Big apple

On August 14, 2003, my wife and I were returning from a trip to Hawaii.  It was a lovely vacation, but the return home was, to put it mildly, fraught with mishaps.  The most spectacular one occurred as we were descending into LaGuardia Airport in New York City.  It was late afternoon and I was watching the lights of the city zooming along below us, when, all of a sudden...

... the entire skyline went dark.

I nudged Carol and asked her to confirm that I was, in fact, seeing what I thought I was seeing.  The pilot landed the plane, but the jet bridges weren't working so we deplaned via a rolling ladder.  The entire airport was dark except for a few lights that were kept on by a generator.  Remember that this is a little less than two years after 9/11, so our immediate (and terrifying) thought was that it was a terrorist attack, but it turned out we'd gotten caught up in the Great Northeastern Blackout, which knocked out the electricity to a huge chunk of the northeastern United States and eastern Canada, and which apparently had been triggered by a software bug.

The upshot was we got stuck in the airport overnight with a bunch of other people who were also trying to get back to the Ithaca area, and one of these was a very nice woman who worked for the Apple Genomics Project at Cornell Orchards.  That evening she and I had a real Nerd-O-Rama about the ins and outs of plant genetics, which was a very peculiar way to make the best of a bad situation.

She and her team had a fascinating job -- going all over Europe, the Caucasus, Anatolia, and Central Asia looking for apple germ line -- basically, anything that can be used to reproduce an entire tree (seeds and cuttings being two of the most obvious examples).  They hired translators to accompany them, who asked locals to point out the best apple trees for various uses -- cooking, cider, making wine or vinegar, drying/preserving, or eating fresh -- and they took samples of germ line (along with copious notes) to bring home to the Orchards for growing and hybridizing.  Besides just looking for good fruit quality, they were also interested in finding strains that are resistant to pests and diseases.

The most diversity they discovered was in Kazakhstan and Uzbekistan, which is where apples originate.  ("American as apple pie" is about as inaccurate as you can get; apples not only aren't native to the United States, they were brought into North America in the mid-1600s by a Frenchman, Pierre Martin -- who settled in Nova Scotia.)  And some research out of the Max Planck Institute for the Science of Human History that appeared last week in Frontiers in Plant Science found that the spread of apples from their homeland, thousands of miles across Europe, was due to two factors; megafauna and the Silk Road.

[Image licensed under the Creative Commons Sandstein, Civni-Rubens apple, CC BY 3.0]

The modern apple is the result of hybridization between at least four wild species, followed by centuries of backcrossing and artificial selection.  Let apples cross-pollinate and plant the seeds, and you'll end up with something like a wild crabapple.  Originally, the bright fruits of apples were eaten by large herbivores like horses and wild cattle, and the seeds dispersed long distances, but with the disappearance of the huge herds that used to exist in central Asia, apple seeds were poorly dispersed.  (Apples aren't the only plants that got into trouble when their seed-disperser disappeared, something about which I wrote in more detail a couple of years ago.)  Fortunately for apples, though, their many uses were noted by humans, and when people moved -- especially along the Silk Road -- they took apple germ line with them, just as my Cornell researcher friend did a thousand years later.

The author, Robert Nicholas Spengler, writes:

Large fruits in Rosaceae [the family apples belong to] evolved as a seed-dispersal adaptation recruiting megafaunal mammals of the late Miocene.  Genetic studies illustrate that the increase in fruit size and changes in morphology during evolution in the wild resulted from hybridization events and were selected for by large seed dispersers.  Humans over the past three millennia have fixed larger-fruiting hybrids through grafting and cloning.  Ultimately, the process of evolution under human cultivation parallels the natural evolution of larger fruits in the clade as an adaptive strategy, which resulted in mutualism with large mammalian seed dispersers (disperser recruitment).

Current archaeobotanical evidence seems to suggest that apple domestication took place over a period of less than 100 generations, much less for the earliest morphological changes.  It seems feasible that rapid domestication through hybridization occurred in as little as one or a few generations, and most of the modern diversity in landraces is probably a recent phenomenon, through directed breeding.  Not only do protracted models of domestication fall short when discussing apples, the concept of a “center” of domestication is misleading. Genetic studies illustrate that wild apple populations across Europe and West Asia collectively contributed to the modern domesticated apple in a hybrid complex of species distributed across a continent and a half.

So that's something to think about next time you bite into a crisp apple -- you're enjoying a fruit that has roots reaching back millions of years, the current shape, color, and taste of which were created by megafaunal seed dispersers and the travel of human populations down the Silk Road.

Oh, and we eventually did get back home.  Carol and I, our geneticist friend, and four other people finally decided to hire a limousine when it became obvious that (1) the power, and therefore the airport, was going to be out of commission for a long time, and (2) there wasn't a rental car to be had anywhere in the New York City area.  We figured that splitting the cost of a limousine all the way to Ithaca seven ways wasn't going to be much more than each of us separately hiring a rental car anyhow.  All was going well until the limousine overheated and died in the middle of nowhere in the Poconos, leaving us stranded by the side of the highway with all our luggage.

By then, even my new friend and I didn't feel much like talking about genetics.

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Why the sad face?

Springboarding off Saturday's post about non-human animals having emotions, today we're going to look at a study that came out a couple of weeks ago in Frontiers of Veterinary Science that demonstrates that not only do animals have emotions, they've evolved to be able to play on ours.

In a paper with the rather intimidating title "The Application of Geometric Morphometrics to Explore Potential Impacts of Anthropocentric Selection on Animals' Ability to Communicate via the Face: The Domestic Cat as a Case Study," animal behaviorists Lauren Finka and Mark Farnsworth (of Nottingham Trent University), Stelio Luna (of São Paulo State University), and Daniel Mills (of the University of Lincoln) looked at an interesting phenomenon; the way human selection of animals for pets has led to the animals evolving traits that trigger a nurturing response in the owners.  A particularly interesting one is the "inner eyebrow raising muscle," which in domestic dog breeds is far more highly developed than in wild dogs, and which causes the furrowed brow "sad puppy" look any dog owners out there will no doubt recognize immediately.  My lovable rescue dog Grendel was the past master of this particular expression:

No, he was not spoiled.  Don't even suggest such a thing.

People seeing Grendel usually took one look at him and said, "Oh, you poor poor puppy!  Why the sad face?  Here, puppy, have a cookie."  Which, of course, led him to understand that looking sad got him what he wanted.

Evolution for the win.

The study that came out a couple of weeks ago, however, took a look at cats, which in general have less emotionally expressive faces than dogs do.  My wife's cat, Geronimo, who died a couple of years ago at age eighteen, had a spectrum of facial expressions that ran the gamut from "I'm pissed off" to "I hate you," occasionally reaching the level of "fuck off and die."  I know this is ascribing human thoughts to a non-human animal, but whenever Geronimo looked at me, his yellow eyes narrowed to slits, I always came away with the expression that he was plotting to disembowel me in my sleep.

But the current study shows that most domestic cats have a wider range of emotional communication than Geronimo did.  Interestingly, what the researchers called "pain features" -- movements of the face indicative of distress -- were often present in "baby-faced" breeds like Persians even when the animals were not actually in distress, while long-faced breeds like Siamese showed fewer "pain features" even when the animal was in pain.  I wonder if this is why Siamese cats have a reputation for being "aloof" and "independent," and Persians a reputation for being in need of pampering?

The authors write:

The ability of companion animals to readily solicit care from humans is obviously advantageous.  However, it is possible that permanently vulnerable looking individuals might have a diminished capacity to clearly indicate when care is or is not required, as well as to display other information relevant to their actual state or intentions.  Thus, if certain cat breeds are being selected to display “pain-like” features on their faces, these features may serve to solicit unwanted or inadequate attention from their caregivers.  More generally, such types of anthropocentric selection might lead to increased anthropomorphic tendencies.  If, for example, the animal has the appearance of an expression which humans find relatable on some level, even if it is not necessarily reflective of that animals' affective state, it may be used to attribute emotions or characteristics to them.  For example, “grumpy cat” a cat made famous by her coverage on social media, achieved her moniker due to her perceived “frowning” facial appearance.  However, this was likely a result of a combination of her feline dwarfism and paedomorphic [infant-like] features, rather than an expression of her irritability.

One interesting point the authors make is that one possible reason that cats in general have fewer facial cues to solicit nurturing from humans is that they've been in domestication as companions for a far shorter time than dogs have.  The human/dog relationship goes back millennia; and while cats have been used as mousers for centuries, their use as companion animals is of fairly recent origin.  In fact, a large percentage of current domestic cat breeds are under a hundred years old -- in other words, if you trace most "pure-bred" cats' ancestry back two hundred years, they all descend from a population of generic-looking felines that began to be heavily selected when people started keeping them in their homes, and expecting something more out of them than just ridding the house of rodents.

In any case, as the authors point out, the advantage to the pet is obvious.  In our case, our dogs play us like fiddles.  One of our current dogs, a lovable big galoot named Guinness, knows that to get what he wants all he has to do is put his head in my lap and just stand there.  I've tried ignoring him, but he knows that patience always gets him what he wants (usually petting) in the end.  If I make eye contact with him, the tail starts wagging, because he knows he won.

As usual.

But as my wife points out, the fact that they've evolved to yank on our heartstrings isn't entirely a one-way relationship.  We get companionship and love and lap-warming, and there's real value in that.  So really, I'm perfectly okay with being used.  A petless home would be a lot cleaner and quieter, but it would also be a lot colder, lonelier, and sadder.

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As a biologist, I've usually thought of myself as immune to being grossed out.  But I have to admit I was a little shocked to find out that the human microbiome -- the collection of bacteria and fungi that live in and on us -- outnumber actual human cells by a factor of ten.

You read that right: if you counted up all the cells in and on the surface of your body, for every one human cell with human DNA, there'd be ten cells of microorganisms, coming from over a thousand different species.

And that's in healthy humans.  This idea that "bacteria = bad" is profoundly wrong; not only do a lot of bacteria perform useful functions, producing products like yogurt, cheese, and the familiar flavor and aroma of chocolate, they directly contribute to good health.  Anyone who has been on an antibiotic long-term knows that wiping out the beneficial bacteria in your gut can lead to some pretty unpleasant side effects; most current treatments for bacterial infections kill the good guys along with the bad, leading to an imbalance in your microbiome that can persist for months afterward.

In The Human Superorganism: How the Microbiome is Revolutionizing the Pursuit of a Healthy Life, microbiologist Rodney Dietert shows how a lot of debilitating diseases, from asthma to allergies to irritable bowel syndrome to the inflammation that is at the root of heart disease, might be attributable to disturbances in the body's microbiome.  His contention is that restoring the normal microbiome should be the first line of treatment for these diseases, not the medications that often throw the microbiome further out of whack.

His book is fascinating and controversial, but his reasoning (and the experimental research he draws upon) is stellar.  If you're interested in health-related topics, you should read The Human Superorganism.  You'll never look at your own body the same way again.

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

Tracing the lapse of ages

The evolutionary model is one of the most powerful explanatory devices in biology.  It has led to discoveries that simply blow the mind -- such as the fact that dinosaurs didn't go extinct after all (we still have 'em -- we just call 'em birds).  As Richard Dawkins has demonstrated, all you need is an imperfect replicator (DNA) and a selecting agent (the environment) and you can create massive changes in way fewer generations than you'd think.

Of course, sometimes that may not result in an improvement.

I want to tell you today about two fascinating examples of evolutionary conundrums, both about our friends the erstwhile dinosaurs -- and similar occurrences which had nearly opposite results.

First, let's look at scrub jays.

These smart, pretty birds, bright blue with gray markings, are made up of two populations.  The first (and largest) is represented by Woodhouse's Scrub Jay (Aphelocoma woodhouseii):

[Image licensed under the Creative Commons Peter Wallack, Western Scrub Jay, Santa Fe, CC BY-SA 3.0]

The second is the Florida Scrub Jay:

[Image licensed under the Creative Commons Mwanner at the English language Wikipedia]

Pretty similar, right?  Odd, then, that these two photographs were taken 2,700 kilometers apart -- and there are no scrub jays of any kind in between.

Given the fact that the western scrub jays (which include three other species besides Woodhouse's) are a much larger and more diverse population than their Floridian cousins, it's likely the Florida Scrub Jay's ancestors came from the west rather than the reverse.  But how?  They're not migratory, so they didn't get blown off course on migration (which happens -- for three years running a Pacific Loon showed up in Cayuga Lake in upstate New York).  So what caused the split -- and when?  There's apparently been little drift in the populations since the division occurred, given the fact that they're pretty similar still, but that might be low selection, not short time spans.

The bottom line is, we don't know.  The scrub jays are a textbook example of allopatric range distribution -- related populations that have no range overlap.  And while in some cases these peculiarities have been explained, this one has not.

Even odder -- and virtually the opposite in end result -- came out of a genetic study of skeletons of the adzebills (Aptornis spp.), a pair of species native to New Zealand which went extinct from overhunting after the colonization of the islands by the Maoris.  They were impressive birds -- flightless, predatory, just under a meter tall, with the heavy, sharp, downcurved bills that gave them their common name.

Skeleton of Aptornis defossor in the Auckland Museum [Image licensed under the Creative Commons Auckland Museum, Aptornis defossor (AM LB544) 601651 (cropped), CC BY 4.0]

Their general shape led scientists to think they may be related to moas -- enormous flightless birds that went extinct right around the same time as the adzebills did.  But here, appearance and size are misleading.  The study, published last week in Diversity, has shown the genetics of the adzebills indicates their closest living relatives are a group of birds in Africa...

... the flufftails.

White-spotted Flufftail (Sarothrura pulchra)  [Image licensed under the Creative Commons Francesco Veronesi from Italy, White-spotted Flufftail near Kakum NP - Ghana 14 S4E2889 (16010066588), CC BY-SA 2.0]

"A lot of past genetic research and publicity has focused on the moa, which we know were distant relatives of the ostrich, emu, and cassowary," said study co-author Dr Kieren Mitchell of the University of Adelaide.  "But no one had analysed the genetics of the adzebill, despite a lot of debate about exactly what they were and where they came from."

Study co-author Trevor Worthy of Flinders University added, "We know that adzebills have been in New Zealand for a relatively long time, since we previously discovered a 19 million-year-old adzebill fossil on the South Island...  A key question is whether they've been present since New Zealand broke away from the other fragments of the supercontinent Gondwana or whether their ancestors flew to New Zealand from elsewhere later on."

But... look at these two.  (The birds, not the researchers.)  Even the most diehard scientific type might raise an eyebrow at these being closely related.  However, consider my first example -- the wolf and the pug.  Selective breeding of cats and dogs has produced enormous differences in only a few hundred years.  Imagine you were an alien biologist, come to Earth to catalog all the species of life on this planet, and you ran across a chihuahua and a Saint Bernard.

My guess is if you told the alien biologist they were the same species, he/she/it would laugh in your face.  But they are, in fact, genetically very close, and in fact are even theoretically interfertile.  (Although what a Saint Berhuahua would look like kind of boggles the imagination.  Plus, the mechanics of the conception are a little problematic.  I mean, if it was a male chihuahua and a female Saint Bernard, would they, like, give him a stepladder or something?)

An imperfect replicator plus a selecting agent plus time can create wonders.  It seems fitting to end this post with a quote from Charles Darwin's The Origin of Species which I think sums it up brilliantly:

It may metaphorically be said that natural selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life.  We see nothing of these slow changes in progress, until the hand of time has marked the lapse of ages.

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This week's Skeptophilia book recommendation is a tour-de-force for anyone who is interested in biology -- Richard Dawkins's The Ancestor's Tale.  Dawkins uses the metaphoric framework of The Canterbury Tales to take a walk back into the past, where various travelers meet up along the way and tell their stories.  He starts with humans -- although takes great pains to emphasize that this is an arbitrary and anthropocentric choice -- and shows how other lineages meet up with ours.  First the great apes, then the monkeys, then gibbons, then lemurs, then various other mammals -- and on and on back until we reach LUCA, the "last universal common ancestor" to all life on Earth.

Dawkins's signature lucid, conversational style makes this anything but a dry read, but you will come away with a far deeper understanding of the interrelationships of our fellow Earthlings, and a greater appreciation for how powerful the evolutionary model actually is.  If I had to recommend one and only one book on the subject of biology for any science-minded person to read, The Ancestor's Tale would be it.

[If you purchase the book from Amazon using the image/link below, part of the proceeds goes to supporting Skeptophilia!]

Fuzzy thinking, alarmism, and GMOs

There's a fundamental problem when elected officials are charged with creating laws and policies surrounding issues that they simply do not understand.

This is where we currently stand with GMOs.  GMOs, or "genetically-modified organisms," get a great deal of negative press from the all-natural folks, who have nicknamed GMO crops "frankenfoods," claiming that they cause everything from allergies to autism.  Of course, that by itself is ridiculous; modifying genes isn't going to result in the same risks and benefits every time you do it, because (and it pains me to have to point this out) different genes do different things.  A papaya that has been genetically modified to be resistant to ringspot virus is not going to resemble in any way a strain of corn that produces the caterpillar-killing BT toxin.  The only commonality is that both of them were the result of humans tinkering with DNA.

Another problem, of course, is that we've been tinkering with DNA for a long, long time, which makes the USDA's definition of GMO sound a little ridiculous.  The USDA says that genetic modification is "The production of heritable improvements in plants or animals for specific uses, via either genetic engineering or other more traditional methods."  It's the "more traditional methods" that's a little funny; because by that definition, not only is virtually every food you eat a GMO (unless you're subsisting on wild nuts, berries, and roots), so is your pet dog.  Selective breeding -- which has been done for millennia -- is one of those "more traditional methods" the USDA is referring to, as evidenced by the fact that typical store-variety tomatoes, corn, apples, broccoli, oranges, and soybeans (sorry, tofu-eaters) occur nowhere in the wild.  Nor does this guy:

Trust me, this is not a product of natural selection.  [Image courtesy of the Wikimedia Commons]

So we've got a problem right at the outset, which is that a scientifically-correct definition of GMO includes genetic modification by artificial selection, which means that pretty much everything in the grocery store should be so labeled; and if you include only recently-developed genetically engineered crops, you're throwing together all sorts of products whose only similarity is how they were created.

That's not even the extent of the problem, however.  At the end of last month, Secretary of Agriculture Sonny Perdue announced that the USDA would not label as GMO anything created using the CRISPR/Cas9 gene editing protocol.  The press release gave a rather bizarre justification for this decision:

Under its biotechnology regulations, USDA does not regulate or have any plans to regulate plants that could otherwise have been developed through traditional breeding techniques as long as they are not plant pests or developed using plant pests.  This includes a set of new techniques that are increasingly being used by plant breeders to produce new plant varieties that are indistinguishable from those developed through traditional breeding methods.  The newest of these methods, such as genome editing, expand traditional plant breeding tools because they can introduce new plant traits more quickly and precisely, potentially saving years or even decades in bringing needed new varieties to farmers.

Did you catch that?  The USDA won't regulate crops that "could otherwise have been developed" by traditional techniques, and ones that are "indistinguishable from those developed through traditional breeding methods."  Which, actually, is pretty much every GMO ever created.  How do you figure out whether a particular strain "could otherwise have been developed" or not?  So we've gone from labeling every damn product in the store to labeling nothing at all.

Now, don't get me wrong.  I think CRISPR/Cas9 has phenomenal potential, not only for developing disease-resistant strains of crops that are currently seriously threatened (including, unfortunately, chocolate, oranges, and bananas), but in curing genetic diseases in humans.  And as I said before, it's scientifically inaccurate to regulate -- or even label -- all genetically modified food products the same way, as if the means by which they were produced is the only relevant issue.  My research into the topic has demonstrated to my own satisfaction that the vast majority of GMO foods are completely safe for human consumption, and a great deal of the fear-talk about them comes from people who don't have a very good understanding of what genetic modification is, or how it works.

As Tirzah Duren put it over at Real Clear Science:

Mandatory labeling of GMOs makes no sense both from the technical side and from the practical.  The definition of GMOs is misunderstood even by the organization who made them.  This lack of understanding translates into a sloppy policy that does little to inform consumers.  Examining the regulation of GMOs highlights a truth, which is the government cannot regulate what it does not understand...  [T]he major shortcoming on GMO regulation... is that the people making the rules do not understand what they are making rules about.

And neither, unfortunately, do many of the consumers.  I'm reminded of the situation a few years ago where freeze-resistant strawberries were developed by splicing in a gene for a natural antifreeze protein produced by certain species of fish, and people flipped out, because they believed of one or more of the following:

1. They thought the strawberries would taste like fish.
2. This meant that the strawberries were no longer vegan.
3. They thought the strawberries were produced by some bizarre half-plant, half-fish creature in a lab.  (No, I'm not joking.)

It also gave rise to foolishness like this:

Note that saying that all GMOs are safe is just as ridiculous to say that all of them are harmful.  Each one has to be evaluated and tested on its own merits and risks.  But this kind of alarmism, fear-talk, and elevation of the naturalistic fallacy into the law of the land is simply ignorant, not to mention encouraging us to think with our emotions rather than with our brains.

Anyhow.  I suppose it's no surprise that having a citizenry that is largely ignorant of science results in the election of leaders who are largely ignorant of science.  It's still a little disheartening, though -- especially when those ignorant leaders are charged with developing policy regarding issues that they clearly don't understand.

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This week's featured book on Skeptophilia should be in every good skeptic's library: Michael Shermer's Why People Believe Weird Things.  It's a no-holds-barred assault against goofy thinking, taking on such counterfactual beliefs as psychic phenomena, creationism, past-life regression, and Holocaust denial.  Shermer, the founder of Skeptic magazine, is a true crusader, and his book is a must-read.  You can buy it at the link below!