Stolen glance

Charles Darwin eloquently expressed his own struggle with imagining how the vertebrate eye could have evolved.  If you spend any time reading the writings of creationists or proponents of intelligent design (not recommended unless you have an extraordinary tolerance for pretzel logic), you'll find a quote from The Origin of Species:

To suppose that the eye with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest degree.

This quote causeth much crowing and fist-bumping amongst the holy, lo unto this very day, usually followed by something like "Even Darwin admitted that evolution by natural selection doesn't work."

It's wryly amusing, given the degree to which anti-evolutionists cherry-pick the scientific evidence they accept and the (much larger amount of) evidence they ignore completely, that this quote is itself cherry-picked, as you'd find out if you went on to read the next two sentences of the book:

When it was first said that the sun stood still and the world turned round, the common sense of mankind declared the doctrine false; but the old saying of Vox populi, vox Dei, as every philosopher knows, cannot be trusted in science.  Reason tells me, that if numerous gradations from a simple and imperfect eye to one complex and perfect can be shown to exist, each grade being useful to its possessor, as is certainly the case; if further, the eye ever varies and the variations be inherited, as is likewise certainly the case; and if such variations should be useful to any animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, should not be considered as subversive of the theory.

So the argument -- if I can dignify it by that name -- of the anti-evolutionists boils down to our old friend Argument from Incredulity: "I can't imagine how it could have happened, therefore it must be God."

The truth is, we understand the evolution of the eye pretty well.  Lots of animals (for example, flatworms) have light-sensitive spots; and as Richard Dawkins brilliantly explains in his tour-de-force defense of evolution The Blind Watchmaker, once you have any kind of light-sensing ability at all, incremental improvements can result in some amazingly complex structures.  The eye isn't "irreducibly complex" -- the intelligent design cadre's favorite phrase -- at all; simple photosensitive spots led to "cup eyes" which led to eyes like a pinhole camera, and so on.  In fact, the whole process has been repeated more than once.  Complex eyes have evolved independently at least three times, possibly more.

[Image licensed under the Creative Commons Kamil Saitov, Human eye iris 5, CC BY 4.0]

The vertebrate eye is a particularly interesting case.  The transparent proteins in the lens, appropriately named crystallins, were found in 1988 by molecular biologist Joram Piatigorsky to come from the same genes that produce heat-shock proteins, enzymes that protect other proteins against damage from fluctuating temperature.  Take heat-shock proteins and assemble them in layers, you get a lens.  This is an example of exaptation (also called preaptation or preadaptation), where a gene, protein, or structure that evolved in one context develops a function giving it an entirely different use, and that use kind of moves in and takes over.

It's another example of exaptation in the eye that is why the whole topic comes up; in fact, it's not only exaptation, it's exaptation of a gene that was borrowed from another organism entirely.  A paper this week in Proceedings of the National Academy of Sciences looked at a protein in all vertebrate eyes called IRBP (interphotoreceptor retinoid-binding protein), without which our sense of sight wouldn't work.  When light strikes your eye, protein-bound complexes containing retinol (a derivative of vitamin A) absorb the energy, causing them to kink.  This triggers a neuron to fire, sending a signal to your brain.  However, something needs to unkink the complex, thus resetting the switch so it can respond to the next photon to come along.

That's what IRBP does.  Without it, your retinal cells would be able to respond exactly once, then they'd shut down permanently.

This week's paper found something astonishing.  The gene that codes for IRBP doesn't exist in our nearest invertebrate relatives, nor in any other group studied, with one exception -- certain species of bacteria.  What apparently happened is that the common ancestor of all vertebrates swiped a gene from bacteria that coded for a pepsidase -- an enzyme that breaks down and recycles proteins.  This kind of gene-stealing isn't uncommon.  (I did a post a few years ago about a pair of viral genes that seem to be critical for our forming memories, if you want another good example of this phenomenon.)  But like the heat-shock proteins becoming crystallins, the pepsidase made by the gene our ancestors grabbed was useful for something else -- unkinking the protein complexes in our rapidly-evolving eyes.

So our eyes work not only because of proteins gaining additional functions, but because we stole a gene from bacteria.

"Horizontal gene transfer can help to endow organisms with new functions," said Julie Dunning Hotopp, of the University of Maryland School of Medicine’s Institute for Genome Sciences.  "Once these genes take root in a new species, evolution can tinker with them to produce totally new abilities or enhance existing ones.  It is the biological equivalent of upcycling that happens in my Buy Nothing Group."

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Genes, lost and found

There's a famous anecdote about British biologist J. B. S. Haldane.  Haldane was a brilliant geneticist and evolutionary biology but was also notorious for being an outspoken atheist -- something that during his lifetime (1892-1964) was seriously frowned upon.  The result was that religious types frequently showed up at his talks, whether or not the topic was religion, simply to heckle him.

At one such presentation, there was a question-and-answer period at the end, and a woman stood up and asked, "Professor Haldane, I was wondering -- what have your studies of biology told you about the nature of God?"

Without missing a beat, Haldane said, "All I can say, ma'am, is that he must have an inordinate fondness for beetles."

There's some justification for the statement.  Beetles, insects of the order Coleoptera, are the most diverse order in Kingdom Animalia, with over four hundred thousand different species known.  (This accounts for twenty-five percent of known animal species, in a single order of insects.)  The common ancestor of all modern species of beetles was the subject of an extensive genetic study in 2018 by Zhang et al., which found that the first beetles lived in the early Permian Period, on the order of three hundred million years ago.  They survived the catastrophic bottleneck at the end of the Permian and went on to diversify more than any other animal group.

One striking-looking family in Coleoptera is Buprestidae, better known as "jewel beetles" because of their metallic, iridescent colors.  Most of them are wood-borers; a good many dig into dying or dead branches, but a few (like the notorious emerald ash borer, currently ripping its way through forests in the northern United States and Canada) are significant agricultural pests.

A few of them have colors that barely look real:

An Australian jewel beetle, Temognatha alternata [Image licensed under the Creative Commons John Hill at the English-language Wikipedia]

What's curious about this particular color pattern is that beetles apparently had a gene loss some time around the last common ancestor three hundred million years ago that knocked out the ability of the entire group to see in the blue region of the spectrum.  This kind of thing happens all the time; every species studied has pseudogenes, genetic relics left behind as non-functional copies of once-working genes that suffered mutations either to the promoter or coding regions.  However, it's odd that animals would have colors they themselves can't see, given that bright coloration is very often a signal to potential mates.

That's not the only reason for bright coloration, of course; there is also aposematic coloration (also known as warning coloration), in which flashy pigmentation is a signal that an animal is toxic or otherwise dangerous.  There, of course, it's not important to be seen by other members of your own species; all that counts is that you're visible to potential predators.  But jewel beetles aren't toxic, so their bright colors don't appear to be aposematic.

The puzzle was solved in a paper in Molecular Biology and Evolution that came out last week, in which a genetic study of jewel beetles found that unlike other beetles, they can see in the blue region of the spectrum -- and in fact, have unusually good vision in the orange and ultraviolet regions, too.  What appears to have happened is that a gene coding for a UV-sensitive protein in the eye was duplicated a couple of times (another common genetic phenomenon), and those additional copies of the gene were then free to accrue mutations and take off down their own separate evolutionary paths.  One of them gained mutations that altered the peak sensitivity of the protein into the blue region of the spectrum; the other gave their hosts the ability to see light in the orange region.

The result is that jewel beetles became tetrachromats; their eyes have acuity peaks in four different regions of the spectrum.  (Other than a few people --who themselves have an unusual mutation -- humans are trichromats, with peaks in the red, green, and blue regions.) 

What this shows is that lost genes can be recreated.  The gene loss that took out beetles' blue-light sensitivity was replaced by a duplication and subsequent mutation of a pre-existing gene.  It highlights the fundamental misunderstanding inherent in the creationists' mantra that "mutations can't create new information;" if that's not exactly what this is, there's something seriously amiss with their definition of the word "information."  (Of course, I'm sure any creationists in the studio audience -- not that there are likely to be many left -- would vehemently disagree with this.  But since willfully misunderstanding scientific research is kind of their raison d'être, that should come as no surprise to anyone.)

Anyhow, the jewel beetle study is a beautiful and elegant piece of research.  It showcases the deep link between genetics and evolution, and reminds me of the quote from Ukrainian-American biologist Theodosius Dobzhansky, which seems a fitting place to end: "Nothing in biology makes sense except in light of evolution."

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Seeing in a different light

One of the most influential teachers I've ever had was my high school biology teacher, Jane Miller.  She had a way of making just about everything interesting, from biochemistry to the parts of the cell to the parts of the human body.

I still recall one time she completely boggled my mind.  It was when we were studying the anatomy and physiology of the eye, and she told us that the human eye could only perceive a tiny little slice of the electromagnetic spectrum.  The rest -- radio waves, microwaves, infrared, ultraviolet, x-rays, and gamma rays -- are all light, just like visible light, differing only in frequency and wavelength.  It's just that our eyes aren't built to be sensitive to these other parts of the spectrum.

Further, because of the way light refraction works, the structure of our eyes would have to be different if they could detect different frequencies.  To see in the radio region of the spectrum, for example, we would need to have eyes larger than wagon wheels.  Which would be a little cumbersome.

Nevertheless, there are animals that can see at least some parts of the spectrum we can't.  Mosquitoes can see in the infrared region -- one of several ways the little buggers find you in the dark.  Bees can see into the ultraviolet, and in fact some bee-pollinated flowers have coevolved to reflect in the ultraviolet region.  These flowers might look white or solid-colored to our eyes, but to a bee, they're spangled with spots and stripes -- advertisements that there's nectar inside.

"But... does that mean there are other colors, ones we can't see?" I asked Ms. Miller.  "What color would ultraviolet light be?"

"No one knows," Ms. Miller said.  "You'd have to be a bee to find out."

Mind = blown.

While we still don't know what these other regions of the spectrum would look like to animals that can perceive them naturally, we now have devices that can take photographs sensitive to different frequencies -- effectively converting this invisible (to us) light into visible light so we can see the patterns made by light sources emitting in other parts of the electromagnetic spectrum.  This, in fact, is why this subject comes up; just last week, the James Webb Space Telescope returned stunning photographs of the Phantom Galaxy (M74), not only in the visible light region of the spectrum, but in the infrared.  Here's what it looks like to our eyes:

And here's what the same galaxy would look like if our eyes could see in the infrared:

We really are only sensing a vanishingly small part of what's out there -- and we are fortunate to live in a time when our devices are allowing us to get a glimpse of what the world would look like to eyes different from our own.

I don't know how anyone wouldn't be awestruck by the photos being taken by the JWST.  We need to be reminded of the grandeur and majesty of the universe, not only for our aesthetic appreciation, but to force us to realize the pettiness of our own small concerns against the backdrop of the galaxies.  A little humility goes a long, long way.

So check out the ongoing updates from NASA/JPL.  I bet you'll have your mind blown over and over again -- just like mine was back in tenth grade biology when I first realized that everyone doesn't see the world the same way.  Because that's a great thing to be reminded of, too -- that our narrow little viewpoint isn't universal.  It's what I tried to capture in the final conversation between the character of Duncan Kyle and the enigmatic Sphinx, in my novel Sephirot -- when Duncan is trying to argue that of course what he's seeing is real:

"It's a matter of practicality," Duncan said, an edge of anger in his voice.

"No," the Sphinx replied.  "It is a matter of Duncan Kyle deciding that he knows what is possible and what is impossible.  Who appointed you the Arbiter of Truth?"

"Isn't that what all humans do?"

"It's what they stop doing," the Sphinx said, "if they want to know what the Truth actually is.  You really think your puny, nearsighted eyes, your weak ears, your dull and calloused skin, can sense everything there is to sense?  That your feeble brain can know everything there is to know?  How arrogant of you."

"I never thought of it that way."

"So a man who cannot prove that he isn't a reflection of a reflection, who doesn't know whether he is flesh and blood or a character in someone else's tale, sets himself up to determine what is possible."  She chuckled.  "That's rich."

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Color my world

Our ability to perceive color is, when you think about it, a peculiar thing.

First, there's the rather hackneyed question of whether we all see color the same way (exclusive, of course, of people who are colorblind).  The way the question is usually phrased goes something like, "How could we tell if when you look at something red, what you see what I call green, but you still call it red because that's what you've learned?"  In other words, if I were to take a look through your eyes and brain, would the colors of objects be the same as what I see?

The answer is: we can't know for sure.  Thus far there's no way for one person to perceive the world through another person's sensory organs and brain.  But the great likelihood is that we all see colors pretty similarly.  All of our visual receptors are put together the same way, as are the visual cortices in our brains.  To assume that even with this structural and functional similarity, each person is still perceiving colors differently, runs counter to Ockham's Razor -- so without any evidence, it seems like a pretty untenable position.

More interesting is the comparison between how we see the world and how other animals do.  Once again, we run up against the issue that we can't see through another's eyes, but at least here we're on more solid ground because we can see that different animals have differently structured eyes.  Dogs, for example, have retinas with a much higher density of rods (the structures that operate in dim light, but only see in shades of gray) and a much lower density of cones (the structures that operate in bright light, and are able to differentiate by wavelength -- i.e., see colors).  Dogs aren't completely colorblind -- their two types of cones peak in sensitivity in the blue and yellow regions of the spectrum -- but they're relatively insensitive to colors outside that.  (This explains why my dog, Guinness, routinely loses his bright orange tennis ball in the bright green lawn -- to me, it stands out from fifty meters away, but he'll walk right past it without seeing it.) 

Then, there are bees and butterflies, which have eyes sensitive not only in the ordinary visible light spectrum but in the infrared and ultraviolet regions, respectively.  There are flowers that look white to our eyes, but to a butterfly they're covered with streaks and spots -- ultraviolet-reflecting markings that advertising nectar to those who can see it. 

A flower of the plant Potentilla reptans, photographed in ultraviolet light.  To the human eye, the flower looks solid yellow -- this is what it might look like to a butterfly.  [Image licensed under the Creative Commons Wiedehopf20, Flower in UV light Potentilla reptans, CC BY-SA 4.0]

But the winner of the wildly complex vision contest is the mantis shrimp, which has sixteen different color receptors (contrasted with our paltry three), rendering them sensitive to gradations of color we aren't, as well as detecting ultraviolet and infrared light, and discerning the polarization angle of polarized light.  How the world looks to them is a matter of conjecture -- but it certainly must be a far brighter and more varied place than what we see.

The reason all this colorful stuff comes up is because of a paper that appeared last week in Proceedings of the National Academy of Sciences, called "What We Talk About When We Talk About Colors," by Colin Twomey, Gareth Roberts, David Brainard, and Joshua Plotkin of the University of Pennsylvania.  The researchers looked at how words describing different colors vary from language to language.  "The color-word problem is a classical one," Plotkin said, in an interview with Science Daily.  "How do you map the infinitude of colors to a discrete number of words?"

And, more central to this research: does everyone do it the same way?  If you showed me a series of gradations from pure blue to pure green, at what point to I switch from saying "this is blue" to saying "this is green" -- or do I call the intermediate shades by a third, discrete name?

What the researchers found was that across 130 different languages, humans tend to group and name colors the same way.  Further, if you give people tiles with varying shades of red and asked them to pick out "the reddest red," the results show remarkable consistency.

Another interesting result of the research was that the sensitivity of our eyes to color variation isn't the same from color to color; we are much better at picking out subtle variations in red, orange, and yellow than we are at seeing differences in (for example) different shades of brown.  The researchers believe this is due to a difference in what they call communicative need; since reds, oranges, and yellows are the colors of ripe fruit, we've evolved eyes that are most sensitive to variations in those colors.  "Fruits are a way for a plant to spread its seeds, hitching a ride with the animals that eat them," Twomey said.  "Fruit-producing plants likely evolved to stand out to these animals.  The relationship with the colors of ripe fruit tells us that communicative needs are likely related to the colors that stand out to us the most...  No one really cares about brownish greens, and pastels aren't super well represented in communicative needs."

So it seems like the great likelihood is that we all see the world pretty much the same way.  Well, all humans, at least.  What the world looks like to a dog, with their better dim-light vision and better motion detection, but far poorer color discrimination, can only be guessed at; and what colors a mantis shrimp sees is beyond the ability of most of us to imagine.

Study lead author Colin Twomey wonders whether the same techniques could be used to study other facets of sensory perception.  "This is something that could be carried to other systems where there is a need to divide up some cognitive space," he said, "whether it's sound, weight, temperature, or something else."

One I wonder about is the sense of taste.  We know that taste differs a great deal between different individuals, not only because everyone likes (and dislikes) particular flavors, and those preferences differ greatly; but there are some people called "supertasters" who are sensitive to minor variations in flavor that the rest of us don't even notice.  (I am most definitely not a supertaster; the joke in my family is that I have two taste buds, "thumbs up" and "thumbs down.")  The daughter of a friend of mine, for example, has amazingly sensitive taste buds, to the point that she can discern whether the coffee was brewed with filtered water or ordinary tap water.

Me, as long as it's brewed with water and not turpentine, I'm fine with it.

But that's all potential future research.  For now, we have a better idea of how each of us colors our world.  And despite our individual differences, the answer appears to be that what you're seeing and what I'm seeing look very much alike.  

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As someone who is both a scientist and a musician, I've been fascinated for many years with how our brains make sense of sounds.

Neuroscientist David Eagleman makes the point that our ears (and other sense organs) are like peripherals, with the brain as the central processing unit; all our brain has access to are the changes in voltage distribution in the neurons that plug into it, and those changes happen because of stimulating some sensory organ.  If that voltage change is blocked, or amplified, or goes to the wrong place, then that is what we experience.  In a very real way, your brain creates your world.

This week's Skeptophilia book-of-the-week looks specifically at how we generate a sonic landscape, from vibrations passing through the sound collecting devices in the ear that stimulate the hair cells in the cochlea, which then produce electrical impulses that are sent to the brain.  From that, we make sense of our acoustic world -- whether it's a symphony orchestra, a distant thunderstorm, a cat meowing, an explosion, or an airplane flying overhead.

In Of Sound Mind: How Our Brain Constructs a Meaningful Sonic World, neuroscientist Nina Kraus considers how this system works, how it produces the soundscape we live in... and what happens when it malfunctions.  This is a must-read for anyone who is a musician or who has a fascination with how our own bodies work -- or both.  Put it on your to-read list; you won't be disappointed.

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Windows of the soul

I find the science of personality fascinating, not least because we're only in the earliest stages of any kind of comprehensive understanding.  What makes human beings act the way they do is certainly some kind of mix between genetics (nature) and environment (nurture), but in what proportion, and to what extent the two influence each other, are still mysteries.

The situation isn't helped much by "type tests," the best-known of which is the Myers-Briggs Type Indicator.  Research has conclusively demonstrated that the MBTI is unreliable -- the same person at different times can end up with entirely different results -- meaning that as a psychiatric tool, it's fairly useless.

Of course, maybe I'm only saying that because I'm an INTP.

So it's not surprising that psychologists and neuroscientists are eager to find more reliable ways to measure personality, especially with respect to the "Big Five" traits (neuroticism, extraversion, agreeableness, conscientiousness, and openness to experience).  And they may have gotten an unexpected leg up with some recent research indicating that where you fall along those five spectra can be given away by your involuntary eye movements.

In their paper, "Eye Movements During Everyday Behavior Predict Personality Traits," which appeared earlier this year in Frontiers in Human Neuroscience, researchers Sabrina Hoppe (of the University of Stuttgart), Tobias Loetscher (of the University of South Australia), Stephanie A. Morey (of Flinders University), and Andreas Bulling (of the Max Planck Institute) found something fascinating; when a headset kept track of the eye movements of forty-two test subjects as they went about their daily business, an artificial-intelligence program could determine where they ranked on various personality scales with astonishing accuracy.

The authors write:

One key contribution of our work is to demonstrate, for the first time, that an individual's level of neuroticism, extraversion, agreeableness, conscientiousness, and perceptual curiosity can be predicted only from eye movements recorded during an everyday task.  This finding is important for bridging between tightly controlled laboratory studies and the study of natural eye movements in unconstrained real-world environments...  The proposed machine learning approach was particularly successful in predicting levels of agreeableness, conscientiousness, extraversion, and perceptual curiosity.  It therefore corroborates previous laboratory-based studies that have shown a link between personality traits and eye movement characteristics. 

[O]ur work... shed[s] additional light on the close link between personality traits and an individual's eye movements.  Thanks to the machine learning approach, we could automatically analyze a large set of eye movement characteristics and rank them by their importance for personality trait prediction.  Going beyond characteristics investigated in earlier works, this approach also allowed us to identify new links between previously under-investigated eye movement characteristics and personality traits.  This was possible because, unlike classical analysis approaches, the proposed machine learning method does not rely on a priori hypotheses regarding the importance of individual eye movement characteristics... 

[I]mproved theoretical understanding will assist the emerging interdisciplinary research field of social signal processing, toward development of systems that can recognize and interpret human social signals. 

Such knowledge of human non-verbal behavior might also be transferred to socially interactive robots, designed to exhibit human-like behavior.  These systems might ultimately interact with humans in a more natural and socially acceptable way, thereby becoming more efficient and flexible.

Which is absolutely fascinating, and of course raises the question of why my neuroticism and introversion would affect the tiny, involuntary movements of my eyes, but answering that was beyond the scope of this study.  Of course, we already knew that the small, back-and-forth movements of the eyes called microsaccades can give you information about what a person is thinking.  A highly amusing experiment a few years ago monitored test subjects in a crowded pub with head-mounted cameras.  The only instructions were that the person should try to keep focused on the person next to them, with whom they were having a discussion.

Well, a few minutes in, the researchers sent in a gorgeous, scantily-clad individual of the test subject's preferred gender to walk by, and even when the subject made a heroic effort not to look, the microsaccades gave him/her away.  While they were focused on the person they were talking to, their microsaccades were going, "Oh dear god that person is drop-dead sexy look that way look that way LOOK THAT WAY."

So the Hoppe et al. study is a fascinating refinement of what our eyes give away about us.  It does make me wonder, however, how this could be used to reveal information the individual would prefer not to reveal.  If an AI program can successfully determine a person's personality from nothing more than eye movements, it's another potential blow to privacy -- however astonishing the results may be to people who, like me, are fascinated with the intricacies of the human brain.

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In writing Apocalyptic Planet, science writer Craig Childs visited some of the Earth's most inhospitable places.  The Greenland Ice Cap.  A new lava flow in Hawaii.  Uncharted class-5 rapids in the Salween River of Tibet.  The westernmost tip of Alaska.  The lifeless "dune seas" of northern Mexico.  The salt pans in the Atacama Desert of Chile, where it hasn't rained in recorded history.

In each place, he not only uses lush, lyrical prose to describe his surroundings, but uses his experiences to reflect upon the history of the Earth.  How conditions like these -- glaciations, extreme drought, massive volcanic eruptions, meteorite collisions, catastrophic floods -- have triggered mass extinctions, reworking not only the physical face of the planet but the living things that dwell on it.  It's a disturbing read at times, not least because Childs's gift for vivid writing makes you feel like you're there, suffering what he suffered to research the book, but because we are almost certainly looking at the future.  His main tenet is that such cataclysms have happened many times before, and will happen again.

It's only a matter of time.

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