The law of whatever works

One common misconception about the evolutionary model and natural selection is that it always leads to greater fitness.

It's fostered by the way the subject is taught; that evolution always works by "survival of the fittest," so over time organisms always get bigger, stronger, faster, and smarter.  There's a kernel of truth there, of course; natural selection does favor the organisms that survive longer and have more offspring.  But there are a number of complicating factors that make this oversimplified impression far wide of the truth.

First, evolution -- in the sense of changes in gene frequencies in populations -- can happen for other reasons besides fitness-based natural selection.  One common example is sexual selection, when a characteristic having little to nothing to do with fitness is the basis for mate choice, such as bright color in the males of many bird species.  This has led to sexual dimorphism -- males and females have dramatically different external appearance, as the females choose ornately-adorned mates who then pass those genes on to their offspring.

Second, the selecting factors can change when the environment does.  What is an advantage today can be a disadvantage tomorrow.  This can lead to what's called an evolutionary misfire -- when some characteristic that was beneficial turns deadly as the conditions change.  A particularly interesting example of this is the way moths navigate.  Moths, like most insects, have compound eyes, hemispherical structures with multiple radially-oriented facets.  They find their way around at night by using distant light sources (such as stars and the Moon), keeping the light from those objects shining into one facet of the eye.  If the light source is distant, this allows the moth to fly in a straight line.  The problem is, moths evolved in a context where there were no nearby light sources at night; and if you try this orientation trick on a close-up light source, you end up flying in circles.

And this is why moths spiral around, and eventually get fried by, candles, lanterns, and streetlights.

Third, many -- probably most -- genes have multiple effects, a phenomenon called pleiotropy.  A single gene that can provide a benefit in one way can provide a serious disadvantage in another.  This is, in fact, why this topic comes up today; scientists at the University of Chicago showed that a gene -- ERAP2 -- that gave people in the fourteenth century a better shot at surviving the bubonic plague also predisposes them (and their descendants) to Crohn's disease.

The link, of course, is the immune system; Crohn's is an autoimmune disease, one where the body's immune system starts fighting against its own tissue, in this case the lining of the digestive tract.  The improvement in survival during the Black Death was significant -- an estimated forty percent increase in the chances of fighting off the disease -- so during the pandemic, the increase in risk for Crohn's was an acceptable tradeoff for near certain death from the plague.

Evolution is, truly, "the law of whatever works at the time."  It's not forward-looking; the forces of selection act on whatever genes the population has currently got, and the set of genes which is able to make more copies of itself is the one that gets passed on to the next generation.  This can happen because of reasons of fitness, but for many other causes including pure random chance (what is called genetic drift).

And because of this, the genetic hand we were dealt can sometimes have untoward consequences -- in a world where the bubonic plague has in most places been eradicated, a gene that had a beneficial effect now turns out to be a significant disadvantage.

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Microborgs

One of the most terrifying alien species in the Star Trek universe is the Borg, a hive-mind collective of interlinked cyborgs that reproduce by assimilating individuals from other species, not the old-fashioned way (although they may do that, too, judging by how taken the Borg Queen was with Captain Picard in Star Trek: First Contact).  

Turns out the assimilate-your-neighbor approach isn't limited to the world of science fiction.  There are terrestrial species who seem to follow the Borg's mantra of "We will add your biological and technological distinctiveness to our own."  Bacteria are especially good at doing this; they have small, mobile pieces of DNA called plasmids that are capable of being exchanged between cells, allowing gene flow without (strictly speaking) sexual reproduction.  Unfortunately for us, these plasmids frequently contain such human-unfriendly gene constructs as antibiotic resistance sequences and "pathogenicity islands" -- genes that code for a virulent attack on the host, such as the ones in the nasty strains of E. coli that can land you in the hospital.

Recently, however, scientists discovered a species of bacteria that has an assemblage of chunks of assimilated DNA (they actually called these strands "Borgs" after the Star Trek villains) that might prove useful to humans rather than harmful.  A species of Archaea (an odd clade of bacteria relatively unrelated to other, more common species, which includes groups that specialize in living in acidic thermal springs, anaerobic mud, and extremely salty water) called Methanoperedens was discovered in lake mud in western North America, and it was found to consume methane -- and has Borgs that allow it to do so at a spectacular rate.

Methanoperedens is odd even without the superlatives.  Most of the Archaea that metabolize methane don't consume it, they create it.  Methanogens -- Archaea that live primarily in deep ocean sediments -- produce methane as a byproduct of their metabolism, secreting it in the form of methane clathrate (frozen methane hydrate) at such a rate that the abyssal plains are covered with the stuff.  (Some ecologists believe that methanogens are, individual for individual, the commonest organisms on Earth, outnumbering all other species put together.)  

Burning methane clathrate -- "flammable snow" [Image is in the Public Domain courtesy of the United States Geological Service]

Methanoperedens, though, is a different sort of beast.  It lives by breaking down methane.  More interesting still, this ability comes from the fact that it has Borgs almost a third the size of its ordinary complement of DNA, made up of gene fragments assimilated from a dozen different species.

What has sparked interest in this bizarre species is the potential for using it to combat climate change.  Methane is a powerful greenhouse gas -- it has thirty times the heat-trapping capacity that carbon dioxide does -- and there's a significant concern that as the Earth warms, decomposing organic matter in the tundra will trigger a positive feedback loop, releasing more methane and warming the planet further.  If this methane-eating bacteria could consume some of the excess methane, it's possible that it could be turned into a tool for bringing the climate back into equilibrium.

I'm a little dubious, however.  It seems unlikely that any kind of attempt to culture Methanoperedens would be possible on a big enough scale to make a difference.  It'd be nice if we'd just face up to the fact that there is, and always has been, one obvious solution; stop burning so damn much fossil fuel.  We're so desperate to cling to our conspicuous-consumption lifestyle that we can't face the reality of what we're doing to the long-term habitability of the Earth.  (It doesn't help, of course, that a great many of our politicians here in the United States are being funded by the fossil fuel industry.)

Whether or not this bacteria species turns out to have any practical applications, the whole phenomenon of evolution by assimilation of DNA from other species is absolutely fascinating.  We ourselves contain "foreign genes" -- most notably endogenous retroviruses, pieces of viral DNA that have taken up permanent residence in our DNA and which might comprise as much as five percent of our total genome.  (There is good evidence that the activation of certain endogenous retroviruses is connected to the development of multiple sclerosis and some forms of schizophrenia.)

Walt Whitman didn't know how true his words were when he said, "I contain multitudes."

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Mosquito magnets

My wife claims that I only bring her along on tropical vacations to lure the mosquitoes away from me.

She is, to put it bluntly, a mosquito magnet.  If there's an outdoor party, and there is a single lonely mosquito anywhere within a five-mile radius, it will find her.  Worse still, she has a bad allergic reaction to bites; being bitten leaves her itching for days.

Bad combo, that.

I, on the other hand, barely get bothered at all.  The same strange dichotomy got passed to our kids; our older son doesn't seem to get bitten much.  On the other hand, we took a family vacation to Belize when our boys were twelve and fifteen, and I saw our younger son was sitting on his bed one evening examining his legs.  I asked him what he was doing.

Turned out he was counting mosquito bites.  He lost count at around forty.

[Image licensed under the Creative Commons User:Ngari.norway, Mosquito bite4, CC BY-SA 3.0]

The contention that many have, of some people being more attractive to mosquitoes than others, was just demonstrated conclusively in a paper last week in the journal Cell, by a team led by Leslie Vosshall of the Howard Hughes Medical Institute.  What Vosshall and her team did was to have volunteers wear nylon stockings on their arms for six hours, allowing the fabric to pick up any chemicals the person was secreting in their sweat and skin oils.  The nylons were then cut up into squares, and the pieces presented to hungry Aedes aegyptii mosquitoes.

The results were unequivocal.  One subject, #33, had an attractiveness to mosquitoes over a hundred times greater than the least attractive subjects, #19 and #28.

What seems to set apart people like poor #33 is the particular cocktail of carboxylic acids in their skin oils.  Carboxylic acids are small organic molecules characterized by having a carboxyl group -- a carbon atom double-bonded to an oxygen atom and single-bonded to a hydroxyl (-OH) group -- and include such familiar compounds as amino acids and fatty acids.  It turns out that of the hundreds of different kinds of carboxylic acids, each person produces different ones in different amounts -- and this "scent" (not that you or I would notice the difference) is what determines who is a mosquito magnet, and who largely gets left alone.

A little discouraging, though, is their other finding; that this chemical signature is relatively resistant to changes in diet and grooming habits.  None of the contentions you might have heard -- eating foods rich in B vitamins, using unscented soaps and shampoos, and so on -- seemed to make any difference.  The people who were mosquito attractors stayed that way throughout the course of the experiment, regardless what they ate and what cosmetic products they used.

While this study might eventually lead to better repellents, at the moment, we're kind of stuck where we were.  The best mosquito repellent is DEET (diethyltoluamide), which has a pretty good track record for safety, although (as I found out when I was in Ecuador) dissolves plastics.  (Fortunately, the only thing damaged was a ball-point pen; I discovered this when I applied some mosquito repellent, picked up the pen, and it promptly stuck to my hand.)  Some other products, like Avon's "Skin So Soft," seem to have some effect but aren't nearly as reliable as DEET.  

Maybe if Vosshall and her team can pinpoint exactly which carboxylic acids are causing the problem, they could find some kind of repellent that would work by blocking them or breaking them down.  I know my wife would appreciate it.  It's late October in upstate New York, and the eight mosquitoes still left alive around here are still waiting by our back door for one last chance to bite her.

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The walk of life

There are countless different actions we take every day that we do so automatically we're hardly even aware of how complex they are.

Take, for example, walking.  Walking takes the coordination of dozens of muscles, each of which has to contract and relax in exactly the right sequence to propel us forward and adjust for irregularities of the terrain we're navigating.  To avoid falling, we need to keep our center of gravity over our base of support, which is aided by adjustments in posture and such counterbalancing movements as swinging the arms.  But in order to do that we have to keep track of proprioception -- our sense of where our bodies are -- which is accomplished by a whole array of sense organs, including vision, the tactile sensors in the skin, and the semicircular canals -- the balance organs in the inner ear, which work a little like a carpenter's level.

And all of those -- the sense organs that keep track of what's going on and the muscles that use that information to contract and relax at the right times -- are linked by an astonishingly complex set of nerve relays and circuits coordinated by our brains.

All of that, just to get up and walk across the room.

The reason the topic of locomotion comes up is a paper a couple of weeks ago in Current Biology describing a single-celled protist called Euplotes eurystomus that has fourteen leg-like appendages -- and is able to walk.

The scientists studying Euplotes found that the appendages had thirty-two different configurations, which they called"gait states," and that somehow, the little creature was keeping track of which sequence of gait states allowed for the most efficient walking.  It turned out that the internal scaffolding of the cell, made of hollow threads called microtubules, created cross-links from each appendage to the others.  The amount of tension in the microtubules allows the organism to coordinate the movement of all fourteen appendages.

"The fact that Euplotes' appendages are moving from one state to another in a non-random way means this system is like a rudimentary computer," said Wallace Marshall, of the University of California - San Francisco, who co-authored the paper.

Euplotes eurystomus [Image from Larson & Marshall, UCSF]

All of this puts me in mind of the idea of irreducible complexity -- that there are structures in living organisms that would not work if all the parts hadn't been created all at the same time.  It's a favorite salvo of the young-Earth creationists and proponents of intelligent design.  The battle cry usually goes something like, "One percent of an eye isn't good for anything."  Richard Dawkins does a brilliant takedown of this entire argument in his tour-de-force exposition of the evolutionary model The Blind Watchmaker, in which he demonstrates that "one percent of an eye" -- a simple, light-sensing patch -- is indeed better than nothing, and that once you have that one percent, incremental gains in acuity can lead to the complex eyes now found in the animal kingdom.  (More fascinating still, the ability to sense light is such a powerful evolutionary driver that this process may have occurred, independently, dozens of times in different lineages.  For a wonderful overview of the evolution of eyes, check out this article from 2017 in the journal Nature.)

So locomotion, like vision, isn't irreducibly complex at all.  It's complex, yes; but hardly irreducible, because a single-celled organism is able to use chemical reactions and a network of microtubules to accomplish something very much like walking.  Our ability to coordinate motion has a history going back billions of years, during which time it has evolved into an action so complicated and intricate it's a damn good thing we don't have to keep track of it consciously.

Think about that next time you move your muscles.

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The ancestral worm

I live only a few miles from the tallest waterfall in the eastern half of North America, which is not Niagara Falls but Taughannock Falls.

Taughannock (for non-locals, pronounced ta-GAN-uck) Falls is sixty-six meters tall, ten meters higher than Niagara.  It is way narrower than Niagara, and has a far smaller water volume even when it gets rainy around here, but hey, a record is a record.

All that gray rock you see surrounding the narrow thread of the waterfall is Devonian-age shale and limestone, sedimentary rocks deposited about four hundred million years ago when this whole area was at the floor of a shallow sea.  Taughannock Creek has gradually cut its way through the layers of rock, creating a hanging valley at the top of one of the gorges this area is known for -- and exposing literally millions of fossils.

Some of the most common fossils you can find in Taughannock Gorge are brachiopods, shelled animals that look to the untrained eye a bit like a clam.  They're only distantly related to mollusks, however -- the internal structure would make that immediately apparent.  Even the shells show the difference, if you know what to look for.  The easiest way to tell is that bivalve (mollusk) shells are symmetrical across the hinge line, and brachiopods are not.  (Whereas brachiopods are symmetrical across the midline of the shell, and most bivalves aren't.)

Syringothyris texta, an extinct Devonian brachiopod [Image is in the Public Domain]

Although incredibly common as fossils -- I know a couple of places where you can fill your pockets with brachiopod fossils in under fifteen minutes -- they're quite rare as living animals today.  They got hit hard by the Permian-Triassic Extinction (what didn't?) and never really recovered.  There are about thirty thousand species of brachiopods known to the fossil record, of which only a little fewer than four hundred have survived to the day.  Those survivors aren't common anywhere.  They're mainly deep marine species, animals none of us are going to run into on a daily basis.

But that low modern diversity belies what a dominant group they were back before the End Permian Event wiped out an estimated 96% of life on Earth.  Along with trilobites, they were one of the commonest life forms in the planet's oceans before the "Great Dying" of 252 million years ago destroyed them.

What brings all this up is a paper in Current Biology last week describing a fossil found in China that is a good candidate for the common ancestor of brachiopods and the two other groups of lophophorates -- phoronid (horseshoe) worms and bryozoans (moss animals).  Once again, looks are deceiving; these three groups of animals bear little superficial similarity.  The horseshoe worms are sedentary animals that live in U-shaped tubes, and bryozoans are tiny colonial species that look a bit like miniature corals.  But they are alike in internal structure, and all three have a lophophore, a tube-like feeding structure surrounded with tentacles.  And this newly-discovered species, the early Cambrian Wulfengella, looks like it's the right animal in the right place at the right time to be the ancestor of all three groups.

Artist's reconstruction of Wulfengella [Image courtesy of Robert Nicholls, Paleocreations.com]

All of this just goes to show how non-intuitive relationships can be.  Wulfengella doesn't look on first glance anything like any of the three groups it's suppose to be the ancestor to, but its fine structure gives away its kinship.  And it once again highlights how much everything -- the biodiversity, the terrain, the continents themselves -- have changed throughout Earth's history.  We only think things are static because our lives are so short; on the grander scale, the current configurations of the planet will last the blink of an eye.  If you'll indulge me quoting one more time the words of one of my favorite poems, from the eloquent mind of Alfred Lord Tennyson, because I can't think of a better way to close this post:

There rolls the wave where grew the tree.

O Earth, what changes hast thou seen?

There where the long road roars has been

The stillness of the central sea.

The hills are shadows, and they flow

From form to form, and nothing stands --

They melt like mists, the solid lands --

Like clouds, they shape themselves, and go.

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A hostile beauty

William Shatner, of Star Trek fame, wrote some profoundly moving words in his book Boldly Go, about his experience riding into space on Jeff Bezos's Blue Origin shuttle:

I love the mystery of the universe.  I love all the questions that have come to us over thousands of years of exploration and hypotheses.  Stars exploding years ago, their light traveling to us years later; black holes absorbing energy; satellites showing us entire galaxies in areas thought to be devoid of matter entirely… all of that has thrilled me for years… but when I looked in the opposite direction, into space, there was no mystery, no majestic awe to behold... all I saw was death.

I saw a cold, dark, black emptiness.  It was unlike any blackness you can see or feel on Earth.  It was deep, enveloping, all-encompassing.  I turned back toward the light of home.  I could see the curvature of Earth, the beige of the desert, the white of the clouds and the blue of the sky.  It was life.  Nurturing, sustaining, life.  Mother Earth.  Gaia.  And I was leaving her.

Everything I had thought was wrong.  Everything I had expected to see was wrong.

I had thought that going into space would be the ultimate catharsis of that connection I had been looking for between all living things—that being up there would be the next beautiful step to understanding the harmony of the universe.  In the film Contact, when Jodie Foster’s character goes to space and looks out into the heavens, she lets out an astonished whisper, "They should’ve sent a poet."  I had a different experience, because I discovered that the beauty isn’t out there, it’s down here, with all of us.

He's right in one sense; the vast majority of the universe is intrinsically hostile to life.  It's why I've always found the Strong Anthropic Principle a little funny.  The Strong Anthropic Principle claims that the physical constants which are, as far as we currently understand, not derivable from anything else -- such as the strength of the four fundamental forces, the masses of the subatomic particles, the speed of light, the fine structure constant, and so on -- were set with those values in order to make the universe accommodate matter and energy as we know it, and ultimately, life.  The words they use are "fine tuned."  If any of those constants were even a little bit different, life would be impossible.

Typically, the argument progresses from "fine tuning" to "implies a fine tuner" to "implies God."

This whole line of thought, though, ignores three things.  First, of course we live in a universe that has the physical constants set such that life is possible; if they weren't, we wouldn't be here to discuss the matter.  (This is called the Weak Anthropic Principle.)  Second, when I said those constants are not derivable from anything else, you should place the emphasis on the phrase that came before it; as far as we currently understand.  It may be that physicists will eventually find a Grand Unified Theory showing that some -- perhaps all -- of the physical constants are what they are because of a single fundamental principle stating that they aren't arbitrary after all, that they couldn't have any other values.

Third, as Shatner points out, most of the universe -- even most of the Earth, honestly -- is pretty fucking hostile to life as it is.

But I question his statement that this makes the universe any less beautiful.  I was in Iceland this summer and got to see an erupting volcano -- the whole nine yards, with jets of orange lava fountaining up and cascading down the side of the cinder cone.  I could feel the heat on my face from where I stood, about a hundred meters away; much closer, and my skin would have blistered.  The sulfur fumes were only made tolerable by the fact that it was a windy day.  The hillside beneath my feet was vibrating, the air filled with a roar like thunder.  Standing there, I was in no doubt at all about my own frailty.

It was also incredibly, devastatingly beautiful.

I was thinking about the beauty of the universe -- as unquestionably inimical as it is to our kind -- when I saw images from the Hubble Space Telescope of the Cat's Eye Nebula, along with a visualization of what it would look like close up, created by a team led by Ryan Clairemont of Stanford University:

The spirals are thought to be caused by two stars in the center of the nebula orbiting around each other, each emitting a pair of plasma jets that have been twisted by the stars' motion in the fashion of the jets of water sprayed from a spinning garden sprinkler.  But whatever the cause of the pattern, I was immediately struck by its awe-inspiring beauty.

I've never been to space, and I don't mean to gainsay Shatner's experience.  But I find the vast immensity of space to be beautiful even though I know my own existence in it is all but insignificant.  I can look up at the autumn constellations, as I did last night -- Perseus and Andromeda, Pegasus and Pisces and Aquarius -- and appreciate the beauty of those stars glittering in the night sky from the warm safety of my home planet.  Maybe some of them have planets harboring their own frail, fragile life forms, who just like us are dependent on the searing fires of their host stars to survive, and just like us look up into the night sky with awe and wonder.

Frightening?  Sure.  Dangerous, savage, unpredictable?  Undeniable.

But also deeply, overwhelmingly beautiful.

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Jurassic rainbow

Regular readers of Skeptophilia might recall that about a year ago, paleontologists announced the discovery of a bird fossil from northeastern China that had a long, pennant-like tail -- and that from the extraordinary state of preservation, they were able to determine that the outer tail feathers had been gray, and the inner ones jet black.

Determining feather, hair, and skin color of prehistoric animals is remarkably tricky; the pigments in those structures break down rapidly when the animal's body decomposes, and the structures themselves are fragile and rarely fossilize.  The result is that when artists do reconstructions of what these animals may have looked like, they base those features on analogies to modern animals.  This is why in old books on dinosaurs, they were always pictured as having greenish or brownish scaly skin, like the lizards they were thought to resemble, even though dinosaurs are way more closely related to modern birds than they are to modern lizards.  (To be fair, even the paleontologists didn't know that until fairly recently, so the artists were doing their best with what was known at the time.)

But it does mean that if we were to get in the TARDIS and go back to the Mesozoic Era, we'd be in for a lot of surprises about what the wildlife looked like back then.  Take, for example, the late Jurassic Period fossil found by a farmer in China that contained the nearly-complete skeleton of a birdlike dinosaur.  Here's the fossil itself:

What's remarkable about this fossil is that the feathers were so well-preserved that paleontologists were able to get a close look at the melanocytes -- the pigment-containing cells -- and from the arrangement and layering of those cells, they determined that the dinosaur's head feathers were arrayed like a rainbow, similar to modern hummingbirds, sunbirds, and trogons.

So here's the current reconstruction of what this species looked like:

[Reconstruction by artist Velizar Simeonovski, of The Field Museum]

Kind of different from the drab-colored overgrown iguanas from Land of the Lost, isn't it?

The species, christened Caihong juji from the Mandarin words meaning "big rainbow crest," adds another ornate member to the late Jurassic and early Cretaceous fauna of what is now northern China.  And keep in mind that we only know about the ones that left behind good fossils -- probably less than one percent of the total species around at the time.  As wonderful as it is, our knowledge of the biodiversity of prehistory is analogous to a future zoologist trying to reconstruct our modern ecosystems from the remains of a sparrow, a cat, a raccoon, a deer, a grass snake, and a handful of leaves from random plants.

I think my comment about being "in for a lot of surprises" if we went back then is a significant understatement.

Even so, this is a pretty amazing achievement.  Astonishing that we can figure out what Caihong juji looked like from some impressions in a rock.  And it gives us a fresh look at a long-lost world -- but one that was undoubtedly as rainbow-hued and iridescent as our own.

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