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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Quick takes

Today I'd like to look at three topics that came up for one reason or another in the last few days.

First, have you ever thought about catnip?  It's peculiar stuff.  A member of the mint family, Nepeta cataria (no, I didn't make up the species name) is a rather un-showy plant with gray-green stems and off-white flowers.  Its strangest characteristic, as I'm sure you know, is that it produces what amounts to kitty drugs.  The chemical nepetalactone is produced in significant quantities by the plant, and is responsible not only for its musky smell but for its apparent psychedelic effects on cats.  Cats who are susceptible to it -- and some, I understand, are not, although every cat I owned was a total catnip junkie -- purr, roll around in it, become playful and frisky, and their eyes dilate.

[Image licensed under the Creative Commons AlishaLH, Bee on Catnip Flowers, CC BY 4.0]

Clearly this is an accident; it's hard to imagine a plausible scenario in which the trait of producing this chemical evolved for the express reason of making cats flail around.  There's a presumption that it has a repellent effect on insects, which is certainly true about a lot of the aromatic substances produced by plants, but that's unsubstantiated.

The reason this comes up is that scientists at the Max Planck Institute of Chemical Ecology have decoded the genome of catnip, and they found that the nepetalactone gene apparently evolved more than once.  There are inactive "pseudogenes," stretches of DNA whose function has been lost over time to mutations, nearly identical to the current (functional) nepetalactone gene.  So evidently the gene evolved a second time, probably from another gene for producing chemicals of the class nepetalactone belongs to (the iridioids, which sounds like an alien species on Doctor Who but isn't), and then was advantageous enough that it kind of went into overdrive in catnip.

Apparently whatever its function is, it's important for more than getting kitties high.

So we're not the only species that has a strange psychological reaction to various naturally-produced chemicals in plants.  It's a good thing, though, that there's no such thing as (for example) moosenip, because the idea of a bunch of moose frolicking about and rolling around in your front yard is a little terrifying.


The next story comes from some research released last week by NASA's Transiting Exoplanet Survey Satellite (TESS), which made an interesting discovery about a rather odd kind of star.  Called Delta Scuti stars (after the first star identified in this class), they are a pulsating variable that are more common than astronomers thought at first -- there's good evidence that the bright stars Altair and Denebola, in the constellations Aquila and Leo respectively, are also in this class.

What makes these stars so odd is not their fluctuations -- periodic variable stars are actually rather common -- but that some parts of the star move outward and dim, and other parts pull inward and brighten, at the same time.  The whole star, therefore, seems to ripple.  The astrophysicists believe this is because as parts of the star heat up, more of the helium in the outer shell becomes ionized; ionized helium is more opaque to light, so it blocks light trying to escape from the core and balloons outward.  Once it cools, it falls back inward, and since this happens at different times in different places on the surface of the star, there are pulsations in not only the overall brightness of the star, but which parts of the star are bright and which are dim.

A paper in Nature last week showed that their behavior may not be as chaotic as it seemed at first.  Data from TESS has shown that these surface fluctuations have their own kind of periodicity -- some, for example, seem to contract and expand one hemisphere at a time, not at random places on the star.

"Delta Scuti stars have been frustrating targets because of their complicated oscillations, so this is a very exciting discovery," said Sarbani Basu, a professor of astronomy at Yale, who studies asteroseismology but was not involved in the study, in an interview in Science Daily.  "Being able to find simple patterns and identify the modes of oscillation is game changing.  Since this subset of stars allows normal seismic analyses, we will finally be able to characterize them properly."

Last, I was contacted by a reader regarding last week's post about the presence of iridescence in the fossilized feathers of ancient birds, with a question as to whether this discovery might shed any light on the presence of tetrachromacy in birds.  You probably know that (most) humans are trichromats -- we have three different kinds of color-detecting cones in the retina of the eye, sensitive to blue, green, and red wavelengths.  The combination of these three gives us our perception of color.

Mammals, apparently, descend from animals that were tetrachromats -- they had four different cones, and presumably, a more highly refined sense of color detection than humans have.  But in most mammals, such as dogs, there were mutations that knocked out two of the genes responsible -- similar to the loss of the catnip gene described earlier -- leaving behind two functioning cone types, and poorer color discrimination.

Some humans -- almost all are female -- have a fourth working cone, and are true tetrachromats.  This is undoubtedly why when my wife and I are going out, a common comment from her is, "Seriously?  You think that shirt matches those pants?"  Saying my aesthetic sense, especially when it has to do with sartorial matters, is poorly developed is kind of a massive understatement.

Birds -- at least the species that have been tested -- seem to all be tetrachromats, which may be why so much of their display behavior has to do with flashing bright colors around.  The presence of feather iridescence in birds from 52 million years ago may be an indication that they've been able to do this for a very long time.

It must be said, however, that the record holder for number of different kinds of color-sensitive photoreceptor is the mantis shrimp, which (depending on species) has between twelve and sixteen independent kinds of cones.  You have to wonder what the world looks like to them, don't you?

So that's three quick takes from the world of science.  And thanks to the reader who suggested a post on tetrachromacy -- it's a fascinating subject, well worth a look.  So keep those cards and letters comin'.

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This week's Skeptophilia book of the week is six years old, but more important today than it was when it was written; Richard Alley's The Two-Mile Time Machine: Ice Cores, Abrupt Climate Change, and Our Future.  Alley tackles the subject of proxy records -- indirect ways we can understand things we weren't around to see, such as the climate thousands of years ago.

The one he focuses on is the characteristics of glacial ice, deposited as snow one winter at a time, leaving behind layers much like the rings in tree trunks.  The chemistry of the ice gives us a clear picture of the global average temperature; the presence (or absence) of contaminants like pollen, windblown dust, volcanic ash, and so on tell us what else might have contributed to the climate at the time.  From that, we can develop a remarkably consistent picture of what the Earth was like, year by year, for the past ten thousand years.

What it tells us as well, though, is a little terrifying; that the climate is not immune to sudden changes.  In recent memory things have been relatively benevolent, at least on a planet-wide view, but that hasn't always been the case.  And the effect of our frantic burning of fossil fuels is leading us toward a climate precipice that there may be no way to turn back from.

The Two-Mile Time Machine should be mandatory reading for the people who are setting our climate policy -- but because that's probably a forlorn hope, it should be mandatory reading for voters.  Because the long-term habitability of the planet is what is at stake here, and we cannot afford to make a mistake.

As Richard Branson put it, "There is no Planet B."

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

Color my world

I'm guessing that every amateur philosopher has wondered if we all perceive color the same way -- for example, if what I perceive as "red" is the same as what you call "green," but we've just learned to both call it green.

I know I've been asked that probably dozens of times in my neuroscience classes, and my answer was always the same: it's possible, given that I can never see the world through your eyes and brain, but it's pretty unlikely because of the homology that exists between all human brains.  The fact that the visual/perceptive apparatus in your body is awfully similar to the one in mine suggests that we both perceive the world substantially the same way.

You can never prove it, though, which is why this question will keep coming up during late-night sessions in freshman dorms, lo unto the end of time.

Even though I'm making light of it, color perception is still quite a mystery.  It's known that most people (excluding the colorblind) have three different kinds of "cones," which are the cells in the retina that distinguish color, peaking in the red, blue, and green regions of the spectrum.  A few humans -- predominantly women, because the genes for the cone pigments are on the X chromosome -- are tetrachromats, and have a fourth type of cone, making their color acuity considerably more sensitive than the rest of us, and probably explaining the times my wife has said to me, "You actually think that shirt matches those pants?"

Then there's the mantis shrimp, a marine arthropod that is weird in a great many respects, not least because they have between twelve and sixteen different kinds of photoreceptors.  You have to wonder what the world looks like to them, don't you?

[Image is in the Public Domain]

This topic comes up because of a paper that appeared this week in the journal Cell, called "Color Categorization Independent of Color Naming," by a team led by Katarzyna Siuda-Krzywicka, a neuroscientist at Sorbonne University in Paris.  And what this research shows is that our ability to categorize colors -- to determine, for example, that vermilion and scarlet are both shades of red -- is independent of our ability to assign names to colors.

I know, pretty weird, isn't it?  The way that Siuda-Krzywicka and her team approached it was to give two different tasks to people, the first of which required you to identify by number which patches of color in a sample were shades of the same color (i.e., #1 and 2 are the same color, and they're different from #3), and the second of which was to identify what color a particular sample actually was (i.e., #1 is a shade of blue).  Neurotypical people can do both pretty well, with allowances for the aforementioned differences in color sensitivity between individuals.

Where it got interesting was that they included in their study a subject called "RDS" who had suffered an ischemic stroke involving his left posterior cerebral artery five years ago, damaging part of the left occipito-temporal region of his brain.  This stroke interfered with his ability to read and identify certain objects, but its effects were most pronounced in his ability to recognize colors.  When Siuda-Krzywicka's team tested RDS, a fascinating pattern emerged.

Task #1, where subjects were asked to do color categorization -- determine which patches were shades of the same color -- RDS did quite well on, and in fact was very close to the average for test subjects of his gender and age.  However, he was really awful at task #2, trying to figure out what color the patches actually were.

In other words, he could tell that ultramarine and azure were both shades of the same color, but he couldn't figure out that they were both shades of blue.

What this indicates is something very curious; our ability to name colors and our ability to recognize color categories are independent of each other.  You can impair one without affecting the other.

The most fascinating part is that the researchers noted that many of the times RDS did get the color name correct, it was because he used his relatively intact ability at categorization, plus his knowledge and memory, to arrive at an answer.  "This is the same color as blood," he said, "and I know blood is red, so this must be red as well."  Naming colors had to be done with a cognitive, logical process, not an automatic recognition as it is done by the rest of us.

It reminds me of my issue with recognizing faces, about which I've written here before.  Although I'm essentially face-blind, I can recognize people sometimes -- putting together what I remember of their hairstyle, coloration, whether or not they wear glasses, and even the way they stand or walk.  But it's nowhere near automatic; it's a logical sequence ("he's the guy who's tall and thin, wears wire-rim glasses, and has curly blond hair"), not an instantaneous recognition.  And it's easily foiled if a person changes hairstyles, wears more (or less) makeup than usual, or -- as I found out last year in one of my classes, when I at first didn't recognize a student I'd taught all year -- simply wears a baseball cap.

This research gives us a bit more information about the sometimes non-intuitive mechanisms by which we perceive the world.  The brain is a complex and fascinating machine.  As a former student once put it, "My brain is so complicated it can't even understand itself."  But it could be worse -- think of what it must be like to be a mantis shrimp.

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This week's Skeptophilia book recommendation is a classic: James Loewen's Lies My Teacher Told Me.  Loewen's work is an indictment not specifically of the educational system, but of our culture's determination to sanitize our own history and present our historical figures as if they were pristine pillars of virtue.

The reality is -- as reality always is -- more complex and more interesting.  The leaders of the past were human, and ran the gamut of praiseworthiness.  Some had their sordid sides.  Some were a strange mix of admirable and reprehensible.  But what is certain is that we're not doing our children, nor ourselves, any favors by rewriting history to make America and Americans look faultless.  We owe our citizens the duty of being honest, even about the parts of history that we'd rather not admit to.

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