Birds, bees, etc.

Yesterday I was thinking about sex.

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

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

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

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

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

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

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

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

TOBEORNOTTOBETHATISTHEQUESTION

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

TOBGORNOTTOBETHATISTHEQUESTION

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

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

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

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

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

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

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

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Gender bender

Sex is a pretty cool phenomenon, and it's not just because it's kinda fun.

How exactly sexual reproduction first evolved isn't well understood, but its advantages are clear.  Asexually-reproducing species, like most bacteria, a good many protists, and a handful of plants and animals, result in genetic copies -- clones, really -- of the parent organism.  

The problem with this is twofold.  First, clones (being identical) are susceptible to the same pathogens, so a communicable disease that is deadly to one of them will wipe them all out.  In a genetically-diverse population, chances are there'd be some that were resistant or entirely immune; in a monoculture, one epidemic and it's game over.  (That's basically what caused the Irish Potato Famine; a one-two punch of cold, rainy weather and an outbreak of late blight killed nearly all of the island's potato crop, resulting in massive starvation.)

The second problem, though, is subtler, and causes problems even if there's no external environmental risk involved.  It's called Muller's Ratchet, named after American geneticist Hermann Muller, who first described the phenomenon.  Asexual species still undergo variation because of random mutations; at each generation, the DNA picks up what amount to typos.  The whole thing is like a genetic game of Telephone.  Each time the genes pass on, there are minor replication errors that accrue and ultimately will turn the whole genome into unintelligible garbage.

Various asexual species have evolved mechanisms for coping with Muller's Ratchet.  Some bacteria have multiple copies of critical genes, so if one copy gets knocked out by a mutation, they have other copies that still work.  Some evolved conjugation, which is a primitive form of sexual reproduction in which cells pair up and exchange bits of DNA, with the goal being the sharing of undamaged copies of important genes (as well as copies of any novel beneficial mutations that may have occurred).

So asexual reproduction is fast, efficient, and doesn't require finding a partner, but ultimately makes the species susceptible to the double whammy of disease proneness and Muller's Ratchet; sexual reproduction requires finding a partner, but increases overall fitness by improving genetic diversity.

Is there any way to gain both advantages without picking up the disadvantages at the same time?

This is one of the main drivers of evolution in flowering plants.  Some flowering plants can reproduce both sexually (through flowers) and asexually (through rhizomes, bulbs, and so on).  Grasses, for example, are pretty good at both.  A very few -- the commercial variety of bananas is one of the only ones that comes to mind -- only reproduce asexually.  (Which is why bananas have no seeds, and also why growers are in a panic over the spread of fusarium wilt.)  A lot of plant species only reproduce sexually, and this brings up the problem of finding a partner of the opposite sex -- which is difficult when you are stuck in place.

This is where pollinators come in.  Some flowering plants are wind-pollinated, and rely on the air to carry the pollen (containing the male gametes) to the ovules (containing the female gametes).  Others use nectar or color lures to bring in insects, birds, and even a few mammals to act as couriers.  But this risks having the pollinator simply double back and fertilize a flower on the same plant, meaning that the offspring is (more or less) identical to the parent -- obviating the advantage of sexual reproduction.

So a great many species have evolved mechanisms for facilitating cross-pollination and avoiding self-pollination.  Some of the brightly-colored flowers of plants in the genus Salvia have evolved a mechanism where there's a spring-loaded trigger -- a visiting bee trips the trigger and gets smacked by the pollen-bearing stamen, with the intention of startling it enough that it decides to move along and visit a different individual of the same species.  Many orchids have wildly byzantine mechanisms for maximizing the likelihood of cross-pollination.  Other species, such as some of the fruiting trees of the rose family (including cherries, apricots, and peaches) have bisexual flowers, but the stamens of one tree mature at a different time than the ovules do -- making self-pollination impossible.  Apples have a genetic barrier to self-pollination -- if pollen from an apple flower is brought to another flower on the same tree, it recognizes the ovule as genetically identical and simply doesn't fuse.

The reason this comes up is a study that appeared last week in the journal Science, looking at the genetics of gender and pollination in walnuts.  Walnuts, and most of the other members of the family Juglandaceae (which also includes hickories and pecans), are pollinated by the wind.  

[Image licensed under the Creative Commons Juglans regia Broadview, CC BY-SA 3.0]

Wind-pollinated plants are most at risk for accidental self-pollination; the wind, after all, isn't going to be attracted or deterred by any kind of mechanical contrivance, and wind-pollinated plants often produce tons of pollen (to maximize the likelihood of at least some of it hitting the target, since inevitably a lot of it is simply blown away and wasted).  This is, incidentally, why most allergy-inducing pollen comes from wind-pollinated plants like grasses, willows, birch, oak, cedar, and (especially) ragweed.

Walnuts, it turns out, solve this problem by switching sex every few weeks -- a particular tree only produces male flowers during one interval, then only female ones the next.  The following year, they do it again -- but changing the order of who is male when.  This renders self-pollination not just unlikely, but impossible.  And the paper, which came out of research at the University of California - Davis, describes the genetic mechanism for how this is controlled.

Oh, but you bigots, do go on and explain to me how in the natural world sex and gender are simple and binary, they're both fixed at conception, male-and-female-He-made-them, and so on and so forth.

Even after years of studying biology, and evolutionary biology in particular, I'm still astonished by the diversity of life, and how many solutions species have evolved to solve the problems of survival, nutrition, and reproduction.  It seems fitting to end this with the final paragraph of Charles Darwin's Origin of Species, which echoes that same sense of wonder:

It is interesting to contemplate a tangled bank, clothed with many plants of many kinds, with birds singing on the bushes, with various insects flitting about, and with worms crawling through the damp earth, and to reflect that these elaborately constructed forms, so different from each other, and dependent upon each other in so complex a manner, have all been produced by laws acting around us.  These laws, taken in the largest sense, being Growth with reproduction; Inheritance which is almost implied by reproduction; Variability from the indirect and direct action of the conditions of life, and from use and disuse; a Ratio of Increase so high as to lead to a Struggle for Life, and as a consequence to Natural Selection, entailing Divergence of Character and the Extinction of less improved forms.  Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.  There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.

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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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The floral death trap

One of the most interesting features of evolution is coevolution -- where two unrelated species influence each other's evolutionary pathway.

It's usually framed as benevolent, providing a benefit for both species, as in the whistling thorn (Vachellia drepandolobium) of East Africa, which makes hollow spheres at the base of the spines.  These provide a home for various species of symbiotic ants, which help out the tree by attacking and killing insect pests that might eat the leaves.  (It's called "whistling thorn" because the wind blowing across the holes in the spheres makes a whistling noise.)

There's also the less pleasant sort, the best-known of which is the evolutionary arms race -- such as the cheetah and the impala.  The fastest cheetahs catch and eat the slowest impalas, thus pushing both species to (on average) get faster.  (The general consensus, though, is that the cheetah might have topped out in terms of potential speed -- the combination of their powerful muscles and flexible spine and limbs would make them prone to dislocations and stress fractures if they were driven much harder.)

A relationship that's usually portrayed as entirely positive, though, is the one between flowering plants and their pollinators.  One of the earliest vindications of Darwin's theory of natural selection came with his conjecture that the Star of Bethlehem orchid (Angraecum sesquipedale) of Madagascar, which has a ridiculously long hollow spur at the back of the flower (with the nectar glands all the way at the tip), must have a pollinator with mouthparts that fit it:

[Image licensed under the Creative Commons sunoochi from Sapporo, Hokkaido, Japan, Angraecum sesquipedale Thouars, Hist. Orchid. 66 (1822) (45523703575), CC BY 2.0]

Not long afterward, researchers discovered the Madagascar hawk moth (Xanthopan morganii praedictum), exactly as Darwin said they would:

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

In fact, the coevolution between flowering plants and insects is so varied and complex that some evolutionary biologists claim it's responsible for the explosion in biodiversity in both groups that started during the early Cretaceous Period.  This, they say, is why flowering plants outnumber all other plant species by a considerable margin, and insect species outnumber all the rest of Earth's species put together.  (My own opinion is that it's probably not that simple -- evolutionary drivers seldom are.  But I won't deny that coevolution played a significant role.)

What's kind of interesting, in a grim sort of way, is when the coevolution between plants and their pollinators takes a darker turn.  One example, that is so crazily complicated that I had students tell me I was making the whole thing up, is the bucket orchid (Coryanthes spp.) of South America.  These bizarre-looking flowers have some upright petals, but the lower ones are fused into a "bucket" that fills with sweet-scented nectar.  The pistil (the female part of the flower) is submerged at the bottom.  One genus of bees (Euglossa spp.) is attracted to the scent, but upon landing on the edge of the bucket, finds no place to hang onto and falls in.  It swims around trying to find a way out, but the sides of the bucket are coated with a slick wax that provides no traction.  There's only one place it can get out -- at the back of the bucket is a ladder (I shit you not) made of hairs the bee can hang onto.  But when it gets to the top of the ladder, it finds itself head-first in a long tube with no place to turn around, so it wriggles its way to the end -- in the process gluing the anthers (the male pollen-bearing structures) to its back.  At the end of the tube is a hole (whew), and the bee flies away.  But then -- not having learned its lesson, apparently -- it finds another flower, falls in again, and this time the nectar acts as a solvent.  The anthers it was carrying come loose and settle to the bottom of the bucket (remember, that's where the pistil is), and pollinates the plant.

[Image licensed under the Creative Commons Orchi, Coryanthes hunteriana Orchi 01, CC BY-SA 3.0]

But at least here, it has a happy ending -- the bee escapes eventually.  There are, however, plants that kill their own pollinators -- in fact, that's the reason this whole topic comes up, because another one was just discovered recently.

The first one I ever heard about that pulls this nasty trick is a species of African water lily (Nymphaea capensis).  It's deceptively beautiful:

[Image licensed under the Creative Commons Fan Wen, Nymphaea capensis (14) 1200, CC BY-SA 4.0]

The flowers open twice, on two successive days.  The first day, the pistils are inaccessible beneath a tight cone of stamens (the above photograph was taken on the first day).  Bees landing on the flower are doomed to disappointment, because the nectar is inside the cone, but in trying to get to it they coat themselves with pollen.  The flowers close at night, then when they open on the second day, the cone of stamens opens as well, exposing a tempting pool of nectar with (once again) the pistil at the bottom.  A bee, having just visited a first-day flower and come away with no food but lots of pollen, lands on the edge of the pool in the middle of a second-day flower, and falls in.  This time, though, there's no escape.  It drowns, and the pollen it's carrying settles to the bottom of the pool and fertilizes the flower -- thus ensuring the plant will cross-pollinate, not self-pollinate.

What brought this topic to mind was a paper I stumbled across yesterday in the journal Plants, People, Planet that describes the same sort of fatal deception, but using a different kind of lure.  A Japanese species of the genus Arisaema, which in the United States is best known for the spring wildflower we call Jack-in the-pulpit (Arisaema triphyllum), that is common here in the northeast.  They have bizarre flowers -- a long, inverted cone with a flap on top (it's actually a spathe, a modified leaf), and in the middle a narrow cylinder (containing the actual flowers themselves, which are tiny).  If they're not weird enough from appearance alone, wait till you hear what some of the Japanese species do.

Arisaema angustatum (left) and Arisaema peninsulae (right), two of the tricksters described in the paper [Photograph by Kenji Suetsugu] 

These flowers are pollinated by fungus gnats -- familiar as annoyances to anyone who owns a greenhouse -- pinhead-sized flies that are attracted to moist soil.  Well, the plants don't just lure them by pretending to be a source of food.  The researcher, Kenji Suetsugu of Kobe University, realized something else was going on when he found that inside the cone-shaped spathe there were dozens of dead fungus gnats...

... all of them male.

Suetsugu started analyzing what chemicals the flowers were producing, and found that like the water lily, the Arisaema flowers change during the time they're open.  At first, only the male flowers are open, and fungus gnats that find their way in (presumably lured by the musty smell the plant has) climb about and pick up pollen.  But then the male flowers close and the female ones open -- and the strategy changes.

When the male flowers only are open, there's a little escape hatch at the base of the flower, so the gnats can get out after picking up pollen.  But when the female flowers open, the escape hatch closes.  And that's when the plants start producing a new chemical: an analog to the sexual attractant pheromone female fungus gnats produce to attract the males.

So the poor male gnats, hoping to get laid, find their way into the flower, but there's no way out because (again like the water lily) the interior of the cone is slippery.  They climb around on the female flowers, pollinating them, but eventually die from a combination of exhaustion and frustrated horniness.

If you thought that the relationship between flowers and pollinators was all mutual happiness, think again.  "Nature is red in tooth and claw," as Alfred, Lord Tennyson put it.  He was thinking of predators and prey, but it isn't restricted to the animal kingdom.  There are plants that reward their pollinators with an unpleasant demise -- showing that once again, evolution finds a way to exploit just about every possible innovation you can think of, nice or not.

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A botanical mystery

One of the most pernicious tendencies in human thought is our arrogance.  The attitude that we know all there is to know, understand the universe, have it all figured out, has led to more oversights, blunders, and outright idiocy than anything else I can think of.

What's striking is how often our intuition about things turns out to be wrong.  Consider, for example, the following question: of all the species currently alive on Earth, what percent of them are known to science -- identified, observed, collected, or studied?

The best estimate we have, from a 2011 study that appeared in PLoS Biology, blew my mind, and as a 32-year veteran of teaching biology, I was ready for an answer lower than my expectation.  You ready?

Fourteen percent.

The study estimated the total number of species on Earth at 8.7 million, 86% of which are unknown to science.  This is staggering.  We are fooling around with our climate and ecosystems, bulldozing our way through our own living space, and potentially destroying millions of species we didn't even know existed.

To be fair, our ignorance about the organisms we share the planet with is at least in part not our fault.  If, like me, you live in a comfortable home with amenities and no particular need to venture off into the wilderness, it would be easy to think that our familiar surroundings are all there is.  The truth is a little humbling, and far more interesting.  I remember my first trip to Hawaii, back in 2003, when we spent our time on the lovely island of Kauai.  While we were there, we took a boat trip out to the Na Pali Coast, a stunning terrain that has a few narrow sandy beaches, but almost immediately beyond them wrinkles up into mountains that are in places damn near vertical.

Carol and I at Na Pali

The guide on the boat told us something that I found astonishing; large parts of Waimea Canyon and Koke'e Parks, which lie inland from Na Pali, are completely unexplored.  Not only is it too steep for roads to be built, you can't even land a helicopter.  Hiking might be possible, but it's densely forested.  The combination has made the interior of these parks one of the few places in the United States where we can say with fair confidence that no human being has ever stood.

Add to that the fact that even more unexplored than some of the remote terrestrial regions are the deep oceans.  I've heard it said we know more about the terrain of the Moon than we do about the floor of the deep ocean -- I don't know if that's true, but it sure sounds plausible.

I'd like to consider, though, a more positive thought; that our lack of knowledge of other species on Earth means there is a lot out there that we could still potentially learn.  And sometimes that happens through unexpected channels.  In fact, the reason this whole topic comes up is because of an article last week in Atlas Obscura about a British botanist and biological artist named Marianne North (24 October 1830-30 August 1890), who traveled all over the world painting native plants in intricate detail -- and who captured an image of at least one plant nobody could identify.

The painting in question was made in Sarawak, one of two states of Malaysia that are on the island of Borneo.  Sarawak is a bit like Kauai; inhabited at the perimeter, but with an inland of rugged terrain and dense, nearly impenetrable forest.  Well, this kind of thing didn't stop North, who made some exquisite paintings of plants in Sarawak, including this one:

[Image is in the Public Domain]

The plant with the blue berries was unidentified -- some botanists thought it might be a member of the tropical genus Psychotria (in the coffee family, Rubiaceae).  But something about that didn't ring true.  None of the 1,582 catalogued species of Psychotria has blue berries -- all the known ones are red or pink -- and the arrangement of the leaves didn't look quite right.  So either (1) this one was an anomaly, (2) North painted the plant inaccurately, or (3) the identification was wrong.

Option (1) was a little far-fetched, but not outside the realm of possibility.  Option (2) struck most knowledgeable people as outright impossible; North was known for her absolute painstaking attention to minute detail.  So botanist and illustrator Tianyi Yu decided (3) had to be correct.  But how to find a single species of plant in an overgrown wilderness on the island of Borneo, which had avoided detection by other scientists for over a century?

Yu had a brainstorm; maybe it hadn't completely flown under the radar.  He decided to spend some time in the herbarium at Kew Gardens.  If you are ever in England, Kew is a must-see; it is home to one of the most amazingly complete collection of plants in the world, and is also stunningly beautiful, especially in spring and summer.  The herbarium contains collections of preserved plants stretching back to its founding in the middle of the nineteenth century, and currently houses over eight million specimens.

So saying it was a needle in a haystack is an understatement.  Yu had one thing going for him; North had been not only a meticulous artist, she was also conscientious about writing down where her paintings had been made.  This one was labeled "Matang Forest, Sarawak," and since the Kew specimens are catalogued not only by species but by location, it significantly narrowed down Yu's search.

And he found it.  A sprig of it was collected in 1973 and sent back to Kew, but was unidentified.  Yu studied both the specimen and North's painting, and concluded that it was a member of the genus Chassalia -- also in Rubiaceae, so the guess of Psychotria hadn't been that far off.

Further analysis by botanists confirmed Yu's surmise.  As the person who identified it as a previously-unrecorded species, Yu was given the honor of naming it.

And last year, it went down in the taxonomic records as Chassalia northi, in recognition of Marianne North's contributions to the field of botany.

So out there on the island of Borneo is a little shrub with white flowers and blue berries that we now have a name for because of a nineteenth-century adventurer/scientist/artist, a happenstance collection from 1973, and a diligent modern botanist determined to put the pieces together.  Just showing that we can still pick away at the sphere of our own ignorance -- but only if we are first willing to admit that there is a lot we still don't know about the world we live in.

**************************************

The mystery from Manu

So much of the damage we've done to the planet hasn't been deliberate destructiveness; it's been due to our carelessly stomping about the place.  We've long had the attitude that resources will never run out, that we can get away with doing whatever we want with no consequences, that nature will rebound like it always does.  There's little awareness of the absolute fragility of it all.

The "bull in a china shop" metaphor seems all too apt.

Of course, that mindset does require a good dollop of willful ignorance.  Just two weeks ago, the United States Fish and Wildlife Service declared that 22 species in the US that were previously classified as critically endangered are now officially considered extinct.  The most famous of them is the Ivory-billed Woodpecker, the largest woodpecker species native to North America, victim to habitat loss as the wetland forests where it lived were drained, the trees felled for lumber.  A full nine of the 22 are bird species endemic to Hawaii, eight of them part of the unique group called Hawaiian honeycreepers that were decimated by the double whammy of habitat loss and susceptibility to avian malaria, carried by the introduced Asian tiger mosquito.

So to think "everything's just fine" you have to make a practice of not paying attention.

One of the problems is that in some of the most vulnerable places in the world, species are disappearing before they're even identified and studied.  Take, for example, the species of tree native to the Amazon basin of Peru that was first seen by scientists in 1973 -- and that has just now been classified and named.

Robin Foster of the Smithsonian Tropical Research Institute was the one who noticed it, while walking in Manu National Park -- and despite a thorough knowledge of Amazonian flora, he couldn't figure out what it was.  "When I first saw this little tree, while out on a forest trail leading from the field station, it was the fruit -- looking like an orange-colored Chinese lantern and juicy when ripe with several seeds -- that caught my attention," Foster said.  "I didn't really think it was special, except for the fact that it had characteristics of plants in several different plant families, and didn't fall neatly into any family.  Usually I can tell the family by a quick glance, but damned if I could place this one."

So Foster sent a branch of the plant to the Field Museum of Chicago, where it sat in the herbarium for almost fifty years.  When DNA analysis became de rigueur for doing taxonomy, back in the 1990s, researchers tried extracting DNA from the dried leaves -- unsuccessfully.  Then last year, scientist Patricia Álvarez-Loayza, who is part of the team that studies the ecosystem in Manu National Park, found a living specimen of the tree, and this time the DNA extraction worked.

Aenigmanu alvareziae

The results were a shock to botanists, because it showed beyond any question that the little tree belonged to an obscure tropical family called Picramniaceae, made up of 48 (now 49) species native to northern South America, Central America, and the Caribbean, but not common anywhere.  "When my colleague Rick Ree sequenced it and told me what family it belonged to, I told him the sample must have been contaminated.  I was like, no way, I just couldn't believe it," said Nancy Hensold of the Field Museum, part of the team that studied the plant and finally identified its affinities.  "Looking closer at the structure of the tiny little flowers I realized, oh, it really has some similarities, but given its overall characters, nobody would have put it in that family." 

The plant was christened Aenigmanu alvareziae -- the genus name means "mystery from Manu," while the species name honors Patricia Álvarez-Loayza, who found the living specimen that helped to place the species.

What strikes me about this whole story is how easily the branch of this little tree could have been forgotten in the herbarium, or the plant itself overlooked completely.  The Amazon is a big place, large swaths of which are unexplored.  While one odd plant species may not seem all that important, this does give us a sense of the extent to which we're blundering around damaging living ecosystems without even understanding them fully.  "Plants are understudied in general," said Robin Foster, the first scientist who noticed Aenigmanu back in 1973.  "Especially tropical forest plants.  Especially Amazon plants.  And especially plants in the upper Amazon.  To understand the changes taking place in the tropics, to protect what remains, and to restore areas that have been wiped out, plants are the foundation for everything that lives there and the most important to study.  Giving them unique names is the best way to organize information about them and call attention to them.  A single rare species may not by itself be important to an ecosystem, but collectively they tell us what is going on out there."

Conservation isn't some kind of academic game, and rare species shouldn't just be of interest to the taxonomists.  We need to understand on a visceral level that you can't pull threads out of the tapestry of life without the entire thing coming unraveled.  Chief Seattle said it best, back in 1854: "The Earth does not belong to man; man belongs to the Earth.  This we know.  All things are connected like the blood which unites one family...  Whatever befalls the Earth befalls the sons of the Earth.  Man did not weave the web of life; he is merely a strand in it.  Whatever he does to the web, he does to himself."

**********************************

During the first three centuries C.E., something remarkable happened; Rome went from a superpower, controlling much of Europe, the Middle East, and North Africa, to being a pair of weak, unstable fragments -- the Western and Eastern Roman Empires --torn by strife and internal squabbles, beset by invasions, with leaders for whom assassination was the most likely way to die.  (The year 238 C.E. is called "the year of six emperors" -- four were killed by their own guards, one hanged himself to avoid the same fate, and one died in battle.)

How could something like this happen?  The standard answer has usually been "the barbarians," groups such as the Goths, Vandals, Franks, Alans, and Huns who whittled away at the territory until there wasn't much left.  They played a role, there is no doubt of that; the Goths under their powerful leader Alaric actually sacked the city of Rome itself in the year 410.  But like with most historical events, the true answer is more complex -- and far more interesting.  In How Rome Fell, historian Adrian Goldsworthy shows how a variety of factors, including a succession of weak leaders, the growing power of the Roman army, and repeated epidemics took a nation that was thriving under emperors like Vespasian and Hadrian, finally descending into the chaos of the Dark Ages.  

If you're a student of early history, you should read Goldsworthy's book.  It's fascinating -- and sobering -- to see how hard it is to maintain order in a society, and how easy it is to lose it.

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The natural pharmacy

A couple of weeks ago, we looked at the discovery and decipherment of a codex written in Nahuatl, one of the languages spoken by the Aztecs (and still spoken in central Mexico).  The study highlighted the fact that language is one of the most critical pieces of culture, embodying a unique way of describing the world.  When languages disappear, that perspective is forever lost.

It's even worse than that, according to another study, that appeared in Proceedings of the National Academy of Sciences a couple of months ago.  In "Language Extinction Triggers the Loss of Unique Medicinal Knowledge," authors Rodrigo Cámara-Leret and Jordi Bascompte of the University of Zürich look at the role of language in preserving information about medicinal plants -- information that might well be encoded in only a single one of the estimated 6,500 languages currently spoken on Earth.

Cámara-Leret and Bascompte considered indigenous languages in three places -- New Guinea, Amazonia, and North America -- lining up those languages with databases of medicinal native plants.  Specifically, they were looking at whether the knowledge of the medicinal value of native flora crossed linguistic boundaries, and were known (and used) in the cultures of the speakers of different languages.

Some, of course, were.  The use of willow bark as an analgesic was widely known to Native Americans throughout the eastern half of North America.  The sedative nature of poppy sap was also widespread, and has a long (and checkered) history.  (It's no coincidence that these two plants produce compounds -- aspirin and morphine, respectively -- that are part of the modern pharmacopeia.)

Illustration and uses of mandrake (Mandragora officinarum) from Dioscurides's De Materia Medica (7th century C.E.) [Image is in the Public Domain]

But what about the rest of the myriad species of medicinal plants that have been catalogued?  What Cámara-Leret and Bascompte found is simultaneously fascinating and alarming.  They looked at 12,495 species of medicinal flora native to the regions they studied, and found that over 75% of them were only named and known as pharmacologically valuable in a single language.

Worse, the researchers found that there was a correlation between the languages with the rarest medicinal knowledge, and how endangered the language is.  "We found that those languages with unique knowledge are the ones at a higher risk of extinction," Bascompte said, in an interview with Mongabay.  "There is a sort of a double problem in terms of how knowledge will disappear."

That knowledge isn't purely of interest to anthropologists, as a sort of cultural curiosity.  Consider how many lives have been saved by quinine (from the Peruvian plant Cinchona officinalis, used in treating malaria), vincristine (from the Madagascar periwinkle, Catharanthus rosea, used in treating leukemia and Hodgkin's disease), digoxin (from the foxglove plant, Digitalis purpurea, used for treating heart ailments), taxol (from the Pacific yew, Taxus brevifolia, used in treating a variety of cancers), and reserpine (from the south Asian plant Rauvolfia serpentina, used in treating hypertension).  And that's just some of the better-known ones.  The whole point of the Cámara-Leret and Bascompte study is that the majority of pharmacologically-useful plants aren't known outside of a single indigenous ethnic group -- and when those languages and cultures are lost or homogenized into the dominant/majority culture, that information is lost, perhaps forever.

"There is life outside English," Bascompte said.  "These are languages that we tend to forget—the languages of poor or unknown people who do not play national roles because they are not sitting on panels, or sitting at the United Nations or places like that.  I think we have to make an effort to use that declaration by the United Nations [the UNESCO decision that 2022 to 2032 will be the "Decade of Action for Indigenous Languages"] to raise awareness about cultural diversity and about how lucky we are as a species to be part of this amazing diversity."

I can only hope that it works, at least to slow down the cultural loss.  It's probably hopeless to stop it entirely; currently, the top ten most common first languages (in order: Mandarin, Spanish, English, Hindi, Arabic, Portuguese, Bengali, Russian, Japanese, and Punjabi) account for almost fifty percent of the world's population.

The remaining 6,490 languages account for the other half.  

I understand the drive to learn one of the more-spoken languages, from the standpoint of participation in the business world (if that's your goal).  You probably wouldn't get very far international commerce if you only spoke only Ainu.  But the potential for losing unique knowledge from language extinction and cultural homogenization can't be overestimated.  Nor can the purely practical aspects of this knowledge -- including the possibility of life-saving medicinal plants that might only be recognized as such by a single small group of people in a remote area of New Guinea. 

*************************************

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!

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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.

**********************************************

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.

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