The broken branch

When I first became interested in paleontology, I think what came as the biggest surprise was how many lineages had become completely extinct.

I knew about the dinosaurs, of course; everyone knew about the dinosaurs.  But I remember one of my books on prehistoric animals showing a family tree of mammals, and branching off way near the bottom was a line marked multituberculates, that suddenly just... ended.  What on earth were those?

Turns out they're a group of small, superficially rodent-like mammals with strange knobbly teeth, that thrived for 130 million years -- coexisting with the dinosaurs for much of it -- before suddenly and inexplicably vanishing during the Miocene Epoch.  But they were hardly the only broken branch on the tree.  There were also the massive, hulking brontotheres, including the famously slingshot-horned Brontops, that lived during the Paleocene and Eocene, dying out around 34 million years ago.  And around the same time there were the mesonychids, scary-ass carnivorous mammals that looked like a cross between a bear and a wolf but were actually more closely related to horses.

All three groups gone forever, leaving no descendants.

Far from being the common picture of a slow, gradual progression, from something like a worm to a fish to an amphibian to a reptile to a primitive mammal to primates to *trumpet fanfare* Homo sapiens, sitting of course on top of the evolutionary tree as befits the Pinnacle of Creation, the family tree of life is more like an unruly and tangled shrub with thousands of splits and bifurcations -- and just as many snapped-off branches.  Whole groups of organisms have turned into dead ends; I wrote a couple of years ago about the bizarre Ediacaran Assemblage, a group of Precambrian species that are so different than the familiar life forms we see around us today that paleontologists have been unable to determine where exactly they fit in the overall taxonomic scheme, or if perhaps they, too, left no descendants.

But they are hardly the only species that are, as the researchers put it, "of uncertain affinities."  In fact, the whole topic comes up because of a paper by Corentin Loron of the University of Edinburgh et al., that looked at a peculiar life form that was one of the first really huge terrestrial organisms, an eight-meter-tall... um... something called Prototaxites.

From their cell wall structure, they pretty clearly weren't plants.  The hypothesis was that Prototaxites was some kind of enormous fungus; a mushroom the size of a small tree, more or less.  But now... well, here's what Loron et al. found:

Prototaxites was the first giant organism to live on the terrestrial surface, reaching sizes of 8 metres in the Early Devonian.  However, its taxonomic assignment has been debated for over 165 years.  Tentative assignments to groups of multicellular algae or land plants have been repeatedly ruled out based on anatomy and chemistry, resulting in two major alternatives: Prototaxites was either a fungus or a now entirely extinct lineage.  Recent studies have converged on a fungal affinity...  Here we test this by contrasting the anatomy and molecular composition of Prototaxites with contemporary fungi from the 407-million-year-old Rhynie chert.  We report that Prototaxites taiti was the largest organism in the Rhynie ecosystem and its anatomy was fundamentally distinct from all known extant or extinct fungi.  Furthermore, our molecular composition analysis indicates that cell walls of P. taiti include aliphatic, aromatic, and phenolic components most similar to fossilisation products of lignin, but no fossilisation products characteristic of chitin or chitosan, which are diagnostic of all groups of extant and extinct fungi, including those preserved in the Rhynie chert.  We therefore conclude that Prototaxites was not a fungus, and instead propose it is best assigned to a now entirely extinct terrestrial lineage.

After reading this, my brain (being basically like the neural equivalent of a giant, out-of-control pinball game) immediately bounced from there to thinking about the "Abominable Mi-Go" from the Lovecraft mythos, which were giant race of creatures that lived in Antarctica when it was warm and habitable hundreds of millions of years ago, and were "fungoid, more vegetable than animal, but truly allied to neither."  Of course, in Lovecraft's universe, the Mi-Go also had wings and kidnapped people and stored their consciousness in what amounted to big metal test tubes, and I don't think Loron et al. think Prototaxites could do all that.

In any case, the current study is fascinating from a couple of standpoints.  First, that the world in the early Devonian would have looked drastically different than it does today -- no trees, and in fact barely any plants larger than club mosses and (very) early ferns.  And second, that there were these towering things sticking up in the landscape, like giant accusing fingers, bearing only a distant (and as-yet uncertain) connection to any other living organism.

Recent advances in paleontology have shown that the nineteenth-century conception of the Great Chain of Being was missing out on some of the most interesting parts -- organisms so different from today's nine-million-odd species that we can't even figure out quite where to pigeonhole them.  And as we uncover more fossil evidence, we're sure to find others, and add further branches to the snarled and twisted family tree of life on Earth.

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The forest primeval

There are some truly astonishing features of living things that are so familiar we stop even thinking about them, and somewhere near the top of that list are plant roots.

The evolution of true roots, which occurred back in the Silurian Period (444 to 419 million years ago), was a major advance over plants like bryophytes (a modern example is moss) that have only simple, unbranched extensions of the stem to hold them in place.  One of the first vascular plants -- plants with internal plumbing, allowing them to transport materials far more efficiently, and therefore grow much taller -- was Cooksonia, a bizarre-looking leafless plant that was nothing more than a bunch of stems each ending in a bulbous spore-production device.

By the Devonian Period (419 to 359 million years ago), this innovation had spread like wildfire, and plants related to today's ferns, horsetails, and club mosses had pretty much taken over the landscape.  There were still no flowering plants -- those wouldn't show up for another two hundred million years -- but our familiar mental image of prehistoric swamps, thick with giant ferns and conifers, populated by enormous dragonflies and centipedes, isn't so far off from the truth.

The reason this comes up is the recent discovery I learned about from a loyal reader of Skeptophilia, of a fossil site near Gilboa, New York, only a couple of hours east of where I live.  Virtually all of the rock in the southern tier region of New York is Devonian in age, mostly fossil-rich shales and limestones, and in an abandoned quarry paleontologists have discovered the fossils of an intricate (and huge) root network from an ancient forest.

The forest was primarily composed of members of two groups: the genus Archaeopteris, which looked a bit like modern Norfolk Island pines, although much more closely related to tree ferns:

[Image licensed under the Creative Commons Retallack, Archaeopteris reconstruction, CC BY-SA 4.0]

The other were the cladoxylopsids, which look like they were invented by Dr. Seuss:

[Image licensed under the Creative Commons Falconaumanni, Pseudosporochnales reconstruccion, CC BY-SA 3.0]

The site is being studied by a team led by paleontologists at nearby Binghamton University, who have thus far mapped over three thousand square meters of this forest extremely primeval.  They have speculated that when it was at its height, 386 million years ago, it extended all the way down into what is now northern Pennsylvania.

"It is surprising to see plants which were previously thought to have had mutually exclusive habitat preferences growing together on the ancient Catskill delta," said Chris Berry, of Cardiff University's School of Earth and Ocean Sciences, who co-authored the study.  "This would have looked like a fairly open forest with small to moderate sized coniferous-looking trees with individual and clumped tree-fern like plants of possibly smaller size growing between them."

This was toward the end of the Devonian, at which point the Earth was heading into a huge warm-up, leading to the sauna-like climate of the Carboniferous swamps.  During the Carboniferous Period, plants kind of took over the place, leading to oxygen levels of perhaps as high as 35% (compared to our current 21%).  The carbon dioxide sucked from the atmosphere and deposited as coal -- coal we are burning today, returning that primordial carbon to the modern air -- was putting gunpowder in the keg, setting up the biggest cataclysm life ever endured.  All through the Carboniferous and Permian Periods, the coal deposition continued, even as the temperature cooled (because of removal of the carbon dioxide).  Then, at the end of the Permian, one of the largest volcanic eruptions ever, the supervolcano that created the Siberian Traps, poured out an unimaginable four million cubic kilometers of basaltic lava.  That molten rock ripped through enormous swaths of buried Carboniferous and Permian coal, blowing all that carbon back into the atmosphere, along with large quantities of sulfur.

The result?  A sudden and massive jump in temperature, a catastrophic drop in atmospheric oxygen, and widespread oceanic anoxia and acidification.  The Permian-Triassic Extinction ensued, during which an estimated ninety percent of species on Earth went extinct.

But when the quarry site was a thriving, fern-filled forest, that was still all in the future.  What is now the maple and oak woodlands of the Catskills was a swampy, lowland thicket of some very strange-looking trees.  Fascinating that sitting here, 386 million years later, we can get a picture of what life was like back then, when the ecosystem was being shaped by one of the most important developments in plant evolutionary history -- roots.

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Roots of the problem

It's natural enough to think that humans are the only organisms that damage their own habitat.  We certainly seem to be doing a damn good job of it.  But there have been other times living things have sown the seeds of their own destruction.

One good example is the Great Oxidation Event -- sometimes, justifiably, nicknamed the "Oxygen Holocaust."  It occurred just over two billion years ago, and hinges on one rather surprising fact; oxygen is a highly reactive, toxic gas.

There's good evidence that aerobic respiration -- the set of biochemical reactions that allows us to burn the glucose in our food, and which provides us with the vast majority of the energy we use -- evolved first as a mechanism for detoxifying oxygen, and only afterward got co-opted into being an energy pathway.  The problem was that prior to the Great Oxidation Event, all of the organisms had been anaerobes, which are capable of releasing energy without oxygen.  To the vast majority of anaerobes, oxygen is a deadly poison.  That's why when there was a sudden, massive injection of oxygen into the Earth's atmosphere a couple of billions of years ago, the result was that just about every living thing on Earth died.

The tipping point came with the evolution of yet another energetic pathway: photosynthesis.  Photosynthesis was a tremendous innovation, as it allowed organisms to harness light energy instead of chemical energy, but it had one significant downside.  The first part of the reaction chain of photosynthesis breaks up water molecules and releases oxygen.  So when the first photosynthesizers evolved -- probably something like modern cyanobacteria -- oxygen gas began to pour into the oceans and atmosphere.

Something like 99% of life on Earth died.

The survivors fell into three groups: (1) the handful of organisms that had some early form of aerobic respiration as a detoxification pathway; (2) anaerobes that had a way of hiding from the oxygen, like today's methanogens that live in anaerobic mud; and (3) the photosynthesizers themselves.

From the organisms that survived that catastrophic bottleneck came every living thing we currently see around us.

So we're far from being the only organisms that cause ecological problems.  The reason the topic comes up, in fact, is because of another example I'd never heard of until I bumped into a paper in the Geological Society of North America Bulletin last week; the Devonian mass extinctions, which are one of the "Big Five" extinction events that have struck the Earth.  This particular series of cataclysms wiped out an estimated seventy percent of marine species, but it may have been triggered by the evolution of something that seems innocuous, even benevolent.

Tree roots.

Plants had only colonized the land during the previous period, the Silurian, enabled to do so by yet another innovation; the evolution of vascular tissue.  The internal plumbing vascular plants have (the xylem and phloem you probably remember from your biology classes) allow plants to move water farther and faster, so they were no longer so tied to living in ponds and lakes.  Plus, vascular tissue in many plants doubles as support tissue, so this facilitated growing taller (a significant advantage when you're competing with your near neighbors for light).

But if you're taller, you're also more likely to topple when it's windy.  So then there's selection for who's got the best support system.  The winners: plants with roots.

Devonian Forest by Eduard Riou (ca. 1872) [Image is in the Public Domain]

Like vascular tissue, roots are multi-purpose.  They not only provide support and anchoring, they're good at creating lots of absorptive surface area for water and nutrients.  (Some roots are also evolved to store starch -- carrots come to mind -- but that's an innovation that seems to have come much later.)  So now we have a competition between plants for who's got the best supports, and who can access nutrients from the soils the fastest.

Roots very quickly became good at twisting their way into rocks.  You've undoubtedly seen it; tree roots clinging to, and breaking up, rocks, asphalt, cement, pretty much any barrier they can get a foothold into.  When that happened, suddenly there's an erosive force breaking up bedrock and transporting nutrients (especially phosphorus) into plant tissue.  Phosphorus began to leach out of the rock into the soil, and when the plants died all the phosphorus in the tissue was released into rivers, streams, and lakes.

The result was a massive influx of nutrients into bodies of water.

Have you ever seen what happens when chemical fertilizers get into a pond?  It fosters algal blooms, and when the algae dies and decomposes, the oxygen levels plummet and the entire pond dies.

That's what happened during the late Devonian Period -- but planet-wide.

The huge reef-building rugose and tabulate corals and stromatoporid sponges were wiped out en masse.  Other groups, such as trilobites and brachiopods, which depended on the reefs for habitat and food, got knocked back hard as well.

All, the authors claim, because of a nifty innovation in the structure of land plants.

It's tempting to think that the environment is stable; we look around us and think things have always been this way, and will always be this way.  What more of us need to understand is that while the global ecosystem is resilient up to a point, there is always a tipping point.  The scary part is we can pass that point suddenly, without even realizing it.  Then before we're even aware of what's happened, the last chance to turn things around is gone.

The difference between what happened during the Great Oxidation Event and the Devonian Mass Extinctions, and what's happening now, is that back then there was no conscious awareness on the part of the organisms who created the problem and those that were affected.  Now, we have (or should have) the awareness to see what is happening, and enough knowledge to make some smart decisions and halt the self-destructive path we're on.

Let's hope that it's not too late.

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Shake your tail feathers

My wife and I reset some pavers in our front sidewalk a couple of days ago.  In our area, most of the stone used for paving and wall-building is native slate and limestone, which make up the majority of the bedrock in this part of upstate New York; and given slate's tendency to fracture naturally along parallel planes, it makes an obvious good choice for paving stones.

We used a pry-bar to pull up one big stone -- maybe a meter across and two meters long -- and a piece of it sheared off.  Unfortunate but unavoidable.  When I stopped and picked up the chunk, a flat, triangular piece a little larger than the palm of my hand, I noticed something interesting about it.  It had ripple marks, the clear signature of the muddy environment where it formed.

Seeing this sort of thing always makes me imagine what things were like back then.  The rocks in this area are Devonian in age, on the order of four hundred million years old, at which time this whole area was at the bottom of a shallow sea.  So those ripple marks in my sidewalk paving stone were created by water movements that occurred so long ago it's hard to imagine.  At that point, there was virtually no terrestrial life -- a few plants and insect species had colonized the land, but everything else was still aquatic.  The first dinosaurs were still a good 150 million years in the future.

It's kind of cool the way these sorts of moments thrill me from two different perspectives.  Being a biology teacher (retired now), I find it absolutely fascinating to ponder the grand panorama that is the history of life on Earth, and to consider evolution's role in creating what Darwin famously called "endless forms most beautiful and most wonderful."  As a novelist, it never fails to fire my imagination -- to picture what it would be like to stand there on the beach with the bare, treeless Devonian landscape stretching out behind me, looking out over oceans where swam trilobites and bizarre armored fish (ostracoderms) and ammonites, all of which went extinct long, long ago.

The reason this comes up -- besides finding signs of four-hundred-million-year-old ocean waves in my slate sidewalk paver -- is a link sent to me (once again) by the indefatigable Gil Miller, about a fossil discovery found in northeastern China recently.  It's the fantastically well-preserved remains of a little feathered dinosaur from 120 million years ago called Yuanchuavis kompsosoura, which was about the size of a blue jay -- but had a thirty-centimeter-long tail, which is longer than its entire body.

Yuanchuavis kompsosoura

Extravagant tails like this are an interesting case of an evolutionary trade-off.  Modern birds like peacocks have tails so long they're actually a hindrance to flying, but apparently the disadvantages of having such a clumsy appendage are outweighed by the advantage in terms of attractiveness to potential mates (sexual selection).  It's theorized that having elaborate plumage is a way of advertising your overall genetic health.  "Look at me," they say.  "I am so genetically superior I can throw away all sorts of energy and resources on something completely frivolous.  I am totally who you want to have sex with."

Kind of the bird version of driving a Jaguar.

That sort of teleological reasoning, however, is always thin ice when you're talking about evolutionary drivers.  None of that selection is being done because of any kind of conscious weighing of options.  But whatever its basis, we see similar kinds of wild tails in a great many bird species today -- swallowtailed kites, African widowbirds, paradise flycatchers, quetzals, drongos, and a lot of hummingbirds, as just a few examples.  The fact that so many relatively unrelated species have gone down the same path supports the conjecture that whatever is propelling this selection, it's pretty powerful.

Reading the article about this fascinating little dinosaur immediately switched on the other mode, which led me to imagining what it actually looked like when alive, and wondering about its behavior and environment.  Of course, even most well-preserved fossils give you only a hint about what the living creature looked like; all the spots and patterns and colors in movies like Jurassic Park are guesses, as are the behaviors (like the dinosaur with the toxic spit that killed Dennis Nedry).  But here, the preservation is on such a fine scale that the paleontologists do have an idea of what color it was -- traces of pigment-producing cells suggest that the fan part of its tail was gray, and the two long banner feathers in the middle were jet black.

Here, we actually can visualize what it looked like when he was shaking his tail feathers in the early Cretaceous forests.

So that's our imagined trip into deep time for today.  I know I've quoted it here before, but the lines from Tennyson's "In Memoriam" are so poignant and so apposite that I will end with them anyhow:

There rolls the deep where grew the tree.
O Earth, what changes hast thou seen?
There where the long road roars hath been
The stillness of the central sea.

The hills are shadows, and they flow
From form to form, and nothing stands;
They melt like mist, the solid lands,
Like clouds, they shape themselves and go.

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Like graphic novels?  Like bizarre and mind-blowing ideas from subatomic physics?

Have I got a book for you.

Described as "Tintin meets Brian Cox," Mysteries of the Quantum Universe is a graphic novel about the explorations of a researcher, Bob, and his dog Rick, as they investigate some of the weirdest corners of quantum physics -- and present it at a level that is accessible (and extremely entertaining) to the layperson.  The author Thibault Damour is a theoretical physicist, so his expertise in the cutting edge of physics, coupled with delightful illustrations by artist Mathieu Burniat, make for delightful reading.  This one should be in every science aficionado's to-read stack!

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

The forest primeval

One of the reasons I'm so fascinated with paleontology is that it induces me to picture what the Earth looked like a loooooooong time ago -- and to consider a planet that was nothing at all like it is now.

I remember when I first realized something about the three earliest periods of Earth's history -- the Precambrian, Cambrian, and Ordovician -- from a kids' book on prehistory, when I was maybe ten years old.  There was a casual statement that during these periods, there was no life on land.  Every living thing there was lived in the water.

And I thought, "Wait, that can't mean what it sounds like."

But it does.  During those three periods -- which together comprise 90% of the history of the Earth -- the land masses were completely barren.  Rock, sand, dust, dirt (with no organic matter whatsoever), stretching over entire continents.

You think the Sahara is a vast wasteland.  Every square kilometer of the early Earth looked like that, without even the occasional palm tree or camel to break the monotony.

Strange to think of an Earth so unlike what we see around us today.  Even after life colonized the land -- starting with plants living around the margins of bodies of water, in the early Silurian -- it would still have looked pretty foreign, and I'm not just talking about dinosaurs, here.  During the Carboniferous Period there were dragonflies with three-foot wingspans, and centipedes almost big enough to ride.  The Devonian, one step earlier, had some fish called placoderms that look like they're wearing poorly-fitting plate armor.

[Image licensed under the Creative Commons, Nobu Tamura (http://spinops.blogspot.com), Dunkleosteus BW, CC BY 3.0]

In fact, it was a discovery dating to the Devonian that spurred me to write this post.  Last week a paper appeared in Current Biology about a fossilized forest in Xinhang, China that spreads over 250,000 square meters.

Quite a significant find.

Don't, however, picture your typical forest here.  These weren't oaks and maples and pines, they were lycopsids, a group now represented only by club mosses, small and generally unassuming plants you'll find in moist forest understories.  But in the Devonian, they got big.  The largest were over seven meters tall, or about the size of your average dogwood or crabapple tree.

But they didn't look anything like modern trees.  More like something Doctor Seuss would have drawn.

[Image licensed under the Creative Commons Tim Bertelink, Lepidodendron, CC BY-SA 4.0]

Imagine a whole forest of these short, skinny trees and you've got the idea.

"The large density as well as the small size of the trees could make the Xinhang forest very similar to a sugarcane field, although the plants in Xinhang forest are distributed in patches," said Deming Wang, a professor in the School of Earth and Space Sciences at Beijing University, who co-authored the study.  "It might also be that the Xinhang lycopsid forest was much like the mangroves along the coast, since they occur in a similar environment and play comparable ecologic roles."

So our picture of this odd world, when fish were the dominant life-form and the only land animals were primitive amphibians, insects, and arachnids, is becoming more complete.  Think about that next time you go for a walk in the woods.  You might not only ponder what the land you're walking on looked like 400 million years ago, but how different it might look like 400 million years from now -- during which evolution will have had plenty of time to generate, as Darwin put it, "endless forms most beautiful and most wonderful."

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This week's Skeptophilia book recommendation is sheer brilliance -- Jenny Lawson's autobiographical Let's Pretend This Never Happened.  It's an account of her struggles with depression and anxiety, and far from being a downer, it's one of the funniest books I've ever read.  Lawson -- best known from her brilliant blog The Blogess -- has a brutally honest, rather frenetic style of writing, and her book is sometimes poignant and often hilarious.  She draws a clear picture of what it's like to live with crippling social anxiety, an illness that has landed Lawson (as a professional author) in some pretty awkward situations.  She looks at her own difficulties (and those of her long-suffering husband) through the lens of humor, and you'll come away with a better understanding of those of us who deal day-to-day with mental illness, and also with a bellyache from laughing.

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