The origin of venom

We're all aware of animals with venomous bites -- most of the familiar ones being either snakes or spiders.  It's an interesting topic, but before we begin, let's get our definitions straight, as summed up in this online conversation that has since gone viral (deservedly):

There are a lot of animals that are venomous which are neither snakes nor spiders, however.  There are mollusks like the blue-ringed octopus and the deadly cone snails of the south Pacific, many jellyfish (including the phenomenally venomous box jellies, most common in the waters off the east coast of Australia), scorpions, a few lizards (like the gila monster), and even mammals like the bizarre solenodons, which look like scaled-down versions of the Rodents Of Unusual Size from The Princess Bride.

[Image licensed under the Creative Commons Seb az86556, Hispaniolan Solenodon crop, CC BY-SA 3.0]

In fact, it's the mammalian venomous animals, including not only solenodons but various shrews and the oddball primate called the slow loris, that bring the topic up today.  A paper appeared last week in BMC Biology, about some research out of the University of Okinawa supporting the startling conclusion that the noxious proteins in the saliva of venomous mammals are structurally related to the proteins that serve the same function in hemotoxic snakes like rattlesnakes, vipers, and adders.

On first glance, this may not seem that odd, but consider what it means.  Saying the venom proteins have the same function is not the same as saying they have the same structure.  If the proteins have the same structure, it means that the genes that produced them do as well.  And if that's the case, chances are, those genes share a common ancestor -- and then descended (albeit with modifications) through the ensuing three hundred million years since the lineages that led to today's venomous snakes and mammals split.

Venoms in these animals are complex mixtures of chemicals, but both rattlesnakes and solenodons (for example) have venom containing a class of complex proteins called kallikrein serine proteases.  These are protein-degrading enzymes that in many animals have a function in regulating blood pressure -- accounting for the localized tissue breakdown and drop in blood pressure you see in the victim of a rattlesnake bite.

What's curious -- and what touched off this particular piece of research -- is that all mammals, ourselves included, have small amounts of kallikrein serine proteases in the saliva.  In us (and, in fact, in most mammals), they seem to serve no purpose -- they appear to be vestigial remnants from our ancestry.  But in the lineages that led to both venomous snakes and venomous mammals, they increased in concentration until they could be used, injected into a bite, to subdue and digest prey.

"In [last week's] paper, we hypothesized that in the ancestor of snakes and mammals, there was a common group of genes that had a toxic potential," said Agneesh Barua, who was the co-lead-author along with Ivan Koladurov.  "Snakes and mammals then took different evolutionary paths, with snake lineages evolving diverse and increasingly toxic concoctions, while in mammals, venom did evolve, but to a much lesser degree.  But what we wanted to know is whether the toxins within mammal and snake venom evolved from a common ancestral gene...  There are so many different serine proteases that have a high degree of similarity, that until now, it was too difficult to isolate the right genes needed to determine the evolutionary history.  [Our results are] really strong evidence for our hypothesis that venom evolved from a common group of genes in an ancestor that had a toxic potential.  But the most surprising thing was that non-toxic salivary kallikreins, like those found in humans and mice, also evolved from the same ancestral gene."

Yet another nail in the coffin of creationism, if you needed one.

What I find coolest about this is that it's a reminder of the unity of our biodiversity here on Earth -- that the tapestry of life was produced from threads with a common source, a couple of billion years ago.  And, best of all, that in looking at today's organisms, we can still see remnants of that common origin, even in pairs of species that look nothing alike.

I'll end with the prescient quote attributed to Chief Seattle, that seems more apt today given our knowledge from science than it did when he wrote it in 1854: 

This we know: the Earth does not belong to man, man belongs to the Earth.  All things are connected like the blood that unites us all.  Humankind has not woven the web of life.  We are but one strand within it.  Whatever we do to the web, we do to ourselves.  All things are bound together; all things connect.

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One of my favorite writers is the inimitable Mary Roach, who has blended her insatiable curiosity, her knowledge of science, and her wonderfully irreverent sense of humor into books like Stiff (about death), Bonk (about sex), Spook (about beliefs in the afterlife), and Packing for Mars (about what we'd need to prepare for if we made a long space journey and/or tried to colonize another planet).  Her most recent book, Fuzz: When Nature Breaks the Law, is another brilliant look at a feature of humanity's place in the natural world -- this time, what happens when humans and other species come into conflict.

Roach looks at how we deal with garbage-raiding bears, moose wandering the roads, voracious gulls and rats, and the potentially dangerous troops of monkeys that regularly run into humans in many places in the tropics -- and how, even with our superior brains, we often find ourselves on the losing end of the battle.

Mary Roach's style makes for wonderfully fun reading, and this is no exception.  If you're interested in our role in the natural world, love to find out more about animals, or just want a good laugh -- put Fuzz on your to-read list.  You won't be disappointed.

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

Lost in the shadows

Some historical discoveries are in that gray area between evocative and frustrating as hell.  The evocative part because it gives us a glimpse into a long-gone culture; frustrating because the great likelihood is we'll never know anything more about it.

It's why I will never get over the loss of the Great Library of Alexandria.  Destroyed piece by piece, starting with a strike against secular intellectuals by King Ptolemy VIII Physcon in 145 B.C.E. and an apparently accidental fire during Julius Caesar's attack on Egypt a hundred years later, the library lost most of its holdings -- and its reputation -- and was gone entirely by the end of the third century C.E.  At its height it had books from all over Europe, North Africa, the Middle East, and Asia, and almost certainly contained the complete catalogue of works by such luminaries as Aeschylus, Sophocles, Euripides, Theophrastus, and Aristotle -- the vast majority of which no longer exist.

It's as if we only knew about Shakespeare because of fragmentary copies of Cymbeline and Timon of Athens.  All his other works are gone, known only by title -- or perhaps completely unknown.  That's the situation we're in with most early authors.  The most painful part is that they're gone forever, irreclaimable, disappeared beyond rescue into the murky waters of our past.

That was the reaction I had to a discovery I found out about because a friend of mine sent me a link a couple of days ago, regarding an archaeological discovery in Finland.  Near the town of Järvensuo, northwest of Helsinki, a team of archaeologists from the University of Turku and University of Helsinki found a 4,400-year-old shaman's staff, the top of which was carved into the likeness of a snake.  It resembles depictions of ritual staffs in cave art from the area, so there isn't much doubt about what it is.

It's a pretty spectacular discovery.  "My colleague found it in one of our trenches last summer," said research team member Satu Koivisto.  "I thought she was joking, but when I saw the snake’s head it gave me the shivers."

The discovery brings up inevitable questions about how it was used, and what it tells us about religions and beliefs back then.  "There seems to be a certain connection between snakes and people," said team member Antti Lahelma.  "This brings to mind northern shamanism of the historical period, where snakes had a special role as spirit-helper animals of the shaman…  Even though the time gap is immense, the possibility of some kind of continuity is tantalizing: Do we have a Stone Age shaman's staff?"

Tantalizing indeed, in the full sense of the word.  Like the lost books of the Library of Alexandria, the knowledge, culture, and rituals of the people who used this staff are almost certainly gone forever.  While we can speculate, those speculations are unlikely to be complete (or even correct).  Imagine taking a random assortment of objects from our culture -- a pair of glasses, a stop sign, a computer mouse, a spoon, a garden rake -- and from those alone trying to figure out who we were, what we believed, what we did.

Note that I'm not diminishing the significance and interest of the find, which is pretty amazing.  It's just that it makes me even more cognizant of what we've lost.  It's inevitable, I know that -- nothing lasts forever, not artifacts, not knowledge, not culture.  It's just frustrating realizing how little we know, and worse still, how little we can know.

Maybe that's why I became a fiction author.  If you can't figure stuff out, make stuff up, that's my motto.  It doesn't replace what we've lost, but at least it provokes our imaginations to wonder what things were like back then, to ponder the lives of our distant ancestors, to picture what the world must have looked like to them.

It's better than nothing.  And until we create a time machine, I guess that'll have to be enough.

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Most people define the word culture in human terms.  Language, music, laws, religion, and so on.

There is culture among other animals, however, perhaps less complex but just as fascinating.  Monkeys teach their young how to use tools.  Songbirds learn their songs from adults, they're not born knowing them -- and much like human language, if the song isn't learned during a critical window as they grow, then never become fluent.

Whales, parrots, crows, wolves... all have traditions handed down from previous generations and taught to the young.

All, therefore, have culture.

In Becoming Wild: How Animal Cultures Raise Families, Create Beauty, and Achieve Peace, ecologist and science writer Carl Safina will give you a lens into the cultures of non-human species that will leave you breathless -- and convinced that perhaps the divide between human and non-human isn't as deep and unbridgeable as it seems.  It's a beautiful, fascinating, and preconceived-notion-challenging book.  You'll never hear a coyote, see a crow fly past, or look at your pet dog the same way again.

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

Reptilian splits

One of my favorite lectures in my AP Biology class was about how there's no such thing as a reptile.

If you took your last biology class before about 1995, you probably learned about Class Reptilia, containing turtles, lizards, snakes, crocodiles, alligators, and a few other assorted groups.  The class was defined by having dry, scaly skin, internal fertilization, "amniote" eggs with shells, and hearts that had incomplete septa (the wall down the center that separates the oxygenated left side from the deoxygenated right side).

Well, the last one wasn't 100% true, and that should have been a clue to what was going on.  Crocodiles and alligators have four-chambered hearts, and are also partial endotherms -- they show some capacity for internally regulating their own body temperatures, just as birds and mammals do.

It was genetic testing that finally settled who was related to whom, and that was when a lot of us got a shock (not so much the evolutionary biologists, who kind of expected this was how it was gonna work out).  The word "reptile" has no real taxonomic significance, because it lumps together groups that really aren't very closely related, and excludes others that are closer.  Here's how this branch of Kingdom Animalia evolved:

As you can see from the diagram, the problem was birds.  Crocodiles are more closely related to birds than they are to lizards (despite superficial appearance); and if you throw dinosaurs into the mix, it becomes even clearer, because birds are dinosaurs.

Think about that the next time you feed the chickadees.

So if you throw all the reptiles together, by the rules of cladistic taxonomy, you'd have to include birds, and nobody much wanted to call birds reptiles.  So the entire Class Reptilia was broken up, now as three different classes: Lepidosauria (lizards, snakes, and the oddball tuatara of New Zealand), Testudines (turtles), and Crocodilia (obviously crocodiles et al.).  Birds have their own class (Aves).

But what this brings up is how such different-looking animals as turtles and snakes evolved from a common ancestor.  The differences between the different groups of reptiles is pretty dramatic.  The explanation has usually been that it was adaptive radiation, a phenomenon that deserves some explanation.

Adaptive radiation is when a group undergoes rapid diversification to fill many available niches.  The classic example is Darwin's finches, a group of birds on the Galapagos Islands, which descend from a common ancestral group that split up to occupy different niches because of bill size and strength (which determines what they can eat).  That's a pretty drastic oversimplification, but it captures the essence: many available niches, and a population with sufficient genetic diversity to split up and specialize into those niches.

Because of the "many available niches" part, adaptive radiation is most common under two scenarios: a population colonizing a previously-uninhabited territory (as with Darwin's finches), and remnant populations left after a major extinction.  This was what was thought to have powered the split-up of the reptiles -- the "Great Dying," the Permian-Triassic extinction of 252 million years ago that by some estimates wiped out 95% of life on Earth.

Nota bene: there is fairly good evidence that the trigger for the Permian-Triassic extinction was hypercapnia -- a sudden increase in atmospheric carbon dioxide.  This led to drastic warming of the atmosphere and ocean acidification.  The cause -- according to a paper that just came out two weeks ago in the journal Geology -- was massive burning of coal.  Sound familiar?  In this case the cause was natural; it's thought to have been triggered by massive volcanism.  But the end result was the same as what we're doing now by runaway use of fossil fuels.  I'd like to think this would be a cautionary note, but the world's leaders seem to specialize in ignoring science unless it can directly make them money and/or keep them in power, so I'm not holding my breath.

But back to the reptiles.  The study that triggered this post, which came out this week in Nature Communications, points out the flaw in the argument that the adaptive radiation of reptiles was due to the Permian-Triassic extinction.  According to recent analysis, the split up was already well underway before the extinction started.  And the extinction itself was sudden, at least in geological terms; from start to catastrophic finish, the whole event took about a hundred thousand years.  In geological strata, this length of time is a very, very narrow band.

Plus, the different groups of reptiles individually show drastically different rates of specialization. "Our findings suggest that the origin of the major reptile groups, both living and extinct, was marked by very fast rates of anatomical change, but that high rates of evolution do not necessarily align with taxonomic diversification," said study lead author Tiago Simões of Harvard University, in an interview in Phys.Org.  "Our results also show that the origin of snakes is characterized by the fastest rates of anatomical change in the history of reptile evolution -- but that this does not coincide with increases in taxonomic diversity [as predicted by adaptive radiations] or high rates of molecular evolution."

The end result of the study is that the cause of the adaptive radiation is unknown.  It probably was pushed along by the mass extinction -- the species that survived the hypercapnia and the resulting environmental devastation were set up to have a whole empty world to colonize.  But what was driving the split-up of the group prior to the extinction itself?

Unknown, but the current study shows that clearly the adaptive radiation had already started.

I love puzzles like this.  In science, there are almost always more questions than answers, and every answer brings up new questions.  But another feature of science is the conviction that there is an answer even if we don't currently know what it is.  And chances are, further study will elucidate what exactly was going on -- and what led to the fragmentation of a group that now, over 250 million years later, comprises some of the best-known and most familiar critters who have ever walked (or flown across) the Earth.

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This week's Skeptophilia book recommendation of the week is for anyone who likes quick, incisive takes on scientific topics: When Einstein Walked with Gödel: Excursions to the Edge of Thought by the talented science writer Jim Holt.

When Einstein Walked with Gödel is a series of essays that explores some of the deepest and most perplexing topics humanity has ever investigated -- the nature of time, the implications of relativity, string theory, and quantum mechanics, the perception of beauty in mathematics, and the ultimate fate of the universe.  Holt's lucid style brings these difficult ideas to the layperson without blunting their scientific rigor, and you'll come away with a perspective on the bizarre and mind-boggling farthest reaches of science.  Along the way you'll meet some of the key players in this ongoing effort -- the brilliant, eccentric, and fascinating scientists themselves.

It's a wonderful read, and anyone who is an aficionado of the sciences shouldn't miss it.

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