The road not taken

One of the most intriguing sets of life forms I've ever heard of is the Ediacaran Assemblage.

It dates from the late Precambrian Era -- something on the order of 570 million years ago -- and is named after the Ediacara Hills of Australia, where rocks of that age are exposed at the surface.  They're sometimes conflated with the Cambrian Explosion fauna like the ones in the famous Burgess Shale, but any connection between the two is tenuous at best.  Not only are they separated by almost seventy million years, the Burgess Shale animals are (mostly) from phyla we know about.  A few -- like the bizarre and aptly-named Hallucigenia -- have more obscure relationships to modern life, but most of the fossils we find there are identifiably proto-arthropods or proto-annelids or proto-whatnot.  So while the Cambrian Explosion fauna is fascinating in its own right, by and large it's still fairly familiar ground.

Not so the Ediacaran Assemblage.

These things are downright mysterious.  Take, for example, the group called rangeomorphs.

They may have been animals, although they were sessile (fixed to the seafloor) via stalks, and had weird frond-like structures of uncertain purpose (but which may have been a mechanism either for oxygen extraction or for filter feeding).  So if you were to look at a living one, your initial impression might well be that it was some odd sort of seaweed, and not an animal at all.

A 550-million-year-old fossil of the rangeomorph Charnia masoni, from the Mistaken Point Formation in Newfoundland [Image licensed under the Creative Commons Smith609 at English Wikipedia, Charnia, CC BY 2.5]

Not only are they bizarre-looking, many seem to have no living descendants, including Obamus coronatus (which looks like a French cruller) and the hubcap-like Tribrachidium heraldicum, one of the only known animals to have triradial symmetry.

Artist's reconstruction of Obamus coronatus [Image licensed under the Creative Commons Nobu Tamura (http://spinops.blogspot.com/), Obamus NT, CC BY-SA 4.0]

There's a misconception about evolution -- that it's linear and progressive, that one form supersedes another in some kind of stepwise fashion based upon an identifiable "improvement," such as increase in speed, defensive or offensive capabilities, ability to access food, or intelligence.  While you can find examples where this appears to have happened, there's a large measure of the chaotic involved in the history of life.  Not only do we see sudden and drastic changes in the climate and environmental conditions -- which, after all, are the biggest drivers of selective pressure -- random occurrences like volcanic eruptions and meteorite strikes can create a situation where extinction had way less to do with poor evolutionary fitness than simply being in the wrong place at the wrong time.

The Ediacaran Assemblage seems to have been on the unfortunate end of that particular equation.  As I mentioned, the majority of them apparently left no descendants, not only today but even by the beginning of the next geological era.  None of the bizarre Ediacaran life forms appear in the early Cambrian; the dominant animals five hundred million years ago show almost no resemblance to their predecessors seventy million years earlier.

In fact, the subject comes up because of a paper a few weeks ago in Geology suggesting that the wipeout of the Ediacaran Assemblage represents the Earth's first known mass extinction (not counting the Great Oxidation Event, of which the effect on life was uncertain but probably enormous).  The new study uses recently-uncovered late Precambrian fossil beds that greatly add to the described Ediacaran biota, and the analysis found that we may well have been drastically underestimating the magnitude of the crash.

The researchers' data shows that what is known as the Kotlin Crisis, the biotic collapse that took out pretty much all of the Ediacaran life forms, may have wiped out as much as eighty percent of life on Earth.  This easily places it amongst what paleontologists Jack Sepkoski and David Raup called the "Big Five" extinction events (the Late Ordovician, Late Devonian, Permian-Triassic, End Triassic, and Cretaceous-Tertiary extinctions).  In fact, if the eighty percent number is correct, it would be in second place -- handily beating the sixty-odd percent of life destroyed in the famous Cretaceous-Tertiary extinction, and exceeded only by the cataclysmic Permian-Triassic "Great Dying."

So, what caused the Kotlin Crisis?  At the moment, it's uncertain.  It may have been a series of unfortunate events, including climate shifts, changes in oxygenation of the ocean, volcanic eruptions, and possibly the evolution of carnivory, but honestly, we're not sure.  There are few enough rock outcrops of that age available to study that any determination is likely to be slow in coming.

But what's certain is that these (very) distant cousins of ours represent a road not taken -- a branch of the vast evolutionary tree of life on Earth that led to no descendants.  It always makes me wonder what would have happened had they survived, and perhaps outcompeted, the bilateral, mobile forms that superseded them, and who ultimately became our ancestors.  If -- in evolutionary biologist Stephen Jay Gould's evocative words -- we could re-run the tape, who would now be the dominant life forms on Earth?

Wouldn't be us, that's for damn sure.  Maybe something like H. P. Lovecraft's bizarre pentaradial "Great Old Ones:"

[Image licensed under the Creative Commons Tom Ardans - blog - Facebook, Old One by Tom Ardans, CC BY-SA 3.0]

I can virtually guarantee that whatever it would have been, it'd be something so strange to our eyes that it would give even Darwin pause, despite all his blithe talk about "many forms most beautiful and most wonderful."

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A Celtic misfire

An evolutionary misfire occurs when a trait evolved in one context, where it was an advantage to the organism, but then circumstances change -- and it becomes a significant disadvantage.

One common example is the way moths circle point sources of light, like streetlights and candle flames, and often get incinerated if they fly too close.  Why on earth would they do something that foolish?  

The whole thing has to do with the way moths navigate.  They evolved for millions of years in a context where the only point sources of light at night were (very distant) stars, and they used them for navigation.  If there's an extremely distant light source, and you keep it in the same position with respect to you as you move, you'll travel in a straight line.  (Remember how in the movie Apollo 13, the astronauts kept a particular star dead center in their window when their navigational system failed?)  

The problem is, if the point source is much closer, the whole strategy falls apart.  If you keep a light source in the same position in your visual field and it's only a few feet away, you don't travel in a straight line, you travel in a circle around it.  So what started out as a perfectly reasonable way for moths to navigate at night has now made them commit suicide around streetlights.

There's another evolutionary phenomenon called heterozygote advantage.  This is when heterozygous individuals -- those who have two different alleles at a particular gene locus -- have a distinct advantage over homozygotes.  Two commonly-cited examples are sickle-cell anemia, where heterozygotes not only seldom have serious symptoms but are resistant to malaria, and cystic fibrosis, a devastating lung disease for homozygotes, that in heterozygotes results in few respiratory symptoms -- and a lower risk for diarrheal disease, still a major killer of infants in parts of the world with poor medical care.

These two phenomena are often the explanation for what might seem like an evolutionary puzzle; if the fittest survive, why do maladaptive traits persist in populations?  This becomes less puzzling if the maladaptive trait used to be beneficial -- or if having a single copy of the gene confers a benefit over being homozygous for either of the alleles.

But put those two together, and you've got serious trouble.  Which brings us to the odd situation of the "Celtic curse."

It's been known for years that people of Celtic ancestry, particularly those from western Scotland and northern Ireland, have a much higher risk for a genetic disease called hemochromatosis.  People with this disorder absorb iron too quickly, so the iron content of their blood builds up to toxic levels, resulting in eventual liver failure.  Fortunately, the treatment is simple; regular blood donation reduces the red blood cell count and thus the iron levels, and significantly lowers the risk of liver damage.  But why is such a damaging disease so common?  A study this week in Nature Communications mapped out the frequency of the allele, and found three hotspots for the gene -- County Donegal, in the northern part of the Republic of Ireland, the region around Glasgow, and the Outer Hebrides -- where the frequency of the high-risk gene is one in sixty.

That seems really high for a condition that can kill you.

[Image is in the Public Domain]

It turns out that the "Celtic curse" is the result of a combination of a misfire with heterozygote advantage.  Having one copy of the high-risk variant of the gene makes you scavenge iron really efficiently from your food, preventing anemia if you have a poor diet.  And for centuries, people in these regions did have iron-poor diets, largely consisting of cereal grains with little in the way of meat.  So having one copy of this gene did give you a selective advantage, as long as you were living on short commons.

Now that just about everyone in the region has access to much better-quality food, the allele's ability to turbo-charge iron uptake backfires, causing iron loading to the point of illness.

And of course, there's the fact that even if you do have two copies of the gene, the more serious side effects usually don't strike until you're in your forties or fifties -- at which time you've probably already had whatever children you're going to have, and passed the gene on.  So honestly, it's not a double-whammy, it's a triple-whammy.

So there's our genetic curiosity of the day.  Interestingly, I have ancestry from Paisley (near Glasgow), but apparently I lucked out and don't have the hemochromatosis gene.  Good thing, because despite my relative good health, I have serious doctor phobia.  If I had a condition that required people to come at me regularly with stethoscopes and needles -- irrational though it certainly is -- I might just take my chances with being on the receiving end of natural selection.

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Echoes of the ancestor

One of the most persuasive pieces of evidence of the common ancestry of all life on Earth is genetic overlap -- and the fact that the percent overlap gets higher when you compare more recently-diverged species.

What is downright astonishing, though, is that there is genetic overlap between all life on Earth.  Yeah, okay, it's easy enough to imagine there being genetic similarity between humans and gorillas, or dogs and foxes, or peaches and plums; but what about more distant relationships?  Are there shared genes between humans... and bacteria?

The answer, amazingly, is yes, and the analysis of these universal paralogs was the subject of a fascinating paper in the journal Cell Genomics last week.  Pick any two organisms on Earth -- choose them to be as distantly-related to each other as you can, if you like -- and they will still share five groups of genes, used for making the following classes of enzymes:

• aminotransferases
• imidazole-4-carboxamide isomerase
• carbamoyl phosphate synthetases
• aminoacyl-tRNA synthetases
• initiation facter IF2

The first three are connected with amino acid metabolism; the last two, with the process of translation -- which decodes the message in mRNA and uses it to synthesize proteins.

The fact that all life forms on Earth have these five gene groups suggests something wild; that we're looking at genes that were present in LUCA -- the Last Universal Common Ancestor, our single-celled, bacteria-like forebear that lived in the primordial seas an estimated four billion years ago.  Since then, two things happened -- the rest of LUCA's genome diverged wildly, under the effects of mutation and selection, so that now we have kitties and kangaroos and kidney beans; and those five gene groups were under such extreme stabilizing selection that they haven't significantly changed, in any of the branches of the tree of life, in millions or billions of generations.

The authors write:

Universal paralog families are an important tool for understanding early evolution from a phylogenetic perspective, offering a unique and valuable form of evidence about molecular evolution prior to the LUCA.  The phylogenetic study of ancient life is constrained by several fundamental limitations.  Both gene loss across multiple lineages and low levels of conservation in some gene families can obscure the ancient origin of those gene families.  Furthermore, in the absence of an extensive diagnostic fossil record, the dependence of molecular phylogenetics on conserved gene sequences means that periods of evolution that predated the emergence of the genetic system cannot be studied.  Even so, emerging technologies across a number of areas of computational biology and synthetic biology will expand our ability to reconstruct pre-LUCA evolution using these protein families.  As our understanding of the LUCA solidifies, universal paralog protein families will provide an indispensable tool for pushing our understanding of early evolutionary history even further back in time, thereby describing the foundational processes that shaped life as we know it today.

It's kind of mind-boggling that after all that time, there's any commonality left, much less as much as there's turned out to be.  "The history of these universal paralogs is the only information we will ever have about these earliest cellular lineages, and so we need to carefully extract as much knowledge as we can from them," said Greg Fournier of MIT, who co-authored the paper, in an interview with Science Daily.

So all life on Earth really is connected, and the biological principle of "unity in diversity" is literally true.  Good thing for us; the fact that we have shared metabolic pathways -- and especially, shared genetic transcription and translation mechanisms -- is what allows us to create transgenic organisms, which express a gene from a different species.  For example, this technique is the source of most of the insulin used by the world's diabetics -- bacteria that have been engineered to contain a human insulin gene.  Bacteria read DNA exactly the same way we do, so they transcribe and translate the human insulin gene just as our own cells would, producing insulin molecules identical to our own.

This is also, conversely, why the idea of an alien/human hybrid would never work.  Even assuming that some alien species we met was humanoid, and had all the right protrusions and indentations to allow mating to work, there is just about a zero likelihood that the genetics of two species that didn't have a common ancestor would line up well enough to allow hybridization.  Consider that most of the time, even relatively closely-related terrestrial species can't hybridize and produce fertile offspring; there's no way humans could do so with any presumed alien species.

Star Trek's claims to the contrary notwithstanding.

So that's our mind-blowing science news of the day.  The discovery of five gene families that were present in our ancestors four billion years ago, and which are still present today in every life form on Earth.  Some people apparently think it's demeaning to consider that we're related to "lower" species; me, I think it's amazingly cool to consider that everything is connected, that I'm just one part of a great continuum that has been around since not long after the early Earth cooled enough to have liquid water.  All the more reason to take care of the biosphere -- considering it's made up of our cousins.

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Who benefits?

There's an interesting idea from evolutionary theory called the cui bono principle.

Cui bono? is Latin for "who benefits?"  It started out as a legal concept; if a crime has been committed, and you're looking for the suspect, find out who benefitted.  That, very likely, will get you on the right path toward solving the mystery.

Cui bono in the evolutionary model has to do with explaining odd phenomena that seem to have no obvious underlying reason -- or which even induce organisms into self-destructive behavior.  One common example is the strange situation where certain ant species crawl up to the tops of blades of grass and basically just wait there to be eaten by herbivores.  It turns out that the bizarrely suicidal ants are infected with a parasite called a lancet worm that needs to complete its life cycle in the gut of a herbivorous mammal, so it damages the brain of the ant in just such a way as to turn its sense of direction upside down.  The parasitized ant then crawls upward instead of downward to safety, gets eaten -- and the lancet worm, of course, is the one who benefits.

Another, even creepier example, is Toxoplasma gondii, which I wrote about here at Skeptophilia a few years ago.  I encourage you to go back and read the post, but the upshot is this parasite -- which by some estimates infects half of the human population on Earth -- causes different symptoms in its three main hosts, cats, rats, and people.  Each set of symptoms is tailored to change behavior in very specific ways, with one end in mind; allowing the parasite to jump to its next host.

I just found out about another very peculiar (and convoluted) example of cui bono just yesterday, this one involving rice plants.  Many plants, it turns out, have pheromonal signaling, releasing chemicals into the air that then trigger responses in neighboring individuals, either of their own or of different species.  Acacia trees that are browsed by herbivores, for example, emit a signal that triggers nearby trees to produce bitter tannins, discouraging further snacking on the leaves.  Well, it turns out that rice plants have an even niftier strategy; attacked by insect pests, the rice plants emit a chemical called methyl salicylate (better known as oil of wintergreen), which attracts parasitoids -- insects like chalcid wasps that attack and kill the offending pests, usually by laying an egg in or on them and allowing the larvae to eat the pests for lunch.

Okay, but this has yet another layer of complexity, because there's a different set of organisms that have another take on cui bono.  Rice are subject to a group of plant viruses called tenuiviruses, which cause rice stripe disease, weakening or killing plants and severely reducing crop yield.  Tenuiviruses are spread by insect pests like planthoppers, which (much like mosquitoes with malaria, dengue fever, yellow fever, and chikungunya) suck up the sap of infected plants and the virus along with it, move on to an uninfected host, and spread the disease.

Rice stripe tenuivirus [Image credit: A. M. Espinoza]

And new research has found that the tenuiviruses, once in an infected plant's tissues, suppress the plant's ability to produce methyl salicylate.  The result?  The plant can't send a signal to the parasitoids, the planthoppers multiply, and the disease spreads.

The authors write:

[R]ice viruses inhibit methyl salicylate (MeSA) emission, impairing parasitoid recruitment and promoting vector persistence.  Field experiments demonstrate that MeSA, a key herbivore-induced volatile, suppresses vector populations by attracting egg parasitoids.  Viruses counter this by targeting basic-helix-loop-helix transcription factor OsMYC2, a jasmonic acid signaling hub, thereby down-regulating OsBSMT1 and MeSA biosynthesis, responses conserved across diverse rice viruses and vector species.

So once again, we have a parasitic microorganism that is engineering a response in its host that makes it more likely to be passed on, in this case by preventing the host from calling for help.

This kind of strategy brings Tennyson's observation that "nature is red in tooth and claw" to new heights, doesn't it?  Makes you wonder how many other examples there are out there of behavior being manipulated by parasites.  Further evidence that evolution is the Law of Whatever Works -- even if Whatever Works is kind of unsettling.

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The advantage of simplicity

One of the most common misconceptions about evolution is that it is goal-oriented.

You hear it all the time.  Giraffes evolved longer necks so they could reach foliage higher up in tree branches -- as if some poor short-necked giraffes  were trundling about on the African savanna looking longingly up into the canopy and thinking, "Wow, that looks amazing," so their kids were born with longer necks.  It becomes even more insidious when you start talking about human evolution, because the way it's often presented is that waaaaaay back you had something like a jellyfish that evolved into something like a worm, and then into a primitive fish, into an amphibian, into a reptile, into a proto-mammal, into true mammals then primates then...

... us.  Sitting, of course, on the very top as befits the pinnacle of evolution, as if all along we're what the whole process had been aiming at.

This misses the boat in several very important ways.  One is that this linear view of evolution is simply wrong.  Evolution causes repeated branching; in fact, in our own lineage, many of the basic body plans we have today (flatworms, roundworms, jellyfish, annelids, mollusks, echinoderms, arthropods, and primitive vertebrates) all arose at around the same time, during what's called the Cambrian explosion.  During the intervening 540-million-odd years since that happened, some of the branches of the tree of life have changed a great deal more than others; but all living things on Earth have exactly the same length of evolutionary history.

A really critical way that the teleological model for evolution fails is that it misses completely how evolution actually works.  Natural selection isn't forward-looking at all; it operates by the environment selecting the forms that have the highest survival and reproductive potential now, irrespective of what the conditions might be a week from Tuesday.  It is very much the Law of Whatever Works, and what works today might not work at all if conditions change -- something we should pay attention to apropos of climate change.

A third problem is the perception that evolution always leads to higher complexity, strength, and intelligence.  None of these are true.  Consider that insects, especially beetles, are the most numerous and diverse animals on Earth by far -- both species-wise, and individual-for-individual, insects outnumber all other animals put together.  Sometimes simplicity has a higher survival advantage than complexity does, and -- to judge by the natural world, and even a significant fraction of the human part of it -- I'm not convinced that intelligence is always an advantage, either.

As a good example of the advantage of simplicity -- and the reason the topic comes up today -- consider the little plant species Balanophora fungosa.  It's found in warm, moist forests in Taiwan, Japan, and Okinawa, and on first glance it looks like a strange mushroom.  Balanophora is in the family Balanophoraceae, which comprises sixteen genera and is somewhat tentatively placed in order Santalales along with more familiar plants like sandalwood and mistletoe.  All the members of Balanophoraceae are obligate parasites, living off the roots of very specific species of trees.

Balanophora fungosa [Image credit: Petra Svetlikova]

Where it gets interesting is that Balanophora has done what superficially looks like evolution in reverse.  It's lost its ability to produce chlorophyll; it has no conventional root system.  Most of the plant kingdom have on the order of two hundred genes whose job it is to produce and operate plastids, the pigment-containing organelles that include chloroplasts; Balanophora has reduced that number to twenty.  Many species in Balanophoraceae produce seeds without fertilization, obviating the need for flowers.

What's curious is that these odd little plants have been around for a long time.  They branched off from the rest of the plant kingdom in the mid-Cretaceous period, something like a hundred million years ago, and have been quietly doing their thing ever since, gradually evolving to jettison structures (and even genes) they don't need along the way.  "Balanophora has lost much of what defines it as a plant, but retained enough to function as a parasite," said Petra Svetlikova, of the Okinawa Institute of Science and Technology, who led the study.  "It's a fascinating example of how something so strange can evolve from an ancestor that looked like a normal plant with leaves and a normal root system."

Because of its extreme specialization, both in terms of habitat and host species, Balanophora is threatened by habitat change.  "Most known habitats of Balanophora are protected in Okinawa, but the populations face extinction by logging and unauthorized collection," Svetlikova said.  "We hope to learn as much as we can about this fantastic, ancient plant before it's too late.  It serves as a reminder of how evolution continues to surprise us."

So there you have some cool research about an evolutionary holdout from a hundred-million-year-old split in the tree of life.  Here, simplicity, not complexity, seems to have been the key to its long survival.  One can only hope that this strange little plant hasn't lasted so long only to reach the end because of us.

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Scattered to the winds

One of the more puzzling aspects of evolutionary theory is the phenomenon of peripheral isolates.

This term refers to widely-separated populations of seemingly closely-related organisms.  One of the first times I ran into this phenomenon came to my attention because of my obsession with birdwatching.  There's a tropical family of birds called trogons, forest-dwelling fruit-eaters that are prized by birdwatchers for their brilliant colors.  There are trogons in three places in the world... Central and South America (27 species), central Africa (3 species), and southern Asia (11 species).

These are very far apart.  But take a look at three representatives from each group -- it doesn't take an ornithologist to see that they've got to be closely related:

The Elegant Trogon (Trogon elegans) of Central America [Image licensed under the Creative Commons dominic sherony, Elegant Trogon, CC BY-SA 2.0]

The Narina Trogon (Apaloderma narina) of central Africa [Image licensed under the Creative Commons Derek Keats from Johannesburg, South Africa, Narina Trogon, Apaloderma narina MALE at Lekgalameetse Provincial Reserve, Limpopo, South Africa (14654439002), CC BY 2.0]

The Red-headed Trogon (Harpactes erythrocephalus) of southeast Asia [Image licensed under the Creative Commons JJ Harrison (jjharrison89@facebook.com), Harpactes erythrocephalus - Khao Yai, CC BY-SA 3.0]

I know, I've gone on and on in previous posts about how misleading morphology/appearance can be in determining relationships, but you have to admit these are some pretty convincing similarities.

The question, of course, is how did this happen?  Where did the group originate, and how did members end up so widely separated?  To add to the puzzle, the fossil record for the group indicates that in the Eocene Epoch, fifty-ish million years ago, there were trogons in Europe -- fossils have been found in Denmark and Germany -- and the earliest fossil trogons from South America come from the Pleistocene Epoch, only two million years ago.

So are these the remnants of what was a much larger and more widespread group, whose northern members perhaps succumbed due to one of the ice ages?  Did they start in one of their homelands and move from there?

And if that's true, why are there no examples of trogons from all the places in between?

Another example of this is the order of mammals we belong to (Primata).  Primates pretty clearly originated in Africa and spread from there; the earliest clear primates were in the Paleocene Epoch, on the order of sixty million years ago, but the ancestor of all primates was probably at least twenty million years before that, preceding the Cretaceous Extinction by fourteen million years.  From their start in east Africa they seem to have spread both east and west, reaching southeast Asia around fifty million years ago.  Some of the earliest members to split were the lorises and tarsiers, along with the lemurs of Madagascar.

But the next group to diverge -- and the reason the whole topic of peripheral isolates came up -- are the "New World monkeys," the "platyrhines" of Central and South America.  It looks like this split happened during the Oligocene Epoch, around thirty million years ago... but how?

At that point, Africa was separated from South America by nine hundred miles of ocean -- narrower than the Atlantic is today, but still a formidable barrier.  But a paper in Science describes recently-discovered evidence from Peru of some fossilized primate teeth from right around the time the New World/Old World monkey split happened.

What this discovery suggests is staggering; all of the New World monkeys, from the spider monkey to the black howler monkey to the Amazonian pygmy marmoset, are descended from a single group that survived a crossing of the Atlantic, probably on a vegetation raft torn loose in a storm, only a little over thirty million years ago.

"This is a completely unique discovery," said Erik Seiffert, the study's lead author and Professor of Clinical Integrative Anatomical Sciences at Keck School of Medicine of the University of Southern California, in an interview with Science Daily.  "We're suggesting that this group might have made it over to South America right around what we call the Eocene-Oligocene Boundary, a time period between two geological epochs, when the Antarctic ice sheet started to build up and the sea level fell.  That might have played a role in making it a bit easier for these primates to actually get across the Atlantic Ocean."

So here we have a possible explanation for one of the long-standing puzzles of evolutionary biology.  Note that these puzzles aren't a weakness of the theory; saying "we still have some things left to explain" isn't the same as saying "the theory can't explain this."  There will always be pieces to add and odd bits of data to account for, but I have one hundred percent confidence that the evolutionary model is up to the task.

Now, I wish it could just come with an explanation for the trogons, because for some reason that really bothers me.

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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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