Note (12/2015): Hi there! I'm taking some time off here to focus on other projects for a bit. As of October 2016, those other projects include a science book series for kids titled Things That Make You Go Yuck! -- available at Barnes and Noble, Amazon and (hopefully) a bookstore near you!

Co-author Jenn Dlugos and I are also doing some extremely ridiculous things over at Drinkstorm Studios, including our award-winning webseries, Magicland.

There are also a full 100 posts right here in the archives, and feel free to drop me a line at secondhandscience@gmail.com with comments, suggestions or wacky cold fusion ideas. Cheers!

Splice Junctions


· Categories: Biology, Genetics
What I’ve Learned:

Splice junctions: snipping ads out of your favorite programs since many millions of years ago.
“Splice junctions: snipping ads out of your favorite programs since many millions of years ago.”

Your DNA is crap.

Well, mostly it’s crap. But so is mine, and so is everyone else’s. For all the wondrous and amazing things our genetic code can accomplish, most of the really good stuff comes from a tiny little fraction of the genome. The rest is poorly understood, variable in quality and dubious in value.

In other words, your DNA is like cable TV.

Think of it this way: imagine all of your genetic material — three billion DNA base pairs tucked into every one of your cells, and responsible for making you “you” and not me or a goldfish or a head of iceberg lettuce — laid out in a line, like a TV program schedule. The “shows” are the genes — twenty to thirty thousand snippets of code that actually mean something. These can be read to produce proteins, which do just about all of the important work in your body, from grabbing the oxygen you breathe to growing toenails to helping you decide how much of that Buffy the Vampire Slayer marathon to sit through.

(All of it. Duh.)

But what’s between those shows you like, in the great abyss of “five hundred channels and nothing on”? Well, a couple of things. First, there are “pseudogenes” — stretches of DNA that look like they might do something interesting, but which have been mutated and mangled past the point of being useful. These are your knockoff shows and half-assed sequels: Who Wants to Be a Thousandaire?. Seinfarb. Home Alone 9: The Alonening. No good can come from these, clearly.

There are other bits of fluff, too. Near-endless repeats — possibly important in DNA for structure; used in TV as an excuse for USA to cram another NCIS rerun on the schedule. And long, droning stretches of apparently random sequence — the overnight informercials of the human genome.

But back to the genes. These are structured like TV shows in another important way: our genes contain commercials. In the genome, these are called “introns”, and are bits of DNA in between the important parts (which are called “exons”). When the gene is finally translated into a protein, these bits are snipped out in a process called splicing. And the edges of each intron in the line contain a short code called a splice junction, which tells the translation machinery where to snip the nonsense out.

So if a gene is like a television show, then a spliced gene is like watching with TiVo. Which is clearly better, because you can skip the commercials. And it’s made possible at the genetic level by splice junctions.

These splice junctions are tiny two-base sequences — usually GU (in RNA-speak) on one end, and AG on the other — that mark the intron they surround for snipping. But it’s not always a simple matter of lopping out the “commercials”. Many of our genes undergo a process called alternative splicing, where chunks containing multiple introns (and the exons between them) can be yanked out, producing multiple proteins from the same gene — sometimes with very different functions.

Think of alternative splicing as watching through the setup of, say, your favorite cop drama, then skipping to the end when they catch the perp. All that stuff in the middle is just filler and dusting for fingerprints, right? Much better.

So the next time your body translates a gene into a protein — which is all the time, obviously — give a little thanks to the splicing, and splice junctions, that make it possible, by editing out the crap in your cable lineup of a genome.

And then get back to that Buffython. Season 5 isn’t gonna watch itself, sunshine.

Actual Science:
Scitable – RNA splicing: introns, exons and spliceosome
CSHL DNA Learning Center – Transcription and translation: RNA splicing
NobelPrize.org – Alternative splicing
BitesizeBio – What is alternative splicing and why is it important?
Brown University – Lariats: how RNA splicing decisions are made

Image sources: Wikipedia (splicing), The Mental Elf (TV watcher), Uncoached and TimeToast (intron-snipping TiVos), Jack of All Trades… (Buffy squeal)

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Capillary Action


· Categories: Chemistry, Physics
What I’ve Learned:

Capillary action: Is that surface tension in your straw, or are you just happy to see me?
“Capillary action: Is that surface tension in your straw, or are you just happy to see me?”

For a long time, I thought “Capillary Action” was a Tom Clancy novel. That’s partly because I never paid attention in physics class, but mostly because I never paid attention to a Tom Clancy book until Harrison Ford got involved.

As it turns out, capillary action is less about espionage, and more about antigravity. And Alabama Slammers. And sometimes, apple bottom jeans. Yeah. It’s kind of a big deal.

Capillary action, or capillarity, describes the movement of fluids in narrow spaces, without any outside force — including gravity. In fact, capillary action often occurs in a direction opposite gravity — like when a bit of your Alabama Slammer climbs up the inside of the straw while it’s resting in the drink, as though the alcohol was trying to claw its way closer to your brain.

(This is why I only drink margaritas. The salted rims keep the alcohol demons at bay, until you decide you’re ready for tequila.

Also: you’re never ready for tequila. No one’s ready for tequila.)

This seemingly-magical uphill slide is actually caused by two physical forces, which are both attractive: the surface tension of the liquid (caused by mutual attraction of its molecules) and the adhesion (again, molecular attraction) of the liquid to the sides of the tube (or straw, or South American monkey-hunting blowgun, if that’s your thing) it’s in.

The combined action of these forces creates a meniscus, or a curve in the surface of the liquid. In fluids like water, the meniscus is concave, meaning the edges touching the walls are higher than the level in the center. As these edges adhere to the tube, the water is pulled further and further up the sides, and voila — capillary action.

It’s like how when some people put on their “skinny jeans”, some of the fluid around their midsections adheres to — and climbs up, and spills over — the sides. The smaller the container, the more climbing up (and out) is going to happen. So basically, capillary action is the muffin top of the physics world.

Except capillary action is caused by attractive forces, and muffin tops are more often caused by Frito pie. Which is far less attractive. Molecularly speaking, of course.

Capillary action is a pretty important phenomenon, though, and scientists have been poking at it for hundreds of years. Leonardo da Vinci first reported it, and some pretty big scientific cheeses — Robert Boyle, Jacob Bernoulli and Lord Kelvin, for instance — have studied and described it. Albert Einstein’s first scientific paper, in fact, was about capillarity. And that guy was pretty smart. He might have even been ready for tequila. Maybe.

Even outside our caipirinhas and our Calvin Kleins (which don’t technically count, but work with me here), capillary action is everywhere. Sponges use capillary action to suck up liquids; so do paper towels. It’s also how trees get moisture to their leaves. Your tear ducts are tiny straws that use capillary action to drain away tears. And those “wicking” fabrics that are all the rage among gym-goers (if somewhat less so among Frito pie fans)? That’s capillary action sucking the sweat off your body and keeping you cool and dry.

So the next time you’re sipping a Sex on the Beach or aerobicizing in Under Armour, take a moment to think about capillary action.

And also Harrison Ford. If they ever make the Capillary Action spy thriller, he’ll make it a lot more interesting.

Actual Science:
USGS – Capillary action
UC Davis ChemWiki – Capillary action
Scientific American – Frost flowers and hot capillary action
ScienceNews – Chemist tackles complex problems with simplicity
Fuck Yeah Fluid Dynamics – (Tears of wine)

Image sources: MIT (capillary action in action), LoveToKnow (Alabammer slammer), Dude I Want That (Muffin tops [you’re welcome]), Star Warped (Harrison, bemused)

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Quantum Fluctuation


· Categories: Physics
What I’ve Learned:

Quantum fluctuation: If you don't see it, you know it's working.
“Quantum fluctuation: If you don’t see it, you know it’s working.”

Space is pretty empty. You might think you’d like it, if you could get out there away from the traffic and the neighbors and the unending stream of Wendy’s commercials. But empty space isn’t all it’s cracked up to be. There aren’t a lot of wifi hotspots in space, for instance. It’s tough to find a decent cheeseburger out there, too. Also, oxygen, which a lot of us like to breathe now and then. Space is woefully lacking in that.

To be fair, there are also a lot fewer Wendy’s commercials. So empty space isn’t all bad.

On the other hand, “empty space” also isn’t all “empty”. That’s because of quantum fluctuation, tiny twitchy changes in energy coming and going in the ether. There’s no chemical reaction or chain of cause and effect going on. It’s just the cosmos playing peek-a-boo to keep itself entertained.

Quantum fluctuation is sometimes described as a constant barrage of “virtual particles” winking into existence, and near-immediately bumping into a bunch of also-just-winked anti-particles, annihilating both back into nothingness. Like two women entering a swank party, seeing they’re both wearing the same “one-of-a-kind” dress, and beating the hell out of each other in the parking lot. Except one of them is made of antimatter, and nobody’s drinking champagne cocktails.

If that all sounds a little weird, then not to worry: this “virtual particle” business isn’t actually the way quantum fluctuation works, exactly. That’s just a trick physicists use to make the math look prettier. Like most things in quantum physics (and pretty much all of quantum field theory, which this also is), the truth is much, much weirder than the model suggests.

(Also, the burgers at Wendy’s don’t look anything like those sandwiches in the commercials. Just in case you’ve been wondering.)

Rather than virtual particles, which you could imagine but don’t exist, quantum fluctuations are more like jitters in the invisible quantum energy fields stretching across the universe. Those do exist, but they don’t look like anything, and make your brain hurt to think about. You might wish for a rogue anti-particle to fling itself out of the ether and put you out of your misery. But no.

Instead, focus on a few basics. Quantum fluctuation is a consequence of the Heisenberg Uncertainty Principle — which sadly (or happily, depending on your point of view) has nothing to do with a certain meth-peddling chem teacher trying to decide on which pair of tighty whities to wear. Instead, the principle states that it is impossible to know both the current energy and the change in energy in a quantum field at the same time. From this, it follows that there’s going to be jitter — and that it’s unpredictable, uncontrollable and inevitable. Where a field exists, there will be static. The entire universe is like a scrambled soft core porn channel.

Which would frankly explain an awful lot. But not the constant Wendy’s commercials.

Why are quantum fluctuations important? For one, random “jitters” in the very, very early moments of the universe may be responsible for the characteristics we enjoy today. For another, though some quantum fluctuation-predicted measurements are spot on, there’s a many-, many-, many-magnitude of order discrepancy between the energy density of empty vacuum and the observed behavior of the universe. This is called the “cosmological constant problem” and theory-wise, something’s got to give. Even Einstein tangled with it. It’s kind of a big deal.

So the next time you’re staring into empty space, just know that there’s a universally crucial fireworks display happening far below the scale that you can see. But if you could, what would you learn? Is it just static? Is there some pattern, a quantum remnant of the cosmos’ birth?

Or is it just playing another goddamned Wendy’s commercial? Because I totally bet that’s it. Figures.

Actual Science:
Of Particular Significance – Quantum fluctuations and their energy
New Scientist – It’s confirmed: matter is merely vacuum fluctuations
A Review of the Universe – Quantum fluctuation
American Physical Society – Quantum fluctuations affect a row of distant ions
Phys.org – Physicists search for new physics in primordial quantum fluctuations
HETDEX – Vacuum energy, or Einstein’s blunder

Image sources: quantum fluctuations, Mooselicker (Wendy’s chomper), Archie dress scandal), Empty Kingdom (scrambly porn)

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Enantiomer


· Categories: Chemistry
What I’ve Learned:

Enantiomers: mirror, mirror on the wall... hey, who the hell is that?
“Enantiomers: mirror, mirror on the wall… hey, who the hell is that?”

You’d think organic chemistry is hard enough already. It’s all methyl-this and hydroxyl-that; here an H2, there an O2, everywhere a hydrocarbon — just figuring out a chemical formula is exhausting. Then there’s sorting out the structure and atomic bonds, which is a whole other ball of difficult. Surely, that should be enough to characterize a molecule, right?

Wrong. It turns out you can have two organic compounds with the same formula and the same structure — but they’re mirror images of each other. Like how your left hand looks like your right hand, but they’re not quite the same thing. Or how those creepy twins from The Shining look alike, but you just know one is a little bit eviler than the other.

In chemistry, these mirror images are called enantiomers. Most of them come about because carbon is, shall we say, somewhat “promiscuous”. A carbon atom can stably bond to four other atoms at once — which, seriously, who has the energy for that? I have trouble enough keeping just one atom happy at home.

Maybe that’s just me.

In an organic molecule, two of carbon’s potential bonds might be taken up by other carbons, forming a backbone for the molecule. That leaves two other spots for hydrogens, oxygens, carbons or just about any other randy atom with a loose electron to wander by and ask, “how you doin’?”

Meanwhile, the chained-up carbon often has a kink put in the angles of its other possible bonds. So if, say, a hydrogen and an oxygen atom jump in, one of these might end up bonding on a side more “left”, while the other winds up on a side facing more “right”. But the next time around, things could get flipped — the hydrogen could wind up where the oxygen was, and the oxygen where the hydrogen ought to be.

If we were making candy, this might be a Reese’s peanut butter cup. But we’re making organic molecules instead, so the two ever-so-slightly different molecules are called enantiomers. Less delicious, perhaps — but pretty important.

That’s because many enantiomers aren’t like creepy horror movie twins, who behave in exactly the same creepy, twinny way. They’re more like celebrity twins — say, Mary-Kate and Ashley Olsen, for instance. So maybe one enantiomer goes through a little goth phase, while the other does a stint on Weeds and then dabbles with plastic surgery.

Or, you know, maybe they just have different chemical properties. It’s not a perfect analogy.

Enantiomers are a big deal in pharmacology, because many clinical drugs are made from organic compounds and synthesizing these sometimes also means dragging a mirror-image molecule along for the ride. A soup of two enantiomers in equal amounts — called a racemic mixture — isn’t always a problem. Sometimes, the “twin” behaves similarly enough to be of some benefit.

Other times, the enantiomer is completely inactive — so while the dose of such a drug might be twice as high (to make sure enough of the “good twin” is present), it’s otherwise okay. In this case, scientists might leave the compound as-is or decide to purify it further; the compound in Lunesta is an example of a drug made from one enantiomer separated from its mirror twin.

In still other cases, the unintended enantiomer actually causes harmful side effects or competes with the compound in the body. For these drugs to work, they have to be made “enantiopure” — either separated from the mirror compound, or synthesized in such a way that only one form is possible. Imagine a world with a million Ashleys, and no Mary-Kates at all.

If you can.

Actual Science:
University of Calgary – Enantiomers
Rowland Institute / Harvard University – Molecular chirality
Chemhelper – Separation of enantiomers
BrightHub – Enantiopure medications: are chiral drugs more effective?

Image sources: Hemija u Matematickoj gimnaziji (enantiomers), Canvas, Cameras and Chianti (creepy twins), My Semi True Story (Reese’s commercial), Open Vintage (also fairly creepy twins)

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Gravity


· Categories: Physics
What I’ve Learned:

Gravity: what goes up... gets pretty complicated on the way down.
“Gravity: what goes up… gets pretty complicated on the way down.”

Gravity is a bitch. This is true for absent-minded skydivers jumping without their parachutes. But it’s also true for theoretical physicists. Because gravity doesn’t make much sense, and it doesn’t care who gets splatted on the ground trying to figure it out.

Gravity seems like it should easy. Everyone feels the pull of gravity — some of us more than we used to, and on body parts that have themselves “splatted” in shameful, horrifying ways. Discovering what’s underneath all that planetary tugging seems like a no-brainer.

But it is a brainer. A very big-brainer, actually.

Scientists recognize gravity as one of four fundamental forces of nature — and frankly, all four are pretty screwy. There’s the strong nuclear force, which may be mighty — but only works at scales smaller than atomic nuclei, so it’s also really tiny and sad. It’s the Rudy of universal forces.

Then there’s the weak nuclear force, which… I don’t know, holds the atoms of weak things together, maybe? Like that skinny kid in gym class, and Ikea furniture, and the Cleveland Browns. I’m just spitballing here.

Then there’s the electromagnetic force. Electromagnetism gives us light to see, radio waves to hear and microwaves to nuke our frozen burritos. It’s everywhere, and moves at the speed of light. Literally, because it is light, and various other wavelengths.

For all these forces, physicists have discovered corresponding elementary particles. Photons, for instance, which mediate the interaction of electric charges. The photons themselves are a pain to nail down — today they’re particles, tomorrow they’re waves — but at least we’ve found them. Likewise, particles called gluons carry the strong nuclear force, and W and Z bosons carry the weak force. It gets pretty complicated, but everything lines up and can all be explained by quantum mechanics.

Until you get to gravity. Because gravity is a bitch.

First of all, no one’s ever observed a particle — or wave, or aura, or Magic freaking 8-Ball — that carries gravitational force. There’s a predicted one, called a “graviton”, but we won’t be seeing those in a lab any time soon, because practical reasons.

(One estimate holds that we could detect one graviton every ten years, if we had a one hundred percent efficient detector the size of Jupiter. Which we don’t. And it only works if we put it near a neutron star, which we can’t. Also, it has to be shielded from cosmic neutrinos, which requires so much extra matter it would fall into itself and form a black hole. Which is bad.

In other words, gravitons are essentially undetectable. Eat your heart out, Higgs boson.)

We do have a shot at detecting gravitational waves, “ripples” in spacetime made up of many gravitons (if they exist) and produced by various astronomical objects. Some such waves may have been produced soon after the Big Bang, and may tell us something about the early origins of the universe. But we haven’t confirmed any discoveries yet, and interference from various electromagnetic sources on Earth make reliable detection tricky. (Stupid delicious microwave burritos.)

The other issue — theoretical gravitons or no — is you can’t jam the equations dealing with gravity into quantum physics. When you try, you wind up with infinities over here and irreconcilable differences over there and everything goes to hell. You might as well try getting Katie Holmes back together with Tom Cruise. It’s not gonna happen.

That leaves gravity as the “odd force out” — and mathematically speaking, completely separate from the rest of the universe. All sorts of strategies have been devised to pull this crazy loner back into the fold, including string theory, superstring theory and loop quantum gravity. So far, nothing (testable) has worked.

So if you’re planning to prank someone by getting them to jump out of a plane without a ‘chute, you’ve got a fair chance of convincing them gravity doesn’t really exist at all. Bonus if they’re a physicist working on quantum gravity — because at this point, they’ll probably want to jump.

Actual Science:
Fermilab / Inquiring Minds – Is gravity a particle or a wave?
PBS / Nova – What are gravitons?
Universe Today – Can you escape the force of gravity?
Quanta – Physicists eye quantum-gravity interface
New York Times – A scientist takes on gravity
Space.com – Einstein’s gravity waves could be found with new method

Image sources: Physics Is Fun (“Curses!”), ILoveSkydiving.org (lounging jumper), CinemaSips (“Rudy! Rudy!”), Today’s Zaman (giggly Katie, tee-hee Tom)

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