Sponges, bird brains, and ugly plants

There's a story about Socrates, who was asked what he thought about his reputation for being the smartest man in the world.

The great philosopher thought for a moment, and responded, "If I am, it is only because I alone realize how little I know."

I think there's something to this.  Ignorance confers a kind of cockiness sometimes; another great thinker, Bertrand Russell, once said, "The whole problem with the world is that fools and fanatics are always so certain of themselves, and wiser people so full of doubts."  It's inevitable that learning generates some level of humility, because one is always reminded of how much left there is to learn.

This is probably why I was so damn cocky as a college freshman.  Once I got to be a junior, I realized how foolish that was, as I got an inkling of how much I didn't know.  (Of course, nearly failing Classical Mechanics also had a dampening effect on my ego.  That was the moment I realized I didn't have the brains to be a physicist.)

Whenever I start perusing scientific journals -- a common occupation, as I'm looking for topics for Skeptophilia -- I'm amazed at what we've uncovered about the world we live in, and also how much there is left to learn.  That was one of my main takeaways from three scientific papers I came across last week; that, and a sense of wonder at how cool science is.

The first was a link sent to me by my buddy (and fellow writer) Gil Miller.  A paper in Nature by Elizabeth Turner, paleontologist at the Harquail School of Earth Sciences at Laurentian University, describes a find at a dig site in northwestern Canada that seems to contain fossils of one of the earliest and simplest animal groups -- sponges. 

What's mind-boggling about this discovery is that the rocks of the Stone Knife Formation, where the fossils were discovered, are about 890 million years old.  So if confirmed, this would predate the next-oldest undisputed sponge fossils by 350 million years.  This might just get a shoulder shrug, because most people -- myself included, unless I force myself to stop and think about it -- get lost when the numbers get large, so a 350 million year gap falls into the "it's big, but I can't visualize how big" category.  Let me put this number in perspective for you: if you went back 350 million years from today, you'd be in a world where there were no dinosaurs -- the earliest dinosaurs wouldn't appear for another 90 million years or so.

That's how far back Turner's discovery pushes the earliest animals.

If confirmed, this would place the origin of animals prior to the Cryogenian Period (also called the "Snowball Earth") of between 720 and 635 million years ago, one of the most massive worldwide glaciation events known.

The second paper, in Science Advances, is about the evolution of modern dinosaurs -- or, as we usually call them, "birds."  It's striking that the ancestors of today's birds survived a catastrophic bottleneck at the end of the Cretaceous Period 66 million years ago, caused by the double whammy of a massive meteorite collision and a near-simultaneous flood basalt eruption in what is now India.  (Scientists have yet to determine if the two events were connected -- if, perhaps, the collision destabilized the crust and caused the eruption.)

The paper centers on the discovery of a fantastically well-preserved fossil of Ichthyornis, an aquatic bird species of about 70 million years ago.  Picture a  gull with teeth, and you have a pretty good idea of what Ichthyornis looked like.  

Reconstruction of Icthyornis dispar [Image licensed under the Creative Commons El fosilmaníaco, Ichthyornis restoration, CC BY-SA 4.0]

What is remarkable about this fossil is the preservation of the skull, which gives the researchers a good look at the structure of the brain it once enclosed.  What they found is that the likelihood of a bird lineage surviving the bottleneck was largely due to one thing -- brain size.  Put simply, when the extinction came, the big dumb species tended to die out, and the small smart species survived.  

"Living birds have brains more complex than any known animals except mammals," said study lead investigator Christopher Torres, of the University of Texas and Ohio University.  "This new fossil finally lets us test the idea that those brains played a major role in their survival...  If a feature of the brain affected survivorship, we would expect it to be present in the survivors but absent in the casualties, like Ichthyornis.  That's exactly what we see here."

The third paper, in Nature, is about one of the world's weirdest plants -- Welwitschia mirabilis, of the deserts of Namibia.  The number of bizarre features of this plant are too many to list, but include:

• The plant can live thousands of years, but only ever has two leaves.  (The Afrikaans name for the plant, tweeblaarkanniedood means, "two leaves, doesn't die.)  The leaves are strap-like and can eventually grow to four meters in length.  They eventually get shredded by the wind into what looks like a giant pile of seaweed.
• The root is also about four meters in length, and looks like a giant carrot.
• Despite its appearance, its closest familiar relatives are conifers, like pines, spruces, and firs.

To me it falls into the "ugly but fascinating" category.

[Image licensed under the Creative Commons Muriel Gottrop, Welwitschia at Ugab River basin, CC BY-SA 3.0]

The current paper is about the Welwitschia genome, which has a number of interesting features.  First, it seems to have originated when there was a spontaneous duplication of the DNA about 85 million years ago that led to its being genetically isolated from its near relatives, after which it continued to develop along its own lines.  Duplication of the genome has an advantage -- providing extra copies of vital genes, so if mutation knocks out a copy, there's still a functional one available -- but it has the disadvantage of overproduction of gene products (too much of a protein can be as bad as not enough; this is why chromosomal duplications, as in Down syndrome, lead to developmental problems).

Welwitschia solved the disadvantage by a process called methylation, which chemically ties up and shuts down genes.  This is done during normal development in many species, where turning genes on and off at the right times is absolutely critical, and it also knocks out genetic parasites called transposons (a transposon is a segment of DNA that is able to copy itself and splice those copies elsewhere in the DNA -- a sort of copy-and-paste function gone haywire).  So Welwitschia ended up with a huge genome, of which a lot -- the researchers found about 55% -- is composed of shut-down transposons and other methylated (i.e. non-functional) sequences.

Also very weird is the balance between the different nitrogenous bases in Welwitschia's DNA.  You probably know that the "alphabet" of DNA is made up of four bases -- adenine, thymine, cytosine, and guanine -- and that they pair together like puzzle pieces, A with T, C with G.  So in normal DNA, there will always be exactly as much A as T and exactly as much C as G.

But the other ratios -- A to C, for example -- vary by species.  Still, the number of A/T pairs and C/G pairs is usually fairly close.  Unsurprisingly, this plant, which is an exception to so many rules, is an exception to this one as well -- only 29% of its DNA is made up of C/G pairs.

The upshot: this paper shows that an ugly but fascinating plant is even more interesting than we'd realized.

All of this, published just in the last week.  Which brings me back to Socrates.  I'm not claiming to be anywhere near as smart as he was, but I do share one belief with him.

So much to learn, so little time.

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Author and biochemist Camilla Pang was diagnosed with autism spectrum disorder at age eight, and spent most of her childhood baffled by the complexities and subtleties of human interactions.  She once asked her mother if there was an instruction manual on being human that she could read to make it easier.

Her mom said no, there was no instruction manual.

So years later, Pang recalled the incident and decided to write one.

The result, Explaining Humans: What Science Can Teach Us About Life, Love, and Relationships, is the best analysis of human behavior from a biological perspective since Desmond Morris's classic The Naked Ape.  If you're like me, you'll read Pang's book with a stunned smile on your face -- as she navigates through common, everyday behaviors we all engage in, but few of us stop to think about.

If you're interested in behavior or biology or simply agree with the Greek maxim "gnothi seauton" ("know yourself"), you need to put this book on your reading list.  It's absolutely outstanding.

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

Dinosaur redux

For me, one of the coolest things about science is that even once you think you've got something pretty well figured out, you can always find new interesting pieces of the puzzle.

For example, take dinosaurs, which we've known a good bit about for a long while, starting with Mary Anning's discoveries along the "Jurassic Coast" of Dorset, England in the early nineteenth century.  Even the kids' books when I was growing up back in the 1960s and 1970s had a lot of pretty decent information.  Although some of the reconstructions of skeletons, and (especially) our knowledge of the soft tissue that covered it, has changed since that time, it wasn't like I had to completely relearn the science when I studied it more seriously.

That said, we're still learning new stuff and adding to the picture.  Just this week we had two new papers that have sharpened the focus on our understanding of dinosaur evolution -- the first about the mid-Jurassic peak in dinosaur diversity and size, and the second about the event that wiped the entire lineage out, with the exception of the ones we now call birds.

The first paper is from Proceedings of the Royal Society B, and is titled "Extinction of Herbivorous Dinosaurs Linked to Early Jurassic Global Warming Event."  The paper was written by a team led by Diego Pol, paleontologist at the Paleontological Museum Egidio Feruglio in Trelew, Argentina, and looked at a hitherto-unexplained overturning of Jurassic fauna that made way for the rise of the sauropods -- the largest land animals that have ever lived.

Skeleton of Apatosaurus [Image licensed under the Creative Commons Tadek Kurpaski from London, Poland, Louisae, CC BY 2.0]

The early Jurassic had a high dinosaur diversity, but then toward the middle of the period something happened, and a good many of the early Jurassic dinosaurs vanished.  They were replaced by behemoths like the familiar Brachiosaurus and the less-well-known but hilariously-named Supersaurus, which measured an almost unimaginable 33 meters from tip to tail.  (Even better, though, is the name Dreadnoughtus, which was shorter than Supersaurus -- "only" 26 or so meters long -- but is thought to be the heaviest land animal ever, on the order of thirty metric tonnes.)

So what caused the replacement of the earlier species by the giants?  Pol and his team found what they think is the smoking gun, a series of massive volcanic eruptions in southern Gondwanaland (what is now South America and Africa), which spiked the carbon dioxide content of the air, boosting the average temperature and dropping the pH of ocean water.  

The perturbation of the climate affected the plants first.  Earlier groups, like seed ferns and other smaller herbaceous plants, were replaced by conifers, which have tough, lignified stems, small needles or scales instead of leaves, and thick waxy cuticles to prevent water loss.  The problem is -- if you're an early Jurassic herbivorous dinosaur -- having evolved to eat seed ferns, you're not going to do so well trying to munch pine needles.

So as it always does, the change to the base of the food web percolated its way up to the top.  The early dinosaurs were replaced by big sauropods, who had grinding teeth (so tough plant material could be thoroughly pulverized before swallowing) and large stomachs (where food could sit and digest for a long time, extracting all the nutritive value possible).  The result was the arrival on the scene of monsters like Supersaurus and Dreadnoughtus and their cousins, which were the dominant land herbivores for a good hundred million years thereafter.

Sometimes new evidence results in our having to revise our previous models, overturning what we thought we knew.  Take, for example, the research that appeared this week in Royal Society Open Science that conclusively put to rest a commonly-held idea -- that by the time the Chicxulub Meteorite hit the Earth 66 million years ago, dinosaurs were already in a steep decline, so they would have disappeared anyhow, even without the massive impact that was the final death blow.

In "Dinosaur Diversification Rates Were Not in Decline Prior to the K-Pg Boundary," by a team led by Joseph Bonsor of the London Natural History Museum and the University of Bath, we find out that the dinosaurs were actually doing okay before the meteorite hit.  Far from being in decline, they would have been very likely to retain their position as the dominant animals on Earth well into the Cenozoic Era -- with effects on mammalian evolution that can only be imagined.

Bonsor, as befits a good scientist, is cautious about overconcluding.  "The main point of what we are saying is that we don't really have enough data to know either way what would have happened to the dinosaurs," Bonsor said in a press release from the Natural History Museum.  "Generally in the fossil record there is a bias towards a lack of data, and to interpret those gaps in the fossil record as an artificial decline in diversification rates isn't what we should be doing.  Instead we've shown that there is no strong evidence for them dying out, and that the only way to know for sure is to fill in the gaps in the fossil record."

But in the absence of positive evidence for a decline, we're thrown back to the null hypothesis; that they weren't in imminent danger of extinction.  So the whole idea of the dinosaurs as some kind of "failed experiment" in evolution is clearly wrong.  Not only did they kind of run things for a good two hundred million years -- which, by comparison, is something like a thousand times longer than we've been around -- they would probably have persisted for a good long while had a giant rock not interfered.

Me, I always want to know "what if?"  I think it comes from being a novelist; I'm always wanting to play around with reality and see what happens.  If the dinosaurs had stuck around for a long time rather than dying out 66 million years ago, it's hard to see how the rise of mammals -- and ultimately, us -- would have occurred.  Mammals had been around for a long while before the Chicxulub Impact, but they were mostly small, presumably kept that way both by the big carnivores and by competition with herbivores much larger than themselves.  So what would the Earth look like today?

Super-intelligent dinosaurs?  Maybe.  Evolution doesn't always point in the direction of "bigger and smarter;" it's the law of whatever works.  So as fun as it is to speculate, to be fair we have to side with Bonsor and say we just don't know.

Anyhow, that's our look back into the distant past for today.  Cool that we're still assembling new views of an old branch of biology.  Further reinforcing my opinion that if you're interested in science, you will never ever be bored.

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This week's Skeptophilia book-of-the-week is one that has raised a controversy in the scientific world: Ancient Bones: Unearthing the Astonishing New Story of How We Became Human, by Madeleine Böhme, Rüdiger Braun, and Florian Breier.

It tells the story of a stupendous discovery -- twelve-million-year-old hominin fossils, of a new species christened Danuvius guggenmosi.  The astonishing thing about these fossils is where they were found.  Not in Africa, where previous models had confined all early hominins, but in Germany.

The discovery of Danuvius complicated our own ancestry, and raised a deep and difficult-to-answer question; when and how did we become human?  It's clear that the answer isn't as simple as we thought when the first hominin fossils were uncovered in Olduvai Gorge, and it was believed that if you took all of our millennia of migrations all over the globe and ran them backwards, they all converged on the East African Rift Valley.  That neat solution has come into serious question, and the truth seems to be that like most evolutionary lineages, hominins included multiple branches that moved around, interbred for a while, then went their separate ways, either to thrive or to die out.  The real story is considerably more complicated and fascinating than we'd thought at first, and Danuvius has added another layer to that complexity, bringing up as many questions as it answers.

Ancient Bones is a fascinating read for anyone interested in anthropology, paleontology, or evolutionary biology.  It is sure to be the basis of scientific discussion for the foreseeable future, and to spur more searches for our relatives -- including in places where we didn't think they'd gone.

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