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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Cheers!

Humans have been making and consuming alcoholic drinks for a very long time.

We're hardly the only animal species to experience the psychotropic effects.  You may recall that about ten years ago a story from Sweden (Höme of the Majestic Mööse!  Extra points if you know the reference) in which one of the antlered behemoths got drunk eating fermented fallen apples, tried to climb the apple tree, and got stuck.  Not all species experience the same effects, though.  A 2008 study of pen-tailed tree shrews in Malaysia found that they habitually consume naturally-fermented nectar that raises their blood alcohol levels to well above the legal limit for humans, and show no ill effects whatsoever.  Presumably if they've evolved with that kind of diet, they've developed a mechanism for detoxifying the alcohol, or at least avoiding the psychological effects.  The jungles of Malaysia are thick with predators, and for a small furry mammal to spend all its time stumbling around dead drunk would be a good way to end up actually dead.

The earliest hard evidence of humans making wine or beer comes from near Jiahu, in the Yellow River Valley of China.  Pottery dating from about 6800 B.C.E. was found that had residues of fermented rice, honey, grapes, and hawthorn berries; around the same time, there's evidence of grape wine and barley beer being made in the Middle East.  I've often wondered what that stuff tasted like, as compared to our refined and filtered wines, beers, and spirits a lot of us enjoy today.  Back then, they were relying on wild yeasts and bacteria to do the fermenting, and that undoubtedly led to highly variable results (and a lot of spoilage).

The written records of the Greeks and Romans certainly mention wine and beer, and (especially with the Romans) we know a good bit about their winemaking techniques.  Grape juice, sometimes flavored with spices, honey, or other fruit juices, was boiled, then filtered, poured into clay amphorae, the lids sealed with beeswax, and then buried for a period that could vary from weeks to years.  The resulting liquid was then decanted and bottled.  This was when it was discovered that the soil type, climate, and grape variety had huge effects on the outcome; Roman wines ran the spectrum from surrentine (which the Emperor Tiberius sneeringly called "generous vinegar") to falernian (so expensive it was only available to the very rich but potent -- it was not only delicious, but was aged for up to twenty-five years and had an alcohol content of around fifteen percent).

[Image is in the Public Domain]

We just learned a little more about the production of vino from an archaeological find from the harbor of San Felice Circeo, ninety kilometers south of Rome.  Wine jars were unearthed in a seabed deposit that still had residues of the wines they contained.  Both red and white wines were found, along with pollen identifiable as coming from several varieties of wild grapes that grow in the area.  (Whether the vines themselves were cultivated is unknown; but those varieties are still found growing wild nearby.)  Interestingly, the amphorae were sealed not with beeswax but with pine tar, and apparently the pine tar was used not only as a sealant but to flavor the wine itself.  Maybe the result was something like Greek retsina, which people seem either to love or hate (I like the flavor, but my wife's opinion is if she wanted to chew on a pine branch, she'd go do it).

It'd be interesting if we went back to Roman times and attended a feast, where it would fall on the spectrum between delectable and revolting.  I wrote last October about a fellow named Andrew Coletti who has tried to recreate bunches of historical recipes as accurately as possible, and found that one of the Roman dishes bore an uncanny resemblance to french fries with ketchup.  But I have no doubt that some of the food and drink would taste pretty strange to us.  I'd still want to try it, though.  I don't hesitate to try local foods when I travel, and have rarely had a bad experience, although I did draw the line at the Icelandic "delicacy" hákarl, which is fermented shark meat.  It apparently has a "strong ammonia smell," and the late Anthony Bourdain said it was "the single worst, most disgusting, and terrible-tasting thing" he'd ever consumed.  Chef Ainsley Harriott was even more descriptive, describing eating it as being like "chewing on a urine-soaked mattress."

I've heard of "acquired tastes," but that's over the line.  In fact, for me, that's so far over the line that from there I wouldn't be able to see the line using a powerful telescope.

But Roman wine?  Sure, I'd give it a go, even the "generous vinegar" one.  Who knows, maybe I'd love it.  Chacun à son goût, and all that sort of thing.  But think about this if you go out for a pint or a glass of wine with friends tonight -- you're partaking in a tradition that goes back in some form or another for thousands of years.  Pretty cool, when you think about it.

Cheers!

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