Skeptophilia (skep-to-fil-i-a) (n.) - the love of logical thought, skepticism, and thinking critically. Being an exploration of the applications of skeptical thinking to the world at large, with periodic excursions into linguistics, music, politics, cryptozoology, and why people keep seeing the face of Jesus on grilled cheese sandwiches.
Showing posts with label FOX-P2. Show all posts
Showing posts with label FOX-P2. Show all posts

Tuesday, May 20, 2025

Talking to the animals

An Introduction to Language (by Victoria Fromkin and Robert Rodman, Third Edition, 1974) defines language as "rule-governed arbitrary symbolic communication."

The "rule-governed" and "arbitrary" parts might seem contradictory, but they're not.  That language has rules is self-evident whether you are a prescriptivist (someone who believes there are correct and incorrect ways to use language) or a descriptivist (someone who believes that as long as communication is occurring, it's language; so the primary role of the linguist is not to enforce rules but to document them).  Being that my master's degree is in historical linguistics, I'm strongly of a descriptivist bent; if I thought there were an inflexible lexicon and set of grammatical rules that never ever changed, I'd kind of be out of a job.

The arbitrary part is less obvious.  It has to do with the sound-to-meaning correspondence.  Dog in English is inu in Japanese, chien in French, kare in Hausa, and hundur in Icelandic; none of those words are, in fact, especially doggy in nature.  Other than a handful of onomatopoeic words like bang, oink, meow, and hiccup, the connection between a word and its meaning is essentially accidental.

Curiously, humans are the only species on Earth that we are certain have true language, by the Fromkin and Rodman definition.  There's long been a suspicion that dolphin and whale vocalizations might be language, but as of this writing, that remains conjecture.  Recently, there have been some interesting studies of other primates indicating that certain features of language might exist outside of Homo sapiens -- a paper out of the University of Warwick last week suggests that orangutan vocalizations might exhibit recursion, the nesting structure you see in the children's rhyme "This is the House That Jack Built."  The researchers found that the sounds orangutans make are grouped into clusters, and those clusters put together in at least two additional tiers of structure, hinting that their vocalizations might have a much richer information-carrying capacity than we'd thought.

Another recent study, this one out of the University of Vienna, found that chimps might use drumming as a means of long-distance communication -- that the spacing of beats when they drum on tree roots varies but is non-random.  Like the recursion found in orangutans, the fact that the rhythm of drumming in chimps isn't just random noise opens up the possibility that it might be meaningful.  The researchers found that different chimps have different rhythmic styles, and that groups also developed their own unique patterns of drumming -- suggestive that drumming in chimps could be a cultural phenomenon.

How we developed language, and (likely) no other extant species did, is still open to question.  There are some interesting genetic pieces to the puzzle; the forkhead box protein 2 (FOX-P2) gene seems to be an important one, as the human variant of FOX-P2 isn't found in any known living species other than ourselves, and mutations in that sequence result in significant problems with learning and utilizing language.  (Genetic studies of Neanderthal remains found that Neanderthals had an identical FOX-P2 gene to that of modern humans; obviously we can't be sure that they had language, but it seems likely.)

[Image licensed under the Creative Commons Emw, Protein FOX-P2 PDB 2a07, CC BY-SA 3.0]

Actually, it was genetics that got me thinking about this topic today; yet another study, this one out of Rockefeller University and Cold Springs Harbor Laboratory, did a gene insertion on mice, replacing the murine version of the NOVA-1 gene with the human variant.  The human NOVA-1 has only a single base pair substitution as compared with that of other mammals, but -- like FOX-P2, damage to this gene is known to impair language learning and production.

And when you replace a mouse embryo's NOVA-1 gene with a human's, the resulting adult mouse is capable of making strikingly more complex vocalizations than your ordinary mouse can do.

"When adult male mice were genetically altered with the human NOVA-1 variant, their squeaks during courtship didn't become higher pitched like the pups," said Robert Darnell, who was lead author on the paper.  "Instead, their vocalizations included more complex syllables.  They 'talked' differently to the female mice.  One can imagine how such changes in vocalization could have a profound impact on evolution....  NOVA-1 encodes a protein that can cut out and rearrange sections of messenger RNA when it binds to neurons.  This changes how brain cells synthesize proteins, probably creating molecular diversity in the central nervous system...  The 'humanized' mice with the NOVA-1 variant had molecular changes in the RNA splicing seen in brain cells, especially in regions associated with vocal behavior."

So we're one step closer to figuring out a uniquely human phenomenon.  That communication in the animal world exists on a spectrum of complexity is certain, but by the Fromkin/Rodman definition, we're kind of it for true language, as far as we know.  How we gained that ability is still not entirely clear, but its advantages are obvious -- and it may be that mutations in two regulatory genes are what kickstarted a capacity for chatter that in large part is responsible for our dominance of the entire biosphere.

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Monday, September 7, 2020

Dog songs

A couple of nights ago I woke up in the middle of the night (not an unusual occurrence for me) in time to hear our local pack of coyotes whooping it up.

I love coyotes.  Their wild screaming and yapping in the distance on an otherwise still night is an eerie, evocative, primal sound that reminds me that nature is out there, all around me, surrounding my comfortable and civilized life -- and it's far, far bigger than I am.

From another angle, my background in linguistics always makes me wonder what they're saying.  The formal definition of language is "arbitrary symbolic communication;" symbolic in the sense that the word stands as a symbol for the object, action, or concept, and arbitrary in that except for a few onomatopoeic words like "bang" and "splat," the connection between the word and what it symbolizes is more or less accidental and will vary from language to language.  (For example, étoile, stjerne, hoshi, and zvezda mean "star" in French, Norwegian, Japanese, and Russian, respectively, but the sounds of the words have nothing especially stellar about them.)

So by the definition, what the coyotes are doing probably isn't language.  It's communication, yes; it undoubtedly facilitates pack cohesion and performs functions like letting the others know if there's a danger or a potential prey nearby.  But any symbolism there (e.g. a high-pitched yelp means "I see a rabbit") is almost certainly extremely rudimentary and shallow at best.

I'm not running down the dogs, though.  Fortunately, neither of my dogs is an incessant barker, but we can tell the difference between the barks from our elderly hound, Lena, depending on whether she wants to be let inside, she sees a chipmunk, she saw my wife drive up, she's playing with our other dog, or she's standing on the end of the dock barking at the goldfish in the pond.  (Yes, she does that.  Nowhere above did I imply that she's smart.)

She's extremely happy, though.  Which is almost certainly better than being smart.

What brings this up is a fascinating study in Proceedings of the National Academy of Sciences last week showing that an elusive canine long thought to be extinct in the wild -- the New Guinea Singing Dog -- is still out there.

An audio recording of six Singing Dogs in chorus

The Singing Dog -- as you heard if you listened to the audio in the link -- has a mournful, but oddly musical, howl that isn't quite like a wolf's, and certainly nowhere near the wild cacophony of coyotes.  There are Singing Dogs in captivity in zoos, but the small gene pool has meant that they've begun to show signs of degradation from inbreeding, so the discovery that the elusive Highland Wild Dog of New Guinea is almost identical to the Singing Dog provides hope that the subspecies may be a good target for conservation.

Also, a study of the genome of the Singing Dog might give us some clues about where their fantastic repertoire of vocalizations comes from.  It's been known for some time that our own ability to speak is related in some way to the FOX-P2 gene, because mutations in it cause developmental dyspraxia.  But a great many mammals have a similar FOX-P2 gene to that of humans, and even birds do.  Further, mutations in birds' FOX-P2 gene causes problems in songs and calls, indicative that it has an important role in vocal communication throughout the animal world -- and is evolutionarily very old, given that the last common ancestor between birds and mammals was on the order of three hundred million years ago.

So the new discovery about the New Guinea Singing Dog is fascinating from a number of angles.  Not only do we have a chance to save a truly unique population, but the information we've gleaned might shed some light on how vocal communication evolved.

But now I need to go see what Lena's barking at.  Last time she made sounds like this, it turned out she was barking at a stick.  To be fair, it was a very threatening-looking stick.  Just protecting our home from danger, like a good dog should.

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Humans have always looked up to the skies.  Art from millennia ago record the positions of the stars and planets -- and one-off astronomical events like comets, eclipses, and supernovas.

And our livelihoods were once tied to those observations.  Calendars based on star positions gave the ancient Egyptians the knowledge of when to expect the Nile River to flood, allowing them to prepare to utilize every drop of that precious water in a climate where rain was rare indeed.  When to plant, when to harvest, when to start storing food -- all were directed from above.

As Carl Sagan so evocatively put it, "It is no wonder that our ancestors worshiped the stars.  For we are their children."

In her new book The Human Cosmos: Civilization and the Stars, scientist and author Jo Marchant looks at this connection through history, from the time of the Lascaux Cave Paintings to the building of Stonehenge to the medieval attempts to impose a "perfect" mathematics on the movement of heavenly objects to today's cutting edge astronomy and astrophysics.  In a journey through history and prehistory, she tells the very human story of our attempts to comprehend what is happening in the skies over our heads -- and how our mechanized lives today have disconnected us from this deep and fundamental understanding.

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



Wednesday, October 24, 2018

Wired for sound

Staying with the general linguistics angle my posts this week have been taking, today we will consider some new research that has identified the neural circuitry that underpins human language -- and comes to a startling conclusion regarding evolution and our mammalian cousins.

True language is thought to be one of the unique features of Homo sapiens.  No other species, as far as we know, has evolved symbolic communication.  Chimpanzees and gorillas can be taught the rudiments of it, and even have come up with novel expressions that have the same creativity and whimsy as human utterances -- such as Koko the gorilla naming her kitten "All Ball."  Whale and dolphin vocalizations might be symbolic language -- but most ethologists think it's simple vocal signaling, like a dog's bark or a cat's meow.

That's why we tend to think of language as a clear deciding line between "human" and "non-human."  The problem with those lines is that they don't reflect the reality of evolution -- that structures and behaviors can't come out of nowhere, and always result from modification of pre-existing genes (and the traits they generated).  So it should have been no real surprise when the FOX-P2 (forkhead box protein 2) gene was discovered in 1990, and it was found that a defect in this gene in humans causes developmental verbal dyspraxia -- a loss of motor coordination and inability to produce speech.

FOX-P2, the protein that allows us to speak [Image is licensed under the Creative Commons, Emw, Protein FOXP2 PDB 2a07, CC BY-SA 3.0]

So is this the "human language gene?"  That's the way it was described, but this runs up against a truth that is uncomfortable for proponents of human uniqueness -- other animals have a FOX-P2 gene, one that isn't identical to humans, but critical nonetheless.  Knocking out the FOX-P2 gene in mice causes fatal developmental disorders.  But the real kicker was that species that have complex vocalizations -- such as songbird and bats -- have a much greater diversity and much greater activity of FOX-P2 genes.

Maybe human language isn't as unique as it seemed at first.

This conclusion got another piece of support last week, with the publication in the Proceedings of the National Academy of Sciences called, "Child First Language and Adult Second Language are Both Tied to General-Purpose Learning Systems," by Phillip Hamrick (of Kent State University), Jarrad A. G. Lum (of Deakin University, Melbourne, Australia), and Michael T. Ullman (of Georgetown University).  And what their research suggests is that the parts of our brain that allow us to use language are not novel, and (very much) not unique to humans -- they are found in many other species and serve a variety of purposes.  The authors write:
Do the mechanisms underlying language in fact serve general-purpose functions that preexist this uniquely human capacity?... The results, which met the predicted pattern, provide comprehensive evidence that language is tied to general-purpose systems both in children acquiring their native language and adults learning an additional language. Crucially, if language learning relies on these systems, then our extensive knowledge of the systems from animal and human studies may also apply to this domain, leading to predictions that might be unwarranted in the more circumscribed study of language.  Thus, by demonstrating a role for these systems in language, the findings simultaneously lay a foundation for potentially important advances in the study of this critical domain...  The results have broad implications. They elucidate both the ontogeny (development) and phylogeny (evolution) of language.  Moreover, they suggest that our substantial knowledge of the general-purpose mechanisms, from both animal and human studies, may also apply to language.

"Our conclusion that language is learned in such ancient general-purpose brain systems contrasts with the long-standing theory that language depends on innately-specified language modules found only in humans," said Michael Ullman, senior author of the study.  "Researchers still know very little about the genetic and biological bases of language learning, and the new findings may lead to advances in these areas.  We know much more about the genetics and biology of the brain systems than about these same aspects of language learning...  Since our results suggest that language learning depends on the brain systems, the genetics, biology, and learning mechanisms of these systems may very well also hold for language."

"These brain systems are also found in animals — for example, rats use them when they learn to navigate a maze," added study co-author Dr. Phillip Hamrick.  "Whatever changes these systems might have undergone to support language, the fact that they play an important role in this critical human ability is quite remarkable."

So yet another blow to our sense of uniqueness, that we are somehow different from the rest of the natural world.  The same forces that generated the wombat and the cactus and the slime mold generated us, and we are deeply tied to our nearest relatives not only on the genetic level, but on the level of brain structure.  The idea that evolution could take the same basic neural circuitry and adapt it in one animal species into the ability to navigate a maze, and in a different one into allowing Shakespeare to write Macbeth, is nothing short of astonishing.

It seems fitting to end with the famous quote from Charles Darwin, the last paragraph of The Origin of Species.  "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling 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 Skeptophilia book recommendation of the week is a must-read for anyone interested in languages -- The Last Speakers by linguist K. David Harrison.  Harrison set himself a task to visit places where they speak endangered languages, such as small communities in Siberia, the Outback of Australia, and Central America (where he met a pair of elderly gentlemen who are the last two speakers of an indigenous language -- but they have hated each other for years and neither will say a word to the other).

It's a fascinating, and often elegiac, tribute to the world's linguistic diversity, and tells us a lot about how our mental representation of the world is connected to the language we speak.  Brilliant reading from start to finish.




Wednesday, November 23, 2016

Mouse talk

Being a linguistics geek, I've always been fascinated with the mechanisms of communication.  My interests span such topics as the evolution of human language, how one language (or culture) influences another (the topic of my master's thesis), the question of how we would understand language in a signal from an extraterrestrial intelligence, and whether vocal communication in other species is actually language.

The conventional answer to the last question has usually been "no."  Language, as defined by linguistics, is "arbitrary symbolic communication."  The arbitrary part is because except in certain rare cases, such as onomatopoeic words ("pop," "splat," "bang," etc.), there is no logical connection between the sound of a word and its referent.  Except in our minds, there is nothing especially doggy about the sound of the word "dog."

So is vocal communication in other animals language?  The singing of songbirds is clearly communication, but it lacks one important characteristics of human language; the flexible productive ability of language to communicate different concepts in different contexts.  Birdsong is for the most part (within a species) limited in range to a few different sounds, and once learned, never changes.

Some species, however, get closer to language than that.  Some birds, notably corvids, have a wide range of vocalizations, and are also some of the most intelligent birds.  Dogs vary their tones depending on context -- I can tell from the tone of my dog's barks whether he's seen a squirrel, someone's knocked on the front door, he wants to be let in, he's hungry, or my wife's just come home.  One step closer are whales and dolphins, whose vocal communication appears to be complex and responsive -- but whether it qualifies as true language is an unsettled question.

However, a new study, which appeared this week in Frontiers in Behavioral Neuroscience, suggests that human language may not be as far removed from vocalizations in other animals as we may have thought.  The paper, entitled "A FOX-P2 Mutation Implicated in Human Speech Deficits Alters Sequencing of Ultrasonic Vocalizations in Adult Male Mice," by Jonathan Chabout, Erich D. Jarvis et al., has shown that mice have the "Forkhead Box Protein 2" (FOX-P2) gene, just as humans do -- and a mutation in that gene impairs vocal communication in mice, just as it does in humans.

[image courtesy of the Wikimedia Commons]

"This study supports the ‘continuum hypothesis,’ which is that FOX-P2 affects the vocal production of all mammals, and not just humans," Jarvis said.  "Mice do not have the complex vocal learning behavior of humans and song-learning birds.  Nonetheless, we find that the same FOX-P2 mutation in mice and in humans leads to overlapping effects on sequencing of vocalizations. In particular, against a background of preserved syllable acoustic structure, we see reductions in the length and complexity of syllable sequences."

I find this fascinating, because I've always been of the opinion that there's a lot more going on inside the brains of non-human animals than we've typically been willing to acknowledge, and a great deal more similarity than difference between human cognition and cognition in other mammals.  So in a way, I find this result unsurprising.

But still, what was drilled into me in my college linguistics classes -- that humans were the only animals that had language, and that there was a hard-and-fast divide between the vocalizations of humans and those in other species -- was a surprisingly deep-seated bias.  It's one I'm glad to jettison, however.  My other geeky passion is evolutionary biology, so the idea that there is an unbroken continuum in the animal world in terms of what we have to say, and the genetic underpinning thereof, is pretty damn cool.