Butterfly effect

Most of you probably know the basic story you were taught in high school biology; DNA has information-containing chunks called genes, which sit in specific places in packages called chromosomes.  Each of those genes is the instruction set for building a specific protein, and the instructions are read by creating an intermediary copy (called mRNA) of the specific gene in question, which then is transported to a structure in the cell called the ribosome, where the sequence is read and used to assemble the protein from smaller bits called amino acids.  The protein thus created -- it could be an enzyme, a structural protein, an energy carrier, a pigment, or any of dozens of other types -- goes on to do its specific job in the organism.

This pattern -- gene (DNA) to mRNA to protein -- was thought to be more or less the whole story by the people who unraveled the pattern, James Watson and Francis Crick, so in their typical self-congratulatory fashion they called it the "Central Dogma of Molecular Genetics."  (And if you know anything about their history, you'll understand why I'm calling it "typical.")  So it was a considerable shock when researchers found out that there was DNA in the genome of every species studied that didn't work this way.

It was a considerably bigger shock when it was found that the amount of DNA that did work this way was around one percent.

You read that right; between ninety-eight and ninety-nine percent of your genome is non-coding DNA.  It does not encode the instructions for building proteins.  Watson and Crick's "Central Dogma" only applies directly to less than two percent of an organism's DNA.  When this was discovered in the 1960s and 1970s, researchers (speaking of arrogance...) called it "junk DNA," following the apparent line of reasoning, "If we don't know what it does right now, it must be useless."

The whole "junk DNA" moniker never made sense to me, especially with the discovery of short tandem repeats, chunks of DNA between two and ten base pairs long that repeat over and over again (the average number of repeats is twenty-five).  Short tandem repeats are common in eukaryotic DNA, and their function is unknown.  That they do have a function -- and are not, in fact, "junk" -- is strongly supported by the fact that they're evolutionarily conserved.  Mutations happen, and if there really was no function at all for STRs, over time the pattern would get lost as mutations altered one base pair after another.  The fact that the pattern has been maintained argues that they have an important function of some kind, and mutations knock that function out and are heavily selected against.

We just don't know what it is yet.

The reason all this comes up is the discovery by a team right here in my neck of the woods, at Cornell University, that at least some of the patterns in butterfly wings are controlled by "genetic switches" in their non-coding DNA.  The team, led by Anyi Mazo-Vargas, looked at forty-six regions of non-coding DNA, and found out that a significant number of them, when disabled (a technique called gene knockout), cause huge changes in the butterfly's wing pattern.  Take, for example, the brightly-colored Heliconius butterflies:

[Image licensed under the Creative Commons Heliconius mimicry, CC BY 2.5]

Knock out a DNA sequence called WntA, and the stripes disappear; disable Optix, and the wings come out jet black.

Other than the obvious deduction -- that these non-coding sequences are acting as switches determining deposition of pigments and arrangements of the cells that generate iridescence -- not much is known about how these sequences work.  "We see that there's a very conserved group of switches that are working in different positions and are activated and driving the gene," Mazo-Vargas said.  

"We have progressively come to understand that most evolution occurs because of mutations in these non-coding regions," added Robert Reed, who co-authored the paper.  "What I hope is that this paper will be a case study that shows how people can use this combination of ATAC-seq and CRISPR [two techniques used in gene modification and knockout] to begin to interrogate these interesting regions in their own study systems, whether they work on birds or flies or worms."

So once again, as we look more closely at things, we find intricacies we never dreamed of.  What I love about research like this is that a seemingly small discovery -- that small stretches of non-coding DNA control macroscopic traits like coloration -- could have an impact on our understanding of how genetics works in general.

Truly -- a "butterfly effect."

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It's all becoming clear

The phenomenon of transparency is way more interesting than it appears at first.

I remember thinking about the concept when I was a kid, the first time I watched the classic horror/science fiction film The Invisible Man.  Coincidentally, I was in high school and was in the middle of taking biology, and we'd recently learned how the human eye works, and Claude Rains's predicament took on an added layer of difficulty when it occurred to me that if he was invisible -- including his retina -- not only would we not be able to see him, he wouldn't be able to see anything, because the light rays striking his eye would pass right through it.  Since it's light being absorbed by the retina that stimulates the optic nerve, and Rains's retinas weren't absorbing any light (or we'd have seen them floating in the air, which is kind of a gross mental image), he'd have been blind.

So an invisibility potion isn't nearly as fun an idea as it sounds at first.

It wasn't until I took physics that I learned why some objects are transparent, and why (for example) it's harder to see a glass marble underwater than it is in the air.  Transparency results from a molecular structure that neither appreciably absorbs nor scatters light; more specifically, when the substance in question has electron orbitals spaced so that they can't absorb light in the visible region of the spectrum.  (If not, the light passes right through it.)  Note that substances can be transparent in some frequency ranges and not others; water, for example, is largely transparent in visible light, but is opaque in the microwave region -- which is why water heats up so quickly when you put it in a microwave oven.

The second bit, though, is where it really gets interesting.  Why are some transparent objects still clearly visible, and others are nearly invisible?  Consider my example of glass in air as compared to glass under water.  You can see through both, but it's much harder to discern the outlines of the glass underwater than it is in air.  Even more strikingly -- submerge a glass object in a colorless oil, and it seems to vanish entirely.

The reason is something called the index of refraction -- how much a beam of light is bent when it passes from one transparent medium to another.  A vacuum has, by definition, an index of refraction of exactly 1.  Air is slightly higher -- 1.000293, give or take -- while pure water is about 1.333.  The key here is that the more different the two indices are, the more light bends when crossing from one to the other (and the more the light tends to reflect from the surface rather than refract).  This is why the boundary between air and water is pretty obvious (and why those amazing photographs of crystal-clear lakes, where you can see all the way to the bottom and boats appear to be floating, are always taken from directly overhead, looking straight down; even at a slight angle from perpendicular, you'd see the reflected portion of the light and the water's surface would be clearly visible).

Likewise, the more similar the indices of refraction are, the less light bends (and reflects) at the boundary, and the harder it is to see the interface.  Glass, depending on the type, has an index of refraction of about 1.5; olive oil has an index of 1.47.  Submerge a colorless glass marble in a bottle of olive oil, and it seems to disappear,

The reason all this comes up has to do with the evolution of transparency in nature -- as camouflage.  It's a pretty clever idea, that, and is used by a good many oceanic organisms (jellyfish being the obvious example).  None of them are completely transparent, but some are good enough at index-of-refraction-matching that they're extremely hard to see.  It's much more difficult for terrestrial organisms, though, because air's lower index of refraction -- 1, for all intents and purposes -- is just about impossible to match in any conceivable form of living tissue.

Some of them come pretty close, though.  Consider the "skeleton flower," Diphylleia grayi, of Japan, which has white flowers that become glass-like when they're wet:

The transparency of the flower petals is likely to be a fluke, as it's hard to imagine how it would benefit the plant to evolve a camouflage that only works when the plant is wet.  An even cooler example was the subject of a paper in the journal eLife last week, and looked at a group of butterflies called (for obvious reasons) "glasswing butterflies."  These are a tropical group with clear windows in their wings -- but, it turns out, they're not all closely related to each other.

In other words, we're looking at an example of convergent evolution and mimicry.

The study found that some of the clear-wings are toxic, and those lack an anti-glare coating on the "windows."  This makes the light more likely to reflect from the surface, rather than pass through; think about the glare from a puddle in the road on a sunny day.  Those flashes of light act as a warning coloration -- an advertisement to predators that the animal is toxic, distasteful, or dangerous.

The glasswing butterfly Greta oto of Central and South America [Image is licensed under the Creative Commons David Tiller, Greta oto, CC BY-SA 3.0]

The coolest part of last week's paper was in looking at the mimics; the species that had the transparent windows but weren't themselves toxic.  Unlike the toxic varieties, those species had evolved anti-glare coatings on the windows, so the mimicry was obvious in bright light -- but in shadow, the lack of glare made them seem to disappear completely.  In other words, the clear parts act as a warning coloration in sunshine, and as pure camouflage in the shade!

Even more amazing is that a number of only distantly-related species have stumbled on the same mimicry -- so this particular vanishing act has apparently evolved independently more than once.  A good idea, apparently, shouldn't just be wasted on one species.

So that's today's cool natural phenomenon, which I hope I've clarified sufficiently.  There seems truly to be no end to the way living things can take advantage of physical phenomena for their own survival -- as Darwin put it, to generate "endless forms most beautiful and most wonderful."

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It's kind of sad that there are so many math-phobes in the world, because at its basis, there is something compelling and fascinating about the world of numbers.  Humans have been driven to quantify things for millennia -- probably beginning with the understandable desire to count goods and belongings -- but it very quickly became a source of curiosity to find out why numbers work as they do.

The history of mathematics and its impact on humanity is the subject of the brilliant book The Art of More: How Mathematics Created Civilization by Michael Brooks.  In it he looks at how our ancestors' discovery of how to measure and enumerate the world grew into a field of study that unlocked hidden realms of science -- leading Galileo to comment, with some awe, that "Mathematics is the language with which God wrote the universe."  Brooks's deft handling of this difficult and intimidating subject makes it uniquely accessible to the layperson -- so don't let your past experiences in math class dissuade you from reading this wonderful and eye-opening book.

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

A genetic cut-and-paste

If I had to pick one technology that I think will make the most different to human quality of life thirty years from now, I would pick CRISPR/Cas9.

CRISPR stands for "Clustered Regularly Interspaced Short Palindromic Repeats," a sequence of repetitive DNA in prokaryotes (bacteria) that interacts with a gene called Cas9 to chop up and inactivate foreign DNA.  At first, it seemed like it would interest only someone with a fascination for bacterial genetics.

Then it was discovered that you could guide CRISPR/Cas9 to specific sequences in DNA using a piece of RNA as a guide.  Think of it as a pair of scissors with a laser sight.  Molecular biologists saw the implications immediately; with that tool, you could cut out any piece of DNA you wanted, insert new genes, inactivate old ones -- you veritably have a cut-and-paste function for the genetic code.

The potential applications to treat human disease are nearly endless.  Disorders where the affected individuals have an inoperative gene, and therefore lack the specific protein it produces, might have the error repaired by splicing in a corrected copy.  (Possible candidates for this are cystic fibrosis and hemophilia.)  On the other hand, disorders where the defective gene makes a damaged end product -- such as sickle-cell anemia and Huntington's disease -- might have the faulty gene cut out and discarded.

All of this is still in the future, however.  At the moment, scientists are playing with CRISPR, seeing what it can do.  And just last week, a team at Cornell University used CRISPR/Cas9 on butterflies to inactivate specific genes...

... and completely changed the color patterns on their wings.

One of the species they worked on was the Gulf Fritillary (Agraulis vanillae), a beautiful black, orange, and gold butterfly native to the southeastern United States.

[image courtesy of photographer Jonathan Zander and the Wikimedia Commons]

When a gene called optix was selectively inactivated by CRISPR/Cas9, the result was stunning.  All of the orange and gold regions turned velvety jet black.  White spots became a metallic silver.  Silencing a different gene, WntA, had a different result -- stripes blurred, eyespots disappeared, edges became indistinct.

Anyi Mazo-Vargas, one of the authors of the paper, calls genes like optix and WntA "paintbrush genes."  "Wherever you put them," Mazo-Vargas said, "you'll have a pattern."

They tested optix deletion on other species, and found similar results, even in species that have been evolutionarily separated for 80 million years.  Colorful butterflies come out looking monochrome. "They just turn grayscale,” said Robert Reed, who led the study.  "It makes these butterflies look like moths, which is pathetically embarrassing for them."

The fact that these genes can be inactivated, almost like flipping a switch, and have such body-wide results is nothing short of spectacular.  Of his earlier work in studying color genes in butterflies, Reed said, "It was convincing but we didn’t know exactly what these genes were doing. Without the ability to delete the genes, and see if their absence changed the butterfly wings, we didn’t have the final proof.  There’s been this frustrating wall that I’ve banged my head against...  CRISPR is a miracle.  The first time we tried it, it worked, and when I saw that butterfly come out ... the biggest challenge of my career had just turned into an undergraduate project."

Of their first success -- the jet-black-and-silver Gulf Fritillary -- Reed said, "It was amazing to see that thing crawl out of the pupa... it was the most heavy metal butterfly I've ever seen."

All of this is one more indication of why we should all be in support of pure research.  On one level, this might sound kind of silly to the layperson -- some scientists tinkering around and changing the color of butterfly wings.  But when you see where such research could lead, and the potential application to human health, it's absolutely stunning.

In my opinion, it won't be long before we're using the same genetic cut-and-paste not to fiddle with "paintbrush genes" in butterflies, but to repair genetic defects in humans.  And that would be the biggest leap in medical science since the invention of vaccines.