The biochemical symphony

Sometimes I run into a piece of scientific research that's so odd and charming that I just have to tell you about it.

Take, for example, the paper that appeared in ACS Nano that ties together two of my favorite things -- biology and music.  It has the imposing title, "A Self-Consistent Sonification Method to Translate Amino Acid Sequences into Musical Compositions and Application in Protein Design Using Artificial Intelligence," and was authored by Chi-Hua Yu, Zhao Qin, Francisco J. Martin-Martinez, and Markus J. Buehler, all of the Massachusetts Institute of Technology.  Their research uses a fascinating lens to study protein structure: converting the amino acid sequence and structure of a protein into music, then having an AI software study the musical pattern that results as a way of learning more about how proteins function -- and how that function might be altered.

What's cool is that the musical note that represents each amino acid isn't randomly chosen.  It's based on the amino acid's actual quantum vibrational frequency.  So when you listen to it, you're not just hearing a whimsical combination of notes based on something from nature; you're actually hearing the protein itself.

[Image licensed under the Creative Commons © Nevit Dilmen, Music 01754, CC BY-SA 3.0]

In an article about the research in MIT News, written by David L. Chandler, you can hear clips from the Yu et al. study.  I recommend the second one especially -- the one titled "An Orchestra of Amino Acids" -- which is a "sonification" of spider silk protein.  The strange, percussive rhythm is kind of mesmerizing, and if someone had told me that it was a composition by an avant-garde modern composer -- Philip Glass, perhaps, or Steve Reich -- I would have believed it without question.  But what's coolest about this is that the music actually means something beyond the sound.  The AI is now able to discern the difference between some basic protein structures, including two of the most common -- the alpha-helix (shaped like a spring) and the beta-pleated-sheet (shaped like the pleats on a kilt -- because they sound different.  This gives us a lens into protein function that we didn't have before.  "[Proteins] have their own language, and we don’t know how it works," said Markus Buehler, who co-authored the study.  "We don’t know what makes a silk protein a silk protein or what patterns reflect the functions found in an enzyme.  We don’t know the code."

But this is exactly what the AI, and the scientists running it, hope to find out.  "When you look at a molecule in a textbook, it’s static," Buehler said.  "But it’s not static at all.  It’s moving and vibrating.  Every bit of matter is a set of vibrations.  And we can use this concept as a way of describing matter."

This new approach has impressed a lot of people not only for its potential applications, but from how amazingly creative it is.  This is why it drives me nuts when people say that science isn't a creative process. They apparently have the impression that science is pure grunt work, inoculating petri dishes, looking at data from particle accelerators, analyzing rock layers.  But at its heart, the best science is about making connections between disparate ideas -- just like this research does -- and is as deeply creative as writing a symphony.

"Markus Buehler has been gifted with a most creative soul, and his explorations into the inner workings of biomolecules are advancing our understanding of the mechanical response of biological materials in a most significant manner," said Marc Meyers, professor of materials science at the University of California at San Diego, who was not involved in this work.  "The focusing of this imagination to music is a novel and intriguing direction. his is experimental music at its best.  The rhythms of life, including the pulsations of our heart, were the initial sources of repetitive sounds that engendered the marvelous world of music.  Markus has descended into the nanospace to extract the rhythms of the amino acids, the building blocks of life."

What is most amazing about this is the potential for the AI, once trained, to go in reverse -- to be given an altered musical pattern, and to predict from that what the function of a protein engineered from that music would do.  Proteins are perhaps the most fundamental pieces of living things; the majority of genes do what they do by making proteins, which then guide processes within the organism (including frequently affecting other genes).  The idea that we could use music as a lens into how our biochemistry works is kind of stunning.

So that's your science-is-so-freaking-cool moment for the day.  I peruse the science news pretty much daily, looking for intriguing new research, but this one's gonna be hard to top.  Now I think I'm going to go back to the paper and click on the sound links -- and listen to the proteins sing.

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The domino effect

I find it fascinating how many important discoveries were made more or less by accident -- either because a researcher was looking for something and stumbled upon something else, or because (s)he was just playing around in the lab and noticed something cool.

Here are a few of my favorite examples:

1. Two researchers, George Beadle and Edward Tatum, were researching nutrition in a mold called Neurospora, and were particularly interested in why some strains of Neurospora starved to death even when given adequate amounts of food.  Their research generated the concept of "one gene-one protein" -- the basis of our understanding of how genes control traits.
2. Charles Richet was studying how the toxin of a rare species of jellyfish affects the body.  His research led to the discovery of how anaphylactic shock works -- and the development of the epi pen, saving countless lives from death because of bee sting allergies, nut allergies, and so on.
3. Wilhelm Röntgen was researching the newly-invented cathode-ray tube, which at that point had no practical applications whatsoever.  That is, he was playing around.  He noticed that when he activated the tube, even though it was completely covered, some fluorescent papers at the other end of the room began to glow in the dark.  He had just discovered x-rays.
4. In 1945 an engineer named Percy Spencer was working with a device called a magnetron that looked like it might have applications in ground-based radar systems.   While messing about with it, he noticed that a chocolate bar in his pocket had melted.   He patented a design that year that we now call the "microwave oven."
5. Alexander Fleming was something of a ne'er-do-well in the scientific world.  He did a lot of raising of bacteria on plates, and his favorite hobby was to take brightly-colored species of bacteria and paint them on agar media to make pictures.  One day, a mold spore blew in and landed on one of his picture-cultures and spoiled it.  His further investigation of how the mold spoiled the culture led to the discovery of the first antibiotic, penicillin.
6. Roy Plunkett was working with gases that could be used to quickly cool vessels in scientific experiments, and after one failure he found that the vessel was left coated with a slick substance.  He eventually named it "Teflon."

Stuff like this is one good reason to support pure research.  The criticism "I don't see what possible application this can have" is best answered, "you don't see what possible application this can have yet."  We never lose by finding out more about the universe we live in.  My own opinion is that there's a benefit to knowing stuff even if it never does have a practical use; but even if you're a pure utilitarian, there's no question that putting money into pure research pays back far more than it costs.

This came to mind because of a cool study that appeared two weeks ago in the journal Physical Review Applied about what controls the speed of collapse of a row of dominoes.

[Image licensed under the Creative Commons Nara Cute, Wallpaper kartu domino, CC BY-SA 4.0]

It's hard not to be fascinated by the phenomenon.  For example, take five minutes and watch this amazing record-setting collapse -- of thirty-two thousand dominoes:

Watching this is kind of mesmerizing, but it did bring up two things: (1) I would never have the patience to do this, and (2) if I did, knowing my luck, I'd be somewhere around domino #31,500 and my dog would come galumphing in, knock the whole thing down, and I'd have to start over.

The researchers into the domino collapse phenomenon found that the speed with which the row collapses is dependent upon two things -- the friction between the dominoes and the surface they're standing on, and the friction between one domino and the next one in line.  If you want the collapse to propagate quickly, you want a high coefficient of friction between the dominoes and the surface, but a low coefficient between the dominoes and each other.  The former means that there won't be much slip-back as the domino falls -- as it tips over, the bottom corner of the domino stays put, and the piece pivots around that fulcrum so that most of the energy of the fall is transmitted into the next domino in line.  The latter means that once a domino hits the next one, the slipping of the two surfaces across each other doesn't get "hung up" and lose energy from friction as the top corner of one domino slides across the surface of the next one.

The result lines up pretty well with common sense, but it's cool to have it confirmed experimentally, and that the researchers actually came up with a mathematical model that predicts the velocity of the collapse.

So, what use is it?  We don't know.  Maybe it could be used as a model of systems you don't want to collapse -- like buildings.  But one of the fantastic things about science is when a model in one area of study turns out to illuminate something completely different.  Maybe the mathematical principles of domino collapse rate could be applied to other phenomena that are caused by a phase transition -- a sudden change between one state and another, often caused by a tiny input of energy (like a finger pushing over a single domino).  There are a number of familiar phenomena that involve rapid phase transitions, including earthquakes, explosive volcanic eruptions, breakup of the ice sheet over a river during the spring thaw, and the firing of a neuron once the stimulus threshold is crossed.

Like I said earlier: the beauty of pure research is that we don't know what kind of applications it might have.  With the brilliant minds in the scientific community, you never know where it might lead.  One little paper on a curiosity of physics might trigger new research and go places you'd never expect.

You might even call it...

... the domino effect.

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The evolution of Little Red Riding Hood

Every once in a while, I'll run across a piece of scientific research that is so creative and clever that it just warms my heart, and I felt this way yesterday when I stumbled onto a link to the article in PLoS ONE called "The Phylogeny of Little Red Riding Hood," by Jamshid Tehrani of the University of Bristol.

The reason I was delighted by Tehrani's paper is that it combines two subjects I love -- evolutionary biology and mythology and folklore.  The gist of what Tehrani did is to use a technique most commonly used to assemble species into "star diagrams" -- cladistic bootstrap analysis -- to analyze worldwide versions of the "Little Red Riding Hood" story to see to what degree a version in (for example) Senegal was related to one in Germany.

Cladistic bootstrap analysis generates something called a "star diagram" -- not, generally, a pedigree or family tree, because we don't know the exact identity of the common ancestor to all of the members of the tree, all we can tell is how closely related current individuals are.  Think, for example, of what it would look like if you assembled the living members of your family group this way -- you'd see clusters of close relatives linked together (you, your siblings, and your first cousins, for example) -- and further away would be other clusters, made up of more distant relatives grouped with their near family members.

So Tehrani did this with the "Little Red Riding Hood" story, by looking at the similarities and differences, from subtle to major, between the way the tale is told in different locations.  Apparently there are versions of it all over the world -- not only the Grimm Brothers Fairy Tales variety (the one I know the best), but from Africa, the Middle East, India, China, Korea, and Japan.  Oral transmission of stories is much like biological evolution; there are mutations (people change the story by misremembering it, dropping some pieces, embellishment, and so on) and there is selection (the best versions, told by the best storytellers, are more likely to be passed on).  And thus, the whole thing unfolds like an evolutionary lineage.

In Tehrani's analysis, he found three big branches -- the African branch (where the story is usually called "The Wolf and the Kids"), the East Asian branch ("Tiger Grandmother"), and the European/Middle Eastern Branch ("Little Red Riding Hood," "Catterinella," and "The Story of Grandmother").  (For the main differences in the different branches, which are fascinating but too long to be quoted here in full, check out the link to Tehrani's paper.)

Put all together, Tehrani came up with the following cladogram:

WK = "The Wolf and the Kids," TG = "Tiger Grandmother," "Catt" = "Catterinella," GM = "The Story of Grandmother," and RH = "Little Red Riding Hood;" the others are less common variations that Tehrani was able to place on his star diagram.

The whole thing just makes me very, very happy, and leaves me smiling with my big, sharp, wolflike teeth.

Pure research has been criticized by some as being pointless, and this is a stance that I absolutely abhor.  There is a completely practical reason to support, fund, and otherwise encourage pure research -- and that is, we have no idea yet what application some technique or discovery might have in the future.  A great deal of highly useful, human-centered science has been uncovered by scientists playing around in their labs with no other immediate goal than to study some small bit of the universe.  Further, the mere application of raw creativity to a problem -- using the tools of cladistics, say, to analyze a folk tale -- can act as an impetus to other minds, elsewhere, encouraging them to approach the problems we face in novel ways.

But I think it's more than that.  The fundamental truth here is that human mind needs to be exercised.  The "what good is it?" attitude is not only anti-science, it is anti-intellectual.  It devalues inquiry, curiosity, and creativity.  It asks the question "how does this benefit humanity?" in such a way as to imply that the sheer joy of comprehending deeply the world around us is not a benefit in and of itself.

It may be that Tehrani's jewel of a paper will have no lasting impact on humanity as a whole.  I'm perfectly okay with that, and I suspect Tehrani would be, as well.  We need to make our brains buckle down to the "important stuff," yes; but we also need to let them out to play sometimes, a lesson that the men and women currently overseeing our educational system need to learn.  In a quote that seems unusually apt, considering the subject of Tehrani's research, Albert Einstein said: "I am enough of an artist to draw freely upon my imagination.  Imagination is more important than knowledge.  Knowledge is limited.  Imagination encircles the world." 

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I was an undergraduate when the original Cosmos, with Carl Sagan, was launched, and being a physics major and an astronomy buff, I was absolutely transfixed.  Me and my co-nerd buddies looked forward to the new episode each week and eagerly discussed it the following day between classes.  And one of the most famous lines from the show -- ask any Sagan devotee -- is, "If you want to make an apple pie from scratch, first you must invent the universe."

Sagan used this quip as a launching point into discussing the makeup of the universe on the atomic level, and where those atoms had come from -- some primordial, all the way to the Big Bang (hydrogen and helium), and the rest formed in the interiors of stars.  (Giving rise to two of his other famous quotes: "We are made of star-stuff," and "We are a way for the universe to know itself.")

Since Sagan's tragic death in 1996 at the age of 62 from a rare blood cancer, astrophysics has continued to extend what we know about where everything comes from.  And now, experimental physicist Harry Cliff has put together that knowledge in a package accessible to the non-scientist, and titled it How to Make an Apple Pie from Scratch: In Search of the Recipe for our Universe, From the Origin of Atoms to the Big Bang.  It's a brilliant exposition of our latest understanding of the stuff that makes up apple pies, you, me, the planet, and the stars.  If you want to know where the atoms that form the universe originated, or just want to have your mind blown, this is the book for you.

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

Skipping the comments

A few days ago I was casting about for topics for Skeptophilia, and was perusing that amazing clearinghouse for everything from the profound to the ridiculous, Reddit.

I ran into a link to a Science Daily article about some delightful research that came out of a collaboration between physicists at four different universities in China, which centered on the physics of skipping rocks.  I absolutely love skipping rocks, and whenever I'm by a lake I will spend inordinate amounts of time finding, and then slinging, the most perfectly flat stones I can find, trying to beat my record (which stands at thirteen skips).

[Image licensed under the Creative Commons Killy Ridols, Stone skimming -Patagonia-9Mar2010, CC BY-SA 2.0]

The math in the original research is way way beyond my ability to understand, despite my bachelor's degree in physics (but to be fair, I kind of sucked as a physics student).  The reader is put on notice that it's going to be rough going immediately, because the first thing the authors do is to define no fewer than 49 different variables they considered in modeling the behavior of a skipping stone.

So I went back to the summary in Science Daily, and found a nicely dumbed-down explanation of what they'd done.  They used an aluminum disk launched by an air compressor in place of the typical round stone and person's arm, with a motorized feature that started the disk spinning at a chosen rate before launch.  Attached to the disk was a set of sensors that monitored the disk while in flight, because -- as you know if you're a rock-skipper -- it can all happen so fast that it's hard to keep track of all-important data like how much the rock's path curves (and which direction), the angle your rock hits the water, and the number of skips you get.

The upshot of it was that the rate of spin is critical, because spinning induces the gyroscopic effect and stabilizes the pitch of the rock as it flies.  Less intuitively obvious, to me at least, is that the vertical acceleration of the rock has to be higher than a certain threshold (which turns out to be about four times the acceleration due to gravity) in order for the stone to bounce.

So I thought all this was pretty cool -- taking a familiar phenomenon and explaining how complex it really is using mathematical modeling.

Then I did what you should never, ever, ever do.

I looked at the comments section.

I swear, I should get fitted out with something like those "Invisible Fence" dog collars, only instead of zapping me when I cross a line on our property, it would zap me when I try to look at the comments section.  Any comments section.  Because I started sputtering with rage almost immediately, when I saw comments like these -- which, for the record, are reproduced here verbatim, because I don't want to write sic over and over:

• This is what scientists do?  Spend their time fucking around throwing rocks in the water.  How about doing stuff that might actually help people.
• I cant believe our tax dollars is going to pay for bullshit "research" like this.
• Whats next, the physics of yoyos?
• Yeah I believe it.  Liberal loonies love this kind of stuff.  Waste of time.
• SMH you can't make this shit up
• Whose approving these grant appliactions?  FFS no wonder nooone trusts scientists to tell the truth when there playing kids games instead of working.

More sensitive readers may want to plug their ears.

WILL ALL OF YOU ANTI-SCIENTIFIC, ILLITERATE YAHOOS KNUCKLE-DRAG YOUR WAY BACK TO YOUR CAVES, AND LEAVE THE INTELLECTUAL COMMENTARY TO PEOPLE WHO HAVE AN ACTUAL INTELLECT?

I mean, really.

First of all, zero American tax dollars were spent on this study, because the entire thing was done in China.  I know we Americans have a regrettable tendency to think "America" = "the entire world," but all you have to do is look at the author affiliation list, or even the line in the Science Daily summary that says the research was done by "scientists from several universities in China."  And while the research itself studied stone-skipping, the model has applications to a lot of important stuff, which you'd have figured out if you bothered to look at the very first line of the original paper: "Although skipping stones seems like a time-honored pastime, an in-depth study of this game is of vital importance for the understanding of the water landing of space flight re-entry vehicles and aircraft, hull slamming, antitorpedo and antisubmarine water entry, etc."

And even if the researchers hadn't pointed out in the introduction to the paper exactly what the potential applications are, I absolutely abhor the attitude that pure research -- investigating a scientific question without regard to immediate utility -- is useless.  It's worth pointing out how many times what seemed like "nothing more than pure research" generated something that turned out to be incredibly important.  Here are a few examples that come to mind:

1. Two researchers, George Beadle and Edward Tatum, were researching nutrition in a mold called Neurospora, and were particularly interested in why some strains of Neurospora starved to death even when given adequate amounts of food.  Their research generated the concept of "one gene-one protein" -- the basis of our understanding of how genes control traits.
2. Charles Richet was studying how the toxin of a rare species of jellyfish affects the body.  His research led to the discovery of how anaphylactic shock works -- and the development of the epi pen, saving countless lives from death because of bee sting allergies, nut allergies, and so on.
3. Wilhelm Röntgen was researching the newly-invented cathode-ray tube, which at that point had no practical applications whatsoever.  That is, he was playing around.  He noticed that when he activated the tube, even though it was completely covered, some fluorescent papers at the other end of the room began to glow in the dark. He had just discovered x-rays.
4. Alexander Fleming was something of a ne'er-do-well in the scientific world. He did a lot of raising of bacteria on plates, and his favorite hobby was to take brightly-colored species of bacteria and paint them on agar media to make pictures.  One day, a mold spore blew in and landed on one of his picture-cultures and spoiled it.  His further messing-about with how the mold spoiled the culture led to the discovery of the first antibiotic, penicillin.
5. Roy Plunkett was working with gases that could be used to quickly cool vessels in scientific experiments, and after one failure he found that the vessel was left coated with a slick substance.  He eventually named it "Teflon."

See why I get a little impatient?

But I think what gets me most about this whole thing, and comments sections in general, is how people who are obviously ignorant on a subject still feel like their opinions have relevance.  I have a lot of faults, but at least I try not to pontificate on topics I know nothing about.

It once again reminds me of the wonderful quote by Isaac Asimov: "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that 'my ignorance is just as good as your knowledge.'"

So, that's my maddening excursion of the day.  To the scientists who did the skipping-stone study, I'll say, "Bravo."  To the people who responded to it with sneers and snarls, I'll say, "Until you learn some science, shut the fuck up."  And to the Invisible Fence people, I'll reiterate my request for a Comments-Section Collar.  I bet you could make some serious cash selling those.

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This week's Skeptophilia book recommendation is pure fun: Arik Kershenbaum's The Zoologist's Guide to the Galaxy: What Animals on Earth Reveal About Aliens and Ourselves.  Kershenbaum tackles a question that has fascinated me for quite some time; is evolution constrained?  By which I mean, are the patterns you see in most animals on Earth -- aerobic cellular respiration, bilateral symmetry, a central information processing system/brain, sensory organs sensitive to light, sound, and chemicals, and sexual reproduction -- such strong evolutionary drivers that they are likely to be found in alien organisms?

Kershenbaum, who is a zoologist at the University of Cambridge, looks at how our environment (and the changes thereof over geological history) shaped our physiology, and which of those features would likely appear in species on different alien worlds.  In this fantastically entertaining book, he considers what we know about animals on Earth -- including some extremely odd ones -- and uses that to speculate about what we might find when we finally do make contact (or, at the very least, detect signs of life on an exoplanet using our earthbound telescopes).

It's a wonderfully fun read, and if you're fascinated with the idea that we might not be alone in the universe but still think of aliens as the Star Trek-style humans with body paint, rubber noses, and funny accents, this book is for you.  You'll never look at the night sky the same way again.

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

Space warp

I honestly don't understand how there are people who don't find science exciting.

Yes, I know that identifies me as a science nerd.  No, I don't care.  I just can't fathom how you wouldn't find it fascinating to comprehend a little more about the way the universe works.

This comes up because of an article by Jake Parks I ran into a couple of days ago over at the site Astronomy, called, "Star is Confirmed Single and Ready to Test Einstein’s Theory."  Despite the sound of the title, this has nothing to do with a nice-looking young Hollywood actor who is ready to go out on the dating circuit.  It's about a confirmation of a corollary of Einstein's General Theory of Relativity -- the idea of gravitational redshift.

The idea here is that the presence of a massive object actually warps the fabric of space -- stretches it in rather the same fashion that a bowling ball would depress the surface of a trampoline.  This, in fact, is what gravity really is; the fact that the Earth travels in an elliptical orbit around the Sun is because the Sun's enormous mass bends space, and the Earth travels along the lines of that curvature. (Picture someone rolling a marble toward the bowling-ball-on-a-trampoline I referenced earlier for a two-dimensional analog.)

[image courtesy of the Wikimedia Commons]

Where it gets really interesting is that if you have a light-emitting object travel past something that's highly massive, not only would its path change, but it would bend the light being emitted.  Because the space itself is stretched by the presence of the more massive object, the light would be stretched out -- red-shifted -- as it tries to "climb out of the gravity well."

It's never been observed before -- but astronomers have a good chance of observing it in a few months.  A star called S0-2 is going to be making a pass in front of Sagittarius A, the supermassive black hole at our galaxy's center.  As the star moves between us and the black hole, its light should be significantly redshifted -- a finding that would be a major win for Einstein's theory.

"It will be the first measurement of its kind,” said Tuan Do, deputy director of the Galactic Center Group, who co-authored the study.  "Gravity is the least well-tested of the forces of nature.  Einstein’s theory has passed all other tests with flying colors so far, so if there are deviations measured, it would certainly raise lots of questions about the nature of gravity!"

It was recently proven that S0-2 is not a binary (double) star system -- an important bit of information, as if it had been, it would have significantly complicated the possibility of observing the predicted redshift.

"We have been waiting 16 years for this," said Devin Chu, study co-author and graduate student of astronomy at UCLA.  "We are anxious to see how the star will behave under the black hole’s violent pull.  Will S0-2 follow Einstein’s theory?  Or will the star defy our current laws of physics?  We will soon find out!"

Can't you just hear the excitement in his voice?

I can already hear the naysayers as well, though -- how much money is being put into this research?  What useful outcome will it generate?  I don't know the answer to the first question, and I don't much care; but the answer to the second is, "we don't know yet -- and that's the point."

There are hundreds of discoveries that were made by scientists doing basic research -- what might appear to the layperson as simple messing around with something that interested them.  Here are a few of my favorites:

1. Henri Becquerel was investigating the effects of phosphorescent minerals on photographic plates in his lab, and used a rock to weight down some plates wrapped in black paper.  When he developed the plates, they had a smudge in the middle, as if they'd been exposed to light, which was impossible.  Turns out the rock was uranium ore.  The result was that he'd just discovered radioactivity.
2. Roy J. Plunkett was experimenting with some chlorofluorocarbon gases he thought might have a use as coolants.  One of his formulations didn't work so well, but condensed out into a solid film on the inside of the container.  He examined it, and found that it had a very low coefficient of friction, and that water and other substances seemed not to adhere to it.  He named it "Teflon."
3. George Beadle and Edward Tatum were studying something few of us would find interesting -- metabolic pathways in a mold species called Neurospora.  They found that there were varieties of the mold that seemed to be unable to metabolize certain nutrients, a finding that was mystifying until they proposed that these varieties were missing a key enzyme.  They made the guess that those enzymes were missing because there was a defect in a specific gene -- and that's how a study of mold led to the "One Gene, One Protein" model of gene expression.
4. Harry Coover was trying to find a new material to use in making the lenses in plastic gun sights.  He was working with a group of chemicals called cyanoacrylates, but found that they were too sticky to be useful in lens making.  One of them, though, struck him as being useful for something else.  He sold the patent to Kodak.  They named it "SuperGlue."
5. In the early 1990s, some researchers at Pfizer were working with a compound called UK92480, which showed promise for opening up blood vessels in patients with angina pectoris.  It worked okay, but the researchers' ears perked up when male test subjects noted an unusual side effect of taking the compound.  They patented it under the trade name "Viagra," which has brought great happiness, lo unto this very day.

And so on and so forth.  My point is, we need to be doing basic research.  No, the gravitational redshift experiment might not ever amount to anything practical.  But then again, it might.  The point is, we don't know, and if we limit research to things we already expect are going to be useful, it's going to hobble science -- and rob us of the next generation of serendipitous discoveries.

Besides, there's a value simply in knowing.  We are at a point in our civilization where we have the technology and insight to unravel the deep secrets of the universe, and it's worthwhile doing that for its own sake.  The inspiration and joy we get from understanding one more bit of the world we live in is a worthwhile end in and of itself.  As the eminent astronomer Carl Sagan put it:  "Somewhere, something incredible is waiting to be known."

Postcards from Pluto

I spend a lot of time, here at Skeptophilia, railing at unscientific, irrational views of the world.  Today, I'd like to celebrate a major accomplishment of humanity: this morning, virtually as I'm writing this, the NASA spacecraft New Horizons is making the closest-ever pass of a spacecraft to Pluto.

The magnitude of this feat isn't obvious at first.  Pluto is a small target -- its radius is estimated at about 1,180 kilometers -- and it's so far away that it's hard to picture.  Pluto's average distance from the sun is about 6,000,000,000 kilometers, although its orbit is so eccentric that it varies from a perihelion of 4.4 billion to an aphelion of 7.3 billion kilometers.  So how amazing a feat is this?

Let me give you an analogy.  This is like hitting an object the size of a tennis ball with an object the size of a speck of dust -- from 175 kilometers away.

Thus far, the information that has been coming back has been breathtaking.  Already we have seen that the surface of the planet is rusty-red in color and has a pattern on its surface shaped like a heart; that it seems to have ice caps of some sort; and that on its surface is a mysterious dark formation that's been nicknamed "The Whale," whose structure is as yet undetermined  We stand to learn more about Pluto's composition and history, and the characteristics of its moon Charon -- which, at a radius of about 630 km, is over half as big as the planet itself.  (In fact, astronomer Neil deGrasse Tyson tweeted this weekend, "Pluto’s primary moon Charon is so large that their mutual center-of-mass lies not within Pluto but in empty space.")

Pluto, as seen from New Horizons on July 11, 2015 [image courtesy of NASA]

But even tiny Pluto -- one-sixth the mass of the Earth's Moon, and one-third its volume -- has four other moons.  They've been named Styx, Nix, Kerberos, Hydra, after other denizens of the Greek underworld (Charon, you'll remember, is the ferryman who brings dead souls across the River Styx).  Its surface seems to be made predominantly of various kinds of ice, including frozen nitrogen, methane, and carbon monoxide.  It's lightweight for its size -- its density is only about 2 grams per cubic centimeter, only twice the density of liquid water -- leading astronomers to conjecture that it has a rocky core, and a mantle composed primarily of liquid water and water ice.  If this is correct, Pluto may have the highest percentage composition of water of any object in the Solar System.

Pluto and Charon -- July 11, 2015 [image courtesy of NASA]

And the fun won't end with its closest pass this morning.  The probe is designed to keep sending back data for another sixteen months.  After that, it will continue sailing out of the Solar System, following Voyager 1, which was launched in 1977, and now zooming out into interstellar space, some 12 billion kilometers away.

Some naysayers -- and there are more than you'd think -- have asked why we put time, effort, and (lots of) money into such endeavors.  So we find out the composition of a celestial body five-some-odd billion kilometers away from us.  So what?  What good does it do us?

I think the reason is that knowledge, in and of itself, is a worthy goal.  Always looking at the profit motive -- what benefit will it bring? -- is ignoring the fact that the inspiration gained from reaching for, and achieving, a lofty goal has a worth that can't be measured in dollars.  How many young minds were inspired by previous successes in pure science -- the discovery of how DNA works, the first humans to reach the Moon, the uncovering of countless bizarre fossil animals by paleontologists, the first manned submarine to descend into the Marianas Trench?

And what did those minds go on to accomplish?

I look at the images coming back from New Horizons with nothing but a sense of wonder and curiosity.  Such missions represent one of humanity's most fundamental drives; the thirst for knowledge.  So when you see the images that are coming back from the furthest reaches of the Solar System, don't just think of them as pictures of a distant denizen of our Solar System.  Think of them as symbols of the highest aspirations of the human mind and spirit.

The evolution of Little Red Riding Hood

Every once in a while, I'll run across a piece of scientific research that is so creative and clever that it just warms my heart, and I felt this way yesterday when I stumbled onto a link to the article in PLoS ONE called "The Phylogeny of Little Red Riding Hood," by Jamshid Tehrani of the University of Bristol.

The reason I was delighted by Tehrani's paper is that it combines two subjects I love -- evolutionary biology and mythology and folklore.  The gist of what Tehrani did is to use a technique most commonly used to assemble species into "star diagrams" -- cladistic bootstrap analysis -- to analyze worldwide versions of the "Little Red Riding Hood" story to see to what degree a version in (for example) Senegal was related to one in Germany.

Cladistic bootstrap analysis generates something called a "star diagram" -- not, generally, a pedigree or family tree, because we don't know the exact identity of the common ancestor to all of the members of the tree, all we can tell is how closely related current individuals are.  Think, for example, of what it would look like if you assembled the living members of your family group this way -- you'd see clusters of close relatives linked together (you, your siblings, and your first cousins, for example) -- and further away would be other clusters, made up of more distant relatives grouped with their near family members.

So Tehrani did this with the "Little Red Riding Hood" story, by looking at the similarities and differences, from subtle to major, between the way the tale is told in different locations.  Apparently there are versions of it all over the world -- not only the Grimm Brothers Fairy Tales variety (the one I know the best), but from Africa, the Middle East, India, China, Korea, and Japan.  Oral transmission of stories is much like biological evolution; there are mutations (people change the story by misremembering it, dropping some pieces, embellishment, and so on) and there is selection (the best versions, told by the best storytellers, are more likely to be passed on).  And thus, the whole thing unfolds like an evolutionary lineage.

In Tehrani's analysis, he found three big branches -- the African branch (where the story is usually called "The Wolf and the Kids"), the East Asian branch ("Tiger Grandmother"), and the European/Middle Eastern Branch ("Little Red Riding Hood," "Catterinella," and "The Story of Grandmother").  (For the main differences in the different branches, which are fascinating but too long to be quoted here in full, check out the link to Tehrani's paper.)

Put all together, Tehrani came up with the following cladogram:

WK = "The Wolf and the Kids," TG = "Tiger Grandmother," "Catt" = "Catterinella," GM = "The Story of Grandmother," and RH = "Little Red Riding Hood;" the others are less common variations that Tehrani was able to place on his star diagram.

The whole thing just makes me very, very happy, and leaves me smiling with my big, sharp, wolflike teeth.

Pure research has been criticized by some as being pointless, and this is a stance that I absolutely abhor.  There is a completely practical reason to support, fund, and otherwise encourage pure research -- and that is, we have no idea yet what application some technique or discovery might have in the future.  A great deal of highly useful, human-centered science has been uncovered by scientists playing around in their labs with no other immediate goal than to study some small bit of the universe.  Further, the mere application of raw creativity to a problem -- using the tools of cladistics, say, to analyze a folk tale -- can act as an impetus to other minds, elsewhere, encouraging them to approach the problems we face in novel ways.

But I think it's more than that.  The fundamental truth here is that human mind needs to be exercised.  The "what good is it?" attitude is not only anti-science, it is anti-intellectual.  It devalues inquiry, curiosity, and creativity.  It asks the question "how does this benefit humanity?" in such a way as to imply that the sheer joy of comprehending deeply the world around us is not a benefit in and of itself.

It may be that Tehrani's jewel of a paper will have no lasting impact on humanity as a whole.  I'm perfectly okay with that, and I suspect Tehrani would be, as well.  We need to make our brains buckle down to the "important stuff," yes; but we also need to let them out to play sometimes, a lesson that the men and women currently overseeing our educational system need to learn.  In a quote that seems unusually apt, considering the subject of Tehrani's research, Albert Einstein said: "I am enough of an artist to draw freely upon my imagination. Imagination is more important than knowledge.  Knowledge is limited.  Imagination encircles the world."