Resurrection

The environmentalists tell us "extinction is forever," and that certainly seems unarguable.  Once a species is lost, evolution will never recreate it.  You may get something that looks like it; there are numerous examples of Elvis taxa, species that evolved to fit vacated niches and underwent convergent evolution resulting in a similarity to some extinct form.  (The name comes from the huge numbers of Elvis impersonators that have popped up since the original's death in 1977.)  But the sad truth is that the original is gone forever.

The issue, though, can be making certain the species actually is extinct.  There are ongoing efforts to find relic populations of a number of presumed-extinct species (two of the best known are the ivory-billed woodpecker and the thylacine).  Naysayers have criticized the efforts to find these species as nothing more than wishful thinking, but it bears keeping in mind that there is a long list of organisms thought to be extinct that have turned out to be very much alive.

They're called Lazarus taxa, after the biblical character Jesus raised from the dead.  Some of them are astonishing.  The one that always comes to mind for most people is the coelacanth, a crossopterygian fish that was only known from fossils preceding the Cretaceous Extinction sixty-six million years ago, which was discovered living in the Indian Ocean in 1938.  But that's only one of many.  Here's a sampler of Lazarus taxa:

• The South American bush dog (now split into three separate species in the genus Speothos) was only known from some Pleistocene-age bones found in a Brazilian cave, but is now known to have a range from southern Central America all the way to northern Paraguay.  Its reclusive habits and rarity still make it the least-studied canid in the world.

A Brazilian bush dog [Image licensed under the Creative Commons Xerini, Waldhund, CC BY-SA 3.0]

• The nightcap oak (Eidothea hardeniana and E. zoexylocarya), which aren't oaks at all but a member of the Protea family (Proteaceae), were known only from fifteen-million-year-old fossils -- and then a stand of them were discovered growing in a remote part of Australia.  The Royal Botanical Gardens in Sydney has a cultivation program for the two species, which are threatened because the seeds are frequently eaten by introduced mice.

Eidothea hardeniana [Image is in the Public Domain]

• The monito del monte, or colocolo opossum (Dromiciops gliroides), was not only thought to have gone extinct eleven million years ago, it was believed that its entire order (Microbiotheria) was gone as well.  It was found -- alive -- in the temperate bamboo forests of the southern Andes Mountains in 1894, and has no near relatives anywhere in the world.  (The closest are the Australian marsupials, but even those are very distant cousins.)

[Image licensed under the Creative Commons José Luis Bartheld from Valdivia, Chile, Monito del Monte ps6, CC BY 2.0]

• In 1898 a fish was discovered that was a near perfect match to Oligocene-age fossils on the order of twenty-eight million years old.  It's Lignobrycon myersi, and is only known from the Rio Braço and Rio Contas in east-central Brazil.  Somehow, it alone of its genus survived through all of those years and made it down to the present day.

[Image licensed under the Creative Commons Alexandre dos Santos Rodrigues et. al., Lignobrycon myersi specimens (9382613) (cropped), CC BY 4.0]

• The monoplacophorans were a group of mollusks common during the Silurian and Devonian Periods, but were last seen in the fossil record in the mid- to late-Devonian, around 375 million years ago.  After that -- nothing.  Reasonably, biologists thought they'd gone extinct, until live monoplacophorans were discovered in deep water off the west coast of Costa Rica.  Further surveys have found no fewer than thirty-seven different species in deep water across the Pacific.

A live specimen of Neopilina filmed off the coast of Samoa by the 2017 Okeanos Explorer mission [Image is in the Public Domain courtesy of NOAA]

• Even the monoplacophorans don't hold the survival record, though.  That honor goes to Rhabdopleura, which is a graptolite -- a (very) distant relative of chordates known mainly through Cambrian-age fossils.  The last Rhabodopleura was thought to have gone extinct in the mid-Cambrian, five hundred million years ago (and the rest of the group didn't make it past the mid-Carboniferous).  In 1869 they were discovered living in the deep water of the Pacific, and since that time nine living species have been identified.

A drawing of Rhabdopleura normani [Image is in the Public Domain]

While the general rule still applies -- extinction is forever -- it's worth keeping in mind that sometimes we find ourselves in a situation a little like Mark Twain did, resulting in his quip, "Rumors of my death were great exaggerations."  The Earth is a big place, and there are still plenty of poorly-explored regions where we might well have lots of surprises in store.

All of which should be encouraging to the folks out there chasing the ivory-billed woodpecker and thylacine.  Don't give up hope.  If Rhabdopleura could survive for five hundred million years unobserved, surely these two could manage a century or so.

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Birdwalking into the Miocene

From the One Thing Leads To Another department, we have: a cute little fuzzy mammal from Madagascar, some thoughts about genetic drift, and a period of geological history during which a lot was happening.

I'd like to say that this kind of twisty mental path is infrequent for me, but unfortunately, it happens pretty much on a daily basis, and has since I was a kid.  When I was around twelve years old, my parents splurged on a set of Encyclopedia Brittanica, ostensibly to assist me with my schoolwork, but they (the Encyclopedia, not my parents) were honestly more of a hindrance than a help.  I'd go to the Brittanica to look up, say, something about the Monroe Doctrine for social studies class, and my mom would find me three hours later with fifteen open volumes spread on the floor around me, with me in the middle immersed in an article about venomous snakes in Malaysia.

It's why conversations with my older son, with whom I seem to share a brain, are like some kind of weird exercise in free association.  We've occasionally tried to reconstruct the pathway by which we got to a particular topic, and there's usually a logical connection between each step and the preceding one, but overall, our discussions give new meaning to the word labyrinthine.

Anyhow, today I started on this particular birdwalk when someone posted a photograph on social media of an animal I'd never heard of: the ring-tailed vontsira (Galidia elegans).  The vontsira is kind of adorable:

[Image licensed under the Creative Commons Charles J. Sharp creator QS:P170,Q54800218, Ring-tailed vontsira (Galidia elegans) 2, CC BY-SA 4.0]

The vontsira and its relative the falanouc are in the family Eupleridae along with a species I had heard of, the fossa, which is a sleek, elegant, weasel-like animal that is only distantly related to other members of the Order Carnivora.  All of the eupleurids live in Madagascar, and like most of the endemic species on the island, they're threatened by habitat loss and competition from non-native species.

What I found most curious about these mammals is that they're a clade -- genetic studies have found that eupleurids all descend from a single small population that arrived in Madagascar something like twenty million years ago, and then diversified into the species you see today.  Chances are, the ancestors of the vontsira, falanouc, fossa, and other eupleurids came over from Africa via rafting in the early Miocene Epoch.  They're distant cousins of the much more common and widespread mongooses, hyaenas, genets, and civets, and it was probably some prehistoric viverroid (the parvorder that includes all five groups) that made its way to Madagascar and gave rise to modern eupleurids.

This led me to looking into what was happening, geology-wise, during the Miocene.  I knew it was a busy time, but I didn't realize just how busy.  Tectonic movement closed off the Mediterranean Sea from the Indian Ocean, and then a shift at the western end of the Mediterranean closed off the Straits of Gibraltar; the result was that the Mediterranean dried up almost completely, something called the Messinian salinity crisis because what was left was a salty desert with an average temperature of something like 110 F and two disconnected lakes of concentrated brine.  At the end of the epoch, another plate movement reopened the Straits, and there was a flood of a magnitude that beggars belief; at its peak, the flow rate was enough to raise the level of the refilling Mediterranean by ten meters per day.

This is also the period during which the Indian subcontinent rammed into Asia, raising the Himalayas and introducing a bunch of African species into Asia (this is why there are lemurs in Madagascar and India, but none in the Middle East).  Also, it's when the Columbia River Flood Basalts formed -- an enormous (175,00 cubic kilometers) blob of igneous rock covering what is now eastern Washington and Oregon, and the west parts of Idaho -- an eruption probably due to the same hotspot which now underlies Yellowstone.

Because of all this, the climate during the Miocene might as well have been attached to a yo-yo.  Warm periods rapidly alternated with cold ones, and wet with dry.  As you might imagine, this played hell with species' ability to adapt, and groups came and went as the epoch passed -- the borophagine ("bone-crushing") canids, the terrifying "hypercarnivorous" hyaenodonts, and the enormous, superficially pig-like entelodonts amongst them.  The first apes evolved, and the split between the ancestors of modern humans and modern chimps occurred in the late Miocene, something like seven million years ago.

If all that wasn't enough, some time during the Miocene -- geologists are uncertain exactly when -- there was an asteroid impact in what is now Tajikistan, forming the twenty-five-kilometer-wide Karakul Crater Lake, which at an elevation of 3,960 meters is higher than the much better-known Lake Titicaca.

So there you have it.  A brief tour of the chaotic paths through my brain, starting with a furry woodland animal from Madagascar and ending with a meteorite impact in Tajikistan.  Hopefully you found some stops along the way interesting.  Now y'all'll have to excuse me, because I need to go look up a single fact in Wikipedia to answer a question a friend asked about linguistics.  You'll find me in a few hours reading about how general relativity applies to supermassive black holes.

I'm sure how I got there will make sense to me, at least.

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Life, complexity, and evolution

Next to the purely religious arguments -- those that boil down to "it's in the Bible, so I believe it" -- the most common objection I hear to the evolutionary model is that "you can't get order out of chaos."

Or -- which amounts to the same thing -- "you can't get complexity from simplicity."  Usually followed up by the Intelligent Design argument that if you saw the parts from which an airplane is built, and then saw an intact airplane, you would know there had to be a builder who put the parts together.  This is unfortunately often coupled with some argument about how the Second Law of Thermodynamics (one formulation of which is, "in a closed system, the total entropy always increases") prohibits biological evolution, which shows a lack of understanding both of evolution and thermodynamics.  For one thing, the biosphere is very much not a closed system; it has a constant flow of energy through it (mostly from the Sun).  Turn that energy source off, and our entropy would increase post-haste.  Also, the decrease in entropy you see within the system, such as the development of an organism from a single fertilized egg cell, does increase the entropy as a whole.  In fact, the entropy increase from the breakdown of the food molecules required for an organism to grow is greater than the entropy decrease within the developing organism itself.

Just as the Second Law predicts.

So the thermodynamic argument doesn't work.  But the whole question of how you get complexity in the first place is not so easily answered.  On its surface, it seems like a valid objection.  How could we start out with a broth of raw materials -- the "primordial soup" -- and even with a suitable energy source, have them self-organize into complex living cells?

Well, it turns out it's possible.  All it takes -- on the molecular, cellular, or organismal level -- is (1) a rule for replication, and (2) a rule for selection.  For example, with DNA, it can replicate itself, and the replication process is accurate but not flawless; the selection process comes in with the fact that some of those varying DNA configurations are better than others at copying themselves, so those survive and the less successful ones don't.  From those two simple rules, things can get complex fast.

But to take a non-biological example that is also kind of mindblowing, have you heard of British mathematician John Horton Conway's "Game of Life?"

In the 1960s Conway became interested in a mathematical concept called a cellular automaton.  The gist, first proposed by Hungarian mathematician John von Neumann, is to look at arrays of "cells" that then can interact with each other by a discrete set of rules, and see how their behavior evolves.  The set-up can get as fancy as you like, but Conway decided to keep it really simple, and came up with the ground rules for what is now called his "Game of Life."  You start out with a grid of squares, where each square touches (either on a side or a corner) eight neighboring cells.  Each square can be filled ("alive") or empty ("dead").  You then input a starting pattern -- analogous to the raw materials in the primordial soup -- and turn it loose.  After that, four rules determine how the pattern evolves:

1. Any live cell that has fewer than two live neighbors dies.
2. Any live cell that has two or three live neighbors lives to the next round.
3. Any live cell that has four or more live neighbors dies.
4. Any dead cell that has exactly three live neighbors becomes a live cell.

Seems pretty simple, doesn't it?  It turns out that the behavior of patterns in the Game of Life is so wildly complex that it's kept mathematicians busy for decades.  Here's one example, called "Gosper's Glider Gun":

Some start with as few as five live cells, and give rise to amazingly complicated results.  Others have been found that do some awfully strange stuff, like this one, called the "Puffer Breeder":

What's astonishing is not only how complex this gets, but how unpredictable it is.  One of the most curious results that has come from studying the Game of Life is that some starting conditions lead to what appears to be chaos; in other cases, the chaos settles down after hundreds, or thousands, of rounds, eventually falling into a stable pattern (either one that oscillates between two or three states, or produces something regular like the Glider Gun).  Sometimes, however, the chaos seems to be permanent -- although because there's no way to carry the process to infinity, you can't really be certain.  There also appears to be no way to predict from the initial state where it will end up ahead of time; no algorithm exists to take the input and determine what the eventual output will be.  You just have to run the program and see what happens.

In fact, the Game of Life is often used as an example of Turing's Halting Problem -- that in general there is no way to be certain that a given algorithm will arrive at a solution in a finite number of steps.  This theorem arises from such mind-bending weirdness as the Gödel Incompleteness Theorem, which proved rigorously that within mathematics, there are true statements that cannot be proven and false statements that cannot be disproven.  (Yes -- it's a proof of unprovability.)

All of this, from a two-dimensional grid of squares and four rules so simple a fourth-grader could understand them.

Now, this is not meant to imply that biological systems work the same way as an algorithmic mathematical system; just a couple of weeks ago, I did an entire post about the dangers of treating an analogy as reality.  My point here is that there is no truth to the claim that complexity can't arise spontaneously from simplicity.  Given a source of energy, and some rules to govern how the system can evolve, you can end up with astonishing complexity in a relatively short amount of time.

People studying the Game of Life have come up with twists on it to make it even more complicated, because why stick with two dimensions and squares?  There are ones with hexagonal grids (which requires a slightly different set of rules), ones on spheres, and this lovely example of a pattern evolving on a toroidal trefoil knot:

Kind of mesmerizing, isn't it?

The universe is a strange and complex place, and we need to be careful before we make pronouncements like "That couldn't happen."  Often these are just subtle reconfigurations of the Argument from Ignorance -- "I don't understand how that could happen, therefore it must be impossible."  The natural world has a way of taking our understanding and turning it on its head, which is why science will never end.  As astrophysicist Neil deGrasse Tyson explained, "Surrounding the sea of our knowledge is a boundary that I call the Perimeter of Ignorance.  As we push outward, and explain more and more, it doesn't erase the Perimeter of Ignorance; all it does is make it bigger.  In science, every question we answer raises more questions.  As a scientist, you have to become comfortable with not knowing.  We're always 'back at the drawing board.'  If you're not, you're not doing science."

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Creepy crawlies

Whenever we have a wet summer -- not an uncommon occurrence in our rainy climate -- we have a plague of little pests trying to get into our house.

They're called millipedes, slinky guys maybe a couple of centimeters long, with lots of legs (not a thousand, though).  They're completely harmless; they don't bite like their cousins the centipedes do, and if you poke at them, they coil up into a ball.  So I guess they're really more of a nuisance than an actual problem.  They don't even damage anything, the way mice can.  Mostly what they seem to do is get in through every crack and crevice (there are lots of these in a big old house like ours), look around for a while, then curl up and die.

[Image licensed under the Creative Commons Totodu74, Anadenobolus monilicornis 03, CC BY-SA 3.0]

So I don't like them, and I wish they stayed outside, but in the grand scheme of things they're no big deal.  Imagine, though, if they were bigger.

A lot bigger.

Recently, paleontologists announced the discovery on a beach in Northumberland, England, of a millipede fossil from the Carboniferous Period.  It's been dated to the middle of the period, about 326 million years ago.  It looks a bit like the millipedes I see trundling across my basement floor in summer.

Only this one was 2.6 meters long (approximately the length of a Mini Cooper), a half a meter across, and weighed something on the order of fifty kilograms.

It's been named Arthropleura, and holds the record as the largest-known arthropod in Earth's history.  Nothing is known for sure about its behavior; if it's like the rest of millipedes, it was a scavenger on leaf detritus, but there's no way to know for certain.  Given its size, it could well have been a lot more dangerous than the ones we have around now.  To paraphrase the old joke about five-hundred-pound gorillas:

Q: What does a fifty-kilogram millipede eat?

A: Anything it wants.

Those of you who are (like me) biology nerds may be frowning in puzzlement at this point.  How on earth could an arthropod get so big?  Their size is limited by the inefficiency of their respiratory system (not to mention the weight of their exoskeletons).  Most arthropods (millipedes included) breathe through pairs of holes called spiracles along the sides of the body.  These holes open into a network of channels called tracheae, which bring oxygen directly to the tissues.  Contrast that with our system; we have a central oxygen-collecting device (lungs), and the hemoglobin in our blood acts as a carrier to bring that oxygen to the tissues.  It's a lot more efficient, which is why the largest mammals are a great deal bigger than the largest arthropods.  (So, no worries that the bad sci-fi movies from the 50s and 60s, with giant cockroaches attacking Detroit, could actually happen.  A ten-meter-long cockroach not only wouldn't be able to oxygenate its own tissues fast enough to survive, it couldn't support its own weight.  It wouldn't eat Detroit, it would just lie there and quietly suffocate.)

So how could there be such ridiculously enormous millipedes?

The answer is as fascinating as the beast itself is.  As the temperature warmed and rainfall increased after the previous period (the Devonian), it facilitated the growth of huge swaths of rain forest across the globe.  In fact, it's the plant material from these rain forests that produced the coal seams that give the Carboniferous its name.  But the photosynthesis of all these plants drove the oxygen levels up -- by some estimates, to around 35% (contrast that to the atmosphere's current 21% oxygen).  This higher oxygen level facilitated the growth of animals who are limited by their ability to uptake it -- i.e., arthropods. (At the same time, there was a dragonfly species called Meganeura with a seventy-centimeter wingspan.  And unlike millipedes, these things were carnivores, just as modern dragonflies are.)

Eventually, though, the system was unsustainable, and a lot of the rain forests began to die off in the Late Carboniferous, leading to a drier, cooler climate.  However, remember the coal seams -- by that time a huge percentage of the carbon dioxide that had fed the photosynthesis of those rain forests was now locked underground.  The fuse was lit for a catastrophe.

Fast forward to the end of the next period, the Permian, 255 million years ago.  What seems to have happened is a series of colossal volcanic eruptions that created the Siberian Traps, a basalt deposit covering most of what is now Siberia.  The lava ripped through the coal seams, blasting all that stored carbon into the atmosphere as carbon dioxide.  The temperature in the late Permian had been cool and dry, and the spike of carbon dioxide created a commensurate spike in the temperature -- as well as a huge drop in oxygen, used up by the burning coal.  The oxygen concentration seems to have bottomed out at around twelve percent, just over half of what it is now.  The extra carbon dioxide dissolved into ocean water, dropping the pH, and the increasing acidity dissolved away the shells of animals who build them out of calcium carbonate -- e.g. corals and mollusks.

Wide swaths of ocean became anoxic, acidic dead zones.  The anaerobic organisms began to eat through all the dead organic matter, churning out more carbon dioxide and another nasty waste product, sulfur dioxide (which gives the horrible smell to rotten eggs, and is also an acidifier).  The result: an extinction that wiped out an estimated ninety percent of life on Earth. In short order, a thriving planet had been turned into a hot, dead, foul-smelling wasteland, and it would take millions of years to recover even a fraction of the previous biodiversity.

Of course, at highest risk would be the big guys like our friends Arthropleura and Meganeura, and the Earth hasn't seen giant arthropods like this since then.  Today, the largest arthropod known is the Japanese spider crab (Macrocheira), topping out at around twenty kilograms -- but crabs and other crustaceans have gills and an oxygen carrier called hemocyanin, so they can boost the efficiency of their respiratory system somewhat over their terrestrial cousins.  The largest insect today is the African Goliath beetle (Goliathus), at about a tenth of a kilogram.  And in today's atmosphere, it's at a pretty significant disadvantage.  They may look big and scary, but in reality, they're slow-moving, harmless creatures.  Kind of a beer can with six legs, is how I think of them.

So that's today's look at creepy-crawlies of the past.  In my opinion it's just as well the big ones became extinct. The last thing I need is having to shoo a fifty-kilogram millipede out of my basement.

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Life converges

One of the most fascinating features of biological evolution -- particularly as it applies to the possibility of life on other planets -- has to do with the concept of constraint.

Which features of life on Earth are, in some sense, inevitable?  Are there characteristics of terrestrial organisms that we might expect to find on any inhabitable world?  Stephen Jay Gould looked at this question in his essay "Replaying the Tape," from his brilliant book on the Cambrian Explosion, Wonderful Life:

You press the rewind button and, making sure you thoroughly erase everything that actually happened, go back to any time and place in the past -– say, to the seas of the Burgess Shale.  Then let the tape run again and see if the repetition looks at all like the original.  If each replay strongly resembles life’s actual pathway, then we must conclude that what really happened pretty much had to occur.  But suppose that the experimental versions all yield sensible results strikingly different from the actual history of life?  What could we then say about the predictability of self-conscious intelligence?  or of mammals?

Some features that have been suggested as evolutionarily constrained, with arguments of varying levels of persuasiveness, are:

• a genetic code based on some kind of nucleic acid (DNA or RNA, or some chemical analogue)
• internal cell membranes made of phospholipids, to segregate competing chemical reactions from each other 
• multicellularity, with some level of tissue specialization
• in more complex organisms, some form of symmetry, with symmetrically-placed organs
• some kind of rapid-transit system for messages, analogous to our nervous system (but perhaps not structured the same way)
• cephalization -- concentration of the central processing centers and sensory organs near the head end

It's interesting when science fiction tackles this issue -- and sometimes comes up with possible pathways for evolution that don't result in humanoids with strangely-shaped ears and odd facial protuberances.  A few that come to mind are Star Trek's silicon-based Horta from the episode"Devil in the Dark," the blood-drinking fog creature from "Obsession," the giant single-celled neural parasites from "Operation Annihilate," and Doctor Who's Vashta Nerada, Not-Things, Gelth, and Midnight Entity.

So the search for extraterrestrial life requires we consider looking not only for "life as we know it, Jim," but life as we don't know it.  Or, more accurately, to consider to what extent our terrestrial biases might be blinding us to the possibility of what evolution could create.

It's worth considering, however, how often evolution here on Earth ends up landing on the same solutions to the problems of survival and reproduction over and over again, a phenomenon called convergent evolution.  Eyes, or analogous light receptor organs, have evolved multiple times -- some biologists have suggested as many as fifty different independent lineages that evolved some form of eye.  Wings occurred separately in four groups of animals -- birds, pterosaurs, insects, and bats.  (If you include structures for gliding, add flying squirrels, sugar gliders, colugos, flying fish, and flying lizards.)

Even biochemical pathways can reappear, something I find astonishing.  Take, for example, the research that came out this week in Nature Chemical Biology, which found that two only distantly-related plants -- ipecac (Carapichea ipecacuanha), in the gentian family, and sage-leaved alangium (Alangium salviifolium), in the dogwood family, have both come up with complex biochemical pathways to generate the same set of bitter, emetic compounds -- ipecacuanha alkaloids.

The last common ancestor of these two species was over a hundred million years ago, so there's a strong argument that they evolved this capacity independently.  And indeed, when the biochemists looked at the enzymatic pathways, they're different -- they found entirely different chemical synthesis methods for producing the same set of end products.  Weirdest of all, they both evolved an enzyme that cleaves a sugar molecule from the alkaloid precursor, and that's what activates it (i.e., makes it toxic).  In the living plant's tissues, the enzyme and the precursor are segregated from each other.  It's only when they're brought together -- such as when a herbivore chomps on the leaves -- that the sugar is split away from the precursor, the alkaloid is activated, and the herbivore starts puking its guts up.

Clever strategy.  So clever, in fact, that it was stumbled upon by two entirely separate lineages of plants.  The rules organisms play by are the same, so perhaps not surprising there are similar outcomes sometimes.

The whole thing highlights the fact that there is a limited range of solutions for the fundamental difficulties of existence.  It has to make you wonder if, when we do find life elsewhere in the universe, it might look a lot more familiar that we're expecting.  I don't think it's likely we'll bump into Romulans or Ice Warriors or Krillitane, but maybe there are features of life on Earth that will re-evolve in just about any conceivable habitable planet.

But hopefully there won't be any Vashta Nerada.  Those things are terrifying.

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The most alien-looking place on Earth

George Wynn Brereton Huntingford was a British anthropologist, linguist, and historian, who traveled widely and was famed for his perceptive observations of societies and cultures.  And if you had to guess which of the many places he traveled during his 77 year life he labeled "the most alien-looking place on Earth," what would you come up with?

His vote was for the island of Socotra, a 132-by-42 kilometer island which lies at at the mouth of the Gulf of Aden.  To the north is the Arabian Sea; to the southwest, the Guardafui Channel separates it from the Horn of Africa.  It's nearer to Africa than to the Arabian Peninsula (232 versus 380 kilometers), but is controlled by the government of Yemen, as much as Yemen's political disaster is currently controlling anything.

Most of Socotra is desert to semi-desert:

[Image licensed under the Creative Commons Rod Waddington from Kergunyah, Australia, Socotra Island (11007223546), CC BY-SA 2.0]

Although it does get more rainfall than either Yemen and Oman (to the north) or Somalia (to the east), so it has a great deal more vegetation than its neighbors:

[Image licensed under the Creative Commons Rod Waddington from Kergunyah, Australia, Wadi, Socotra Island (14495206039), CC BY-SA 2.0]

The main reason for Socotra's uniqueness -- and why evolutionary biologist Lisa Banfield called it "the Galapagos of the Indian Ocean" -- isn't the climate; it's the fact that geologically, it's part of Africa.  During the Miocene Period, about twenty million years ago, Africa and the Arabian Peninsula were joined, but a rift formed that split the two, opening up the Gulf of Aden.  Socotra is a chunk of the Somali Plate that was torn loose and got separated from the rest of the land mass that now forms the easternmost part of Africa.  (Interestingly, the rifting has continued, joining up with a fault system that runs up north through the Red Sea and south into the East African Rift Zone, which one day will tear away a much huger chunk of Africa -- all the way down to Mozambique.)

The issue is that since Socotra's separation from Africa around twenty million years ago, it's been largely isolated, so evolution has veered the community off into its own direction..  This has led to a high degree of endemism -- the fraction of species found nowhere else on Earth.  11% of its bird species, 37% of its plants, 90% of its reptiles, and 95% of its mollusk species are endemic.  One of the most iconic plants is the "dragon's blood tree" (Dracaena cinnabari), which looks like it was invented by Dr. Seuss:

[Image licensed under the Creative Commons Alex38, Dragonblood tree in Socotra 2, CC BY 4.0]

Then, there's the cucumber tree (Dendrosicyos socotranus), which -- as the name would suggest -- is the only species in the cucumber family (Cucurbitaceae) that grows into a tree.  As far as I've heard, though, the fruit isn't edible, which is a good thing, because it'd be a hell of a climb to harvest one for your dinner salad:

[Image licensed under the Creative Commons Gerry & Bonni, Cucumber tree (6407165121), CC BY 2.0]

Like many places with unique and isolated ecosystems, Socotra's oddball assemblage of biota are endangered, from introduced species like cats and rats, from land use by the island's sixty-thousand-odd inhabitants, and from climate change.  The ongoing Yemeni civil war isn't helping, either; the government's priority is certainly not protecting peculiar-looking trees, and the ecotourists whose revenue might help the situation are mostly staying away for their own safety.

In any case, that's one anthropologist's vote for "the most alien-looking place on Earth" -- an island that's geologically African, politically and culturally Arabian, and biologically like nowhere else.  It's a place I'd love to visit one day if the situation calms down.  Adding some bird species to my life list that are found only on one speck of land in the Arabian Sea would be amazing.

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Dire situation

It's estimated that of the five billion species of organisms that have ever existed on Earth, something like 99.99% of them are extinct.  This is with allowances for the fact that -- as I pointed out in a post a couple of years ago -- the word species is one of the mushiest terms in all of science, one of those words that you think you can define rigorously until you realize that every definition you come up with has dozens of exceptions or qualifications.

Be that as it may, there's no doubt that extinction has been the fate of virtually all of the twigs on the Great Tree of Life, from charismatic megafauna like Apatosaurus and the saber-toothed cat all the way down to single-celled organisms that lived and died hundreds of millions of years ago and left no fossil record whatsoever.

Some of the more recent extinctions, though, always strike nature-loving types like myself as a tragedy.  The Dodo usually comes up, and the Thylacine (or "Tasmanian wolf," although it wasn't a wolf and wasn't limited to Tasmania), and the maybe-it-still-exists, maybe-it-doesn't Ivory-billed Woodpecker.  The Passenger Pigeon, which before 1850 was the most abundant bird in eastern North America, comprising flocks of tens of thousands of individuals, was hunted to extinction in only fifty years -- the last wild Passenger Pigeon was shot in Ohio in 1900.

Wouldn't it be cool, many of us have thought, to bring back some of these lost organisms?  The Jurassic Park scenario is a pipe dream; amber notwithstanding, no intact DNA has ever been found from that long ago.  But what about more recently-extinct species?

Well, no need to wonder any more.  It's been done.

A company called Colossal Biosciences, run by Ben Lamm and George Church, claim to have produced three Dire Wolf pups (Aenocyon dirus) using DNA extracted from a tooth and a skull from Idaho and Ohio, respectively -- genetically altering the fertilized eggs of a gray wolf, and gestating the embryos in ordinary female dogs.  Here's one of the results:

[Image credit: Colossal Biosciences]

You're looking at a photograph of an animal that hasn't lived for ten thousand years.

My initial "good lord this is cool" reaction very quickly faded, though, but not because of some sort of "We're playing God!" pearl-clutching.  Lamm, who apparently has huge ambitions and an ego to match, sees no problem with any of it, and has plans to bring back the Dodo and the Woolly Mammoth, and others as well.  All, of course, big flashy animals, because that's what attracts investors; no one is going to put millions of dollars into bringing back the Ouachita pebblesnail.

But even that isn't the actual problem, here.  Lamm himself gave a glancing touch on the real issue in his interview with The New Yorker (linked above), when someone inevitably brought up Jurassic Park.  "That was an exaggerated zoo," Lamm said.  "This is letting the animals live in their natural habitats."

No.  No, it's not.

Because these species' natural habitats don't exist anymore.

Even the Dodo, which went extinct in 1662, couldn't be reintroduced to Mauritius Island today; the feral cats, rats, dogs, and pigs that helped drive it to extinction in the first place still live in abundance on the island.  What would the de-extinction team do?  Create a fenced, guarded reserve for it?

How is that not an "exaggerated zoo?"

And the Dire Wolf is an even more extreme example.  It originally lived throughout much of the continental United States and down into mountainous regions of Central America.  Adults could weigh up to seventy kilograms, so they could take down good-sized prey.  If you could create a breeding population of Dire Wolves, where would you put them that they wouldn't come into contact with livestock, pets... and humans?

The truth is sad but inevitable; the world the Dire Wolf lived in is gone forever.  Whether what we have now is better or worse is a value judgment I'm not equipped to make.  What I do know is that recreating these animals only to have them lead restricted lives in reserves for rich people to come gawk at is morally indefensible.  Ultimately, they can never live in the wild again; so a fenced-in reserve -- or the only other option, to let them go extinct a second time.

As huge as the coolness factor is, we shouldn't be doing this.  How about putting our time, money, and effort into not further fucking up what we still have?  There are plenty of wildlife refuges worldwide that could benefit enormously from the money being sunk into this project.  Or, maybe, working toward fighting Donald Trump's "cut down all the trees and strip mine the world" approach to the environment.

So after the first flush of "Wow," all Lamm and Church's accomplishment did was leave me feeling a little sick.  There seems to be no end to human hubris, and it's sad that these beautiful animals have to be its showpiece.

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Lightning rod

In 1904, biologist Joseph Grinnell formulated what has since become known as the Competitive Exclusion Principle: if two species overlap in their niches, the degree of overlap correlates to the degree of competition between them.  If the competition becomes too high, eventually one of them is outcompeted and dies out.

Contrary to the "Nature is red in tooth and claw" view of the natural world, however, many species solve the problem of competitive exclusion in remarkable peaceable ways.  Some partition the habitat -- for example, species of insect-eating warblers in my part of the world avoid competing for food by splitting up where they forage, with some species mostly staying in the treetops, others in the the forest midstory or undergrowth.  Elaborate cooperative strategies are also remarkably common -- witness lichens, which are a symbiotic pairing of an algae species and a fungus, where the fungus gives the algae housing, and the algae photosynthesizes and donates some of the nutrients to its host.

So despite how it's often characterized, nature doesn't always land on the violent solution.

Sometimes, though...

There's a rain forest tree found in Panama called the almendro (Dipteryx oleifera).  It's in the bean family, Fabaceae, which you can tell if you look at its pinnately-compound leaves and showy flowers:

It can get up to 55 meters tall, which is a necessity in the rain forest.  Dense patches of rain forest have such a thick covering of leaves that only two percent of the incident sunlight reaches the forest floor.  Understory plants have evolved to cope with the perpetual twilight -- this is one of the reasons why rain forest plants often have very dark green leaves.  The density of pigments allows them to trap every photon of light they manage to receive.

Trees, though, compete by elbowing each other out of the way, trying to grow as tall as possible so as to access light, and in the process, shade out the abundant competition.  But not only do rain forest trees have to worry about nearby trees, they also have to deal with lianas, vining species that twine up tree trunks and drape themselves over the canopy, hitching a ride on their taller, sturdier neighbors, and shading them out in the process.

Well, the almendro has evolved a strategy for dealing with all of that at once.

A study this week in New Phytologist looked at a peculiar pattern that ecologist Evan Gora, of the Cary Institute of Ecosystem Studies, had noticed: almendros seemed to have an unusually high likelihood of being struck by lightning, but almost never sustained any significant damage from it.  Well, after a five-year study, Gora and his collaborators found that almendros that were struck usually just lost some leaves and small branches, while other species sustained significant damage, with 64% of the struck trees dying within two years.

Not only that, but the lightning strikes completely wipe out any lianas.  Almendros that were hit by lightning not only recovered quickly, they had their tangle of vines blown to smithereens.  And neighboring trees that were jolted by the strike -- through sparks jumping from the almendro -- often died, too, freeing up more living room.

The data shows that living near an almendro raises a neighboring tree's likelihood of being killed by a lightning strike by 48%.  "Any tree that gets close," Gora said, "eventually gets electrocuted."

How the almendro has managed to evolve into a natural lightning rod is uncertain, but it has been found that the cells in its wood have wider channels for water transport, making the wood more electrically conductive.  Most of the damage to trees from lightning strikes occurs because internal resistance causes the electrical energy to dissipate as heat, making the sap boil and triggering the trunk to explode.  Lowering the electrical resistance allows the current to pass through the trunk and safely into the ground with less heating.  This means that not only does the almendro not suffer as much damage, it actually attracts lightning -- electrical discharges tend to follow the path of least resistance.

So even if sometimes the natural world does evolve nice, friendly, cooperative solutions to the problems of survival, sometimes it... doesn't.  Even the trees don't always.  Like the Ents and Huorns from Tolkien's Fangorn Forest, sometimes the trees deal with their enemies by taking matters into their own... um... branches.

Think about that next time you're going for a nice stroll in the woods.

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Birds, bees, etc.

Yesterday I was thinking about sex.

Not like that.  My intention is to keep this blog PG-13.  I meant sexual reproduction in general, and the topic comes up because I just finished reading Riley Black's lovely new book When the Earth Was Green: Plants, Animals, and Evolution's Greatest Romance, which looks at paleontology through the lens of botany.  It's a brilliant read, the writing is evocative and often lyrical, and it needs to be added to your TBR list if you've even the slightest bit more than a passing interest in the past.

One of the topics she looks at in some detail is how sexual reproduction in plants -- better known as pollination -- led to an inseparable relationship between flowering plants and their pollinators.  A famous example is Darwin's orchid (Angraecum sesquipedale), a Madagascar species with night-scented white flowers whose nectaries are at the base of an impossibly long tube:

[Image licensed under the Creative Commons Bernard DUPONT from France, Darwin's Orchid (Angraecum sesquipedale) (8562029223), CC BY-SA 2.0]

Its discovery prompted Charles Darwin to predict that there must be a moth on the island whose mouthparts fit the flower, and which was responsible for pollinating it.  Sure enough, in a few years, biologists discovered the Madagascar hawk moth (Xanthopan morganii):

[Image licensed under the Creative Commons Nesnad, Xanthopan morganii praedicta Sep 16 2021 03-58PM, CC BY 4.0]

The problem is, such dramatic specialization is risky.  If something happens to either member of the partnership, the other is out of luck.  In fact, sexual reproduction in general is a gamble, but its advantages outweigh the risk, and I'm not just talking about the fact that it's kind of fun.

Asexually-reproducing organisms, like many bacteria and protists, some plants and fungi, and a handful of animals, have the advantages that it's fast, and only requires one parent.  There's a major downside, however; a phenomenon called Muller's ratchet.  Muller's ratchet has to do with the fact that the copying of DNA, and the passing of those copies on to offspring, is not mistake-proof.  Errors -- called mutations -- do happen.  Fortunately, they're infrequent, and we even have enzymatic systems that do what amounts to proofreading and error-correction to take care of most of them.  A (very) few mutations actually lead to a code that works better than the original did, but the majority of the ones that slip by the safeguards cause the genetic message to malfunction.

It's called a "ratchet" because, like the handy tool, it only turns one way -- in this case, from order to chaos.  Consider a sentence in English -- space and punctuation removed:

TOBEORNOTTOBETHATISTHEQUESTION

Now, let's say there's a random mutation on the letter in the fourth position, which converts it to:

TOBGORNOTTOBETHATISTHEQUESTION

The message is still pretty much readable, although the second word is now spelled wrong.  But most of us would have been able to figure out what it was supposed to say.

Now, suppose a second mutation strikes.  There is a chance that it would affect the fourth position again, and purely by accident convert the erroneous g back to an e, but that likelihood is vanishingly small.  This is called a back mutation, and is more likely in DNA -- which, of course, is what this is an analogy to -- because there are only four letters (A, T, C, and G) in DNA's "alphabet," as compared to the 26 English letters.  But it's still unlikely, even so.  You can see that at each "generation," the mutations build up, every new one further corrupting the message, until you end up with a string of garbled letters from which not even a cryptographer could puzzle out what the original sentence had been.

Sexual reproduction is a step toward remedying Muller's ratchet.  Having two copies of each gene (a condition known as diploidy) makes it more likely that at least one of them still works.  Many genetic diseases -- especially the ones inherited as recessives -- are losses of function, where copying errors have caused that stretch of the DNA to malfunction.  But if you inherited a good copy from your other parent, then lucky you, you're healthy (although you can still pass your "hidden" faulty copy on to your children).

This, incidentally, is why inbreeding -- both parents coming from the same genetic stock -- is a bad idea.  It doesn't (in humans) cause problems in brain development, which a lot of people used to think.  But what it does mean is that if both parents have a recent common ancestor, the faulty genes one of them carries are very likely the same ones the other does, and the offspring has a higher chance of inheriting both damaged copies and thus showing the effects of the loss of function.  It's this mechanism that explains why a lot of human recessive genetic disorders are characteristic of particular ethnic groups, such as cystic fibrosis in northern Europeans, Tay-Sachs disease in Ashkenazic Jews, and malignant hyperthermia in French Canadians.  It only happens when both parents are from the same heritage -- which is why "miscegenation laws," preventing intermarriage between people of different races or ethnic backgrounds, are exactly backwards.  Mixed-race children are actually less likely to suffer from recessive genetic disorders -- the mom and dad each had their own "genetic load" of faulty genes, but there was no overlap between the two sets of errors.  Result: healthy kid.

The difficulty, of course, is that despite its genetic advantages, sexual reproduction requires a genetic contribution from two parents.  This is tough enough with mobile species, but with organisms that are stuck in place -- like plants -- it's a real problem.  Thus the hijacking of animals as carriers for pollen, and the evolution of a host of mechanisms for preventing self-pollination (which cancels out the advantage of higher variation, given that once again, both sets of genes come from the same parent).

What's most curious about sexual reproduction is that we don't know how it started.  Even some very simple organisms have genetic exchange mechanisms, such as conjugation in bacteria, which help them not to get clobbered by Muller's ratchet, and something like that is probably how it got going in the first place.  We know sexual reproduction is evolutionarily very old, given that it's shared by the majority of life on Earth, but how the process of splitting up and recombining genetic material every generation first started is still a mystery.

Anyhow, that's our consideration of birds, bees, and others for the day.  I'll end by saying again that you should buy Riley Black's book, because it's awesome, and gives you a vivid picture of life at various times on Earth, not from the usual Charismatic Megafauna viewpoint, but from the perspective of our green friends and neighbors.  It's refreshing to consider how life is experienced from an entirely different angle every once in a while.

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