

And what an organism with that completely different chemistry might look like -- how it would move, eat, sense its environment, reproduce, and think -- well, there'd be an embarrassment of riches.  The possibilities are far beyond even the Star Trek universe, with their fanciful aliens that look basically human but with odd facial structures and funny accents.

The whole thing boggles the mind.  And it further reinforces a conclusion I've held for a very long time; I suspect that we'll find life out there pretty much everywhere we look, and even on some planets we'd have thought completely inhospitable.  The "Goldilocks Zone" -- the region surrounding a star where orbiting planets would have conditions that are "just right" for life to form -- is looking like it might be a vaster territory than we'd ever dreamed.

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Echoes of the ancestors

I recently finished geneticist Bryan Sykes's book, Saxons, Vikings, and Celts: A Genetic History of Britain and Ireland, which describes the first exhaustive study of the DNA of England, Scotland, Wales, and Ireland.  From there, I jumped right into The Ghosts of Cannae: Hannibal and the Darkest Hour of the Roman Republic, by Robert L. O'Connell, which looks at one of the bloodiest battles on record -- the nearly complete massacre of the Roman army by the Carthaginians at the Battle of Cannae in 216 B.C.E.  That book, like Sykes's, considers the large-scale movements of populations.  The Carthaginians, for example, were mostly displaced Phoenicians who had intermarried with Indigenous North African people, and then occupied what is now Spain, adding in a Celtic strain (the "Celtiberians").

One thing that made my ears perk up in O'Connell's book is that Hannibal, in his march toward Rome, crossed through Transalpine Gaul, picking up large numbers of Gaulish mercenaries along the way, who of course had their own grudge with Rome to settle.  And his path took him right near -- perhaps through -- the valley up in the Alps containing the capital of the Celto-Ligurian tribe called the Tricorii, a town then known as Vapincum.

The name Vapincum eventually was shortened, and morphed into its current name, Gap, a modern town of forty thousand people.

It also happens to be about ten kilometers from the little village where my great-great-grandfather was born.

My last name was, like the name of Gap, altered and shortened over time.  It was originally Ariey, and then picked up a hyphenated modifier indicating the branch of the family we belonged to, and we became Ariey-Bonnet.  When my great-great-grandfather, Jacques Esprit Ariey-Bonnet, came over to the United States, the immigration folks didn't know how to handle a hyphenated name, and told him he'd have to use Ariey as his middle name and Bonnet as his surname, so all four of his children were baptized with the last name Bonnet, despite the fact that it wasn't his actual surname.

Just one of a million stories of how immigrants were forced to alter who they were upon arrival.

In any case, about three years ago, I had my DNA analyzed, and one of the things I found out was about my Y-DNA signature.  This is passed down from father to son, so I have the same Y DNA (barring any mutations) as my paternal ancestors as far back as you can trace.  And it turns out my haplogroup -- the genetic clan my Y-DNA belongs to -- is R1b1b2a1a2d3, which for brevity's sake is sometimes called R1b-L2.  And what I learned is that this DNA signature is "characteristically Italo-Gaulish," according to Eupedia, which is a great source of information for the histories of different DNA groups.

Distribution of the larger R1b Y DNA haplogroup [Image licensed under the Creative Commons Maulucioni, Haplogrupo R1b (ADN-Y), CC BY-SA 4.0]

What's most interesting is that as far back as I've traced my paternal lineage, they hardly moved at all.  My earliest known paternal ancestor, Georges Ariey, was born in about 1560 in Ranguis, France, only about a kilometer from the village of St. Jean-St. Nicolas where my great-great-grandfather Jacques Esprit Ariey-Bonnet was born three hundred years later.  And the DNA I carry indicates they'd been there a lot longer than that.

I have to wonder if my paternal ancestors were some of the Gauls who were there to see Hannibal's army headed for their fateful meeting with the Romans -- or even if they may have joined them.  The Tricorii were apparently noted for going into battle wearing nothing but body paint, so maybe this accounts for my own tendency to run around with as little clothing as is legally permissible when the weather's warm.  What's bred in the bone comes out in the flesh, as John Heywood famously said.

So then I had to look at my mtDNA haplogroup.  The mt (mitochondrial) DNA descends only from the maternal line, so we all have mtDNA from our mother's mother's mother (etc.).  Each person's mtDNA differs from another's only by mutations that have accrued since their last common matrilineal ancestor, and this can provide an idea of how long ago that was (in other words, when the two lineages diverged from each other).  Simply put, more differences = a longer time span since the two shared a common ancestor, making both mtDNA and Y DNA something geneticists call a molecular clock.  The mtDNA from my earliest known maternal ancestor, Marie-Renée Brault, who was born in 1616 in the Loire Valley of western France, belongs to haplogroup H13a1a.  Once again according to Eupedia, this lineage goes back a very long way -- it's been traced to populations living in eastern Anatolia and the Caucasus, and from there spread through the mountains of Greece, across the Alps, and all the way to western France where my maternal great-great (etc.) grandmother lived.

So that genetic signature was carried in the bodies of mothers and daughters along those travels, then crossed the Atlantic to Nova Scotia, then went back across to France when the British expelled the Acadians in the Grand Dérangement, and crossed a third time to southern Louisiana in the late eighteenth century, finally landing in the little town of Raceland where my mother was born.  My dad's Y DNA took a different path -- staying put in the Celto-Ligurian populations of the high Alps for millennia, and only in the nineteenth century jumping across the Atlantic to Louisiana, eventually to meet up with my mother's DNA and produce me.

It's astonishing to me how much we now can figure out about the movement of people whose names and faces are forever lost to history, echoes of our ancestors left behind in our very genes.  However much I'd like to know more about them -- a forlorn hope at best -- at least I've gotten to find out about the shared heritage of our genetic clans, and can content myself with daydreams about what those long-ago people saw, heard, and felt.

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The legacy of the seafarers

One of the (many) things I find fascinating about science is how often research involves crossing the boundaries between disciplines.  Ideas from one realm cross-fertilize with ideas from somewhere else, and the result is often unexpected and eye-opening.

Of course, to be honest, a lot of those boundaries are artificial constructs in the first place.  I run into this all the time as a book sorter for our local Friends of the Library used book sale.  Is a donated book anthropology?  Or sociology?  Or gender studies?  You can probably think of examples of books that could plausibly go in any of the three.  The same is true for a lot of books and scholarly papers.  Many of them -- often some of the best ones -- represent a drawing together of ideas from disparate sources, and blending them together to get something fresh and new.

The reason this comes up is because of a study sent to me by a friend and frequent contributor of topics for Skeptophilia, that combines genetics, linguistics, and archaeology.  Led by Andrés Moreno-Estrada of the National Laboratory of Genomics for Biodiversity in Guanajuato, Mexico, the team used genomic studies, patterns of languages, stone building techniques, and even such things as the distribution of certain food crops (like sweet potatoes) across the Pacific to reconstruct the movements of the extraordinary explorers who settled those islands centuries ago.

I mean the "extraordinary" part quite literally.  What these people did is almost unimaginable.  The Pacific is enormous.  The islands of Polynesia are widely-spaced specks of land, some only a few square kilometers in area, separated by hundreds or thousands of kilometers of open ocean.  In nothing more than hand-built wooden canoes, these people launched out into the sea, somehow using natural phenomena (like patterns of clouds and the movements of seabirds) to find their way from one island to the next.  How many of them died trying is unknown and unknowable; but that any succeeded is astonishing.  And enough did succeed that one at a time, they settled all the habitable islands between Samoa and Rapa Nui (Easter Island) -- a distance of 6,600 kilometers.

I don't know about you, but I can't even begin to imagine what kind of incentive it would take for me to jump into an open canoe, leave behind home and family, and try to paddle my way to a hoped-for speck of land five hundred kilometers away.  I've done a lot of traveling, including to some pretty exotic places, but that'd be a big old nope for me.

[Image licensed under the Creative Commons David Eccles (Gringer, Polynesian Migration, CC BY 4.0]

The team used not only genetic evidence from current residents of the islands, but archaeological evidence -- especially the habit of the Polynesians of building stone monoliths.  The most famous ones are the giant stone heads on Rapa Nui, but the Polynesian culture took this art form wherever they went.  Monolithic human statues are found all across the Pacific, and even in the ones on the distant Marquesas Islands, you can see the connection with the iconic moai.

What's coolest is that the pattern of the linguistic evolution and the map of the genetic relatedness between the people on the islands of Polynesia line up pretty much perfectly.  Put more simply, more closely-related people speak more closely-related languages, and therefore both the languages and the people who speak them diverged from a more recent common ancestor.  The alignment of the genetic and linguistic studies supports the usefulness of both for determining patterns of migration -- and clearly could be applied to studying the history of other cultural groups.

Anyhow, the whole thing is pretty amazing, and a great example of what happens when you have creative hybridization between research in different fields.  A fascinating study of the legacy of the fearless seafarers of Polynesia who set off into an uncharted ocean -- and ended up colonizing islands all the way across the Pacific.

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The family tree of dogs

We've had both our dogs DNA tested -- purely for our own entertainment, not because we have any concern about "pure breeding" -- and both of them gave us results that were quite a shock.

First, there's Guinness, whom the rescue agency told us was a black lab/akita mix.  You can see why:

Turns out he is neither -- he's American Staffordshire terrier, husky, chow, and Dalmatian.

Then there's Rosie, who we thought sure would turn out to be fox terrier/beagle:

Once again, not even close.  She came out to be a mix of about ten different breeds in which Australian cattle dog predominates.  Not a trace of hound, which is surprising not only because of her facial features, but her temperament.  We've had hounds several times before, and they are sweet and loving... and stubborn, headstrong, and selectively deaf, all of which describe Rosie perfectly.

I'm not sure that it's reasonable to expect a fifty-dollar mail-order dog DNA test to be all that reliable, mind you.  In Guinness's case, though, there are features that do make sense -- the ebullient disposition and square face of the AmStaff, and the curly tail and thick, silky undercoat of his husky/chow ancestry.  Whatever its accuracy, though, it's fascinating that any signal of ancestry at all shows up in a simple saliva test.

Especially given that just about every dog breed in existence traces back to wild dog populations in only a few thousand years.  That's an extremely short time to have any evolutionary divergence take place.  But genetic testing has become sophisticated enough that we can now retrace the steps in dog evolution -- creating a family tree of dog relationships encompassing 321 different dog breeds (including several sorts of wild dogs).

A team of geneticists led by Jeff Kidd of the University of Michigan, Jennifer R. S. Meadows of Uppsala University, and Elaine A. Ostrander of the NIH National Human Genome Research Institute did a detailed study of two thousand different DNA samples containing over forty-eight million analyzable sequences.  They identified three million SNPs -- single nucleotide polymorphisms, or "snips" -- that were characteristic of certain breeds. 

"We did an analysis to see how similar the dogs were to each other," Kidd said.  "It ended up that we could divide them into around twenty-five major groups that pretty much match up with what people would have expected based on breed origin, the dogs' type, size and coloration."

Interestingly, wild dogs and "village dogs" -- dogs that are somewhere between domesticated and feral, something you find in a lot of towns in developing countries -- have significantly more genetic diversity than domestic breeds do.  This, of course, contributes to their vigor (and, conversely, is why many "pure" dog breeds are susceptible to particular health problems).  It's also why it's so easy to identify behavioral characteristics of particular breeds, like the cheerfulness of golden retrievers, the intelligence and independent nature of huskies, and the nervousness of chihuahuas.

And the fact that if you want to partake in an exercise in frustration, try to housebreak a cocker spaniel.

If you take the time to read the original paper -- highly recommended, because it's amazingly cool -- you'll get to see the final "family tree" of dog breeds and see who's related to whom.

Now y'all'll have to excuse me, because Guinness wants to go outside and play.  I wonder what gene controls the trait of Wanting To Retrieve Tennis Balls For Hours.  Because whatever it is, I think Guinness has like fifty copies of it.

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