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!

DNA Origami


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

DNA origami: when you're done with your genes, fold 'em up.
“DNA origami: when you’re done with your genes, fold ’em up.”

You may be familiar with origami, the ancient Japanese art of paper folding. In modern Western society, origami usually pops up in one of three places:

  • fancy folded paper in art classes I’m not talented enough to get into
  • fancy folded napkins in restaurants I can’t get reservations for
  • fancy folded towels in hotels I can’t afford

Needless to say, I don’t have a lot of origami experience.

However. Clever scientists — who presumably can’t get into swanky hotels or eateries, either — have recently found something else to fold: DNA.

Like its predecessor, DNA origami started mostly as an art project. Biologists knew that the four bases in DNA — represented by the letters A, C, G and T — pair up in a very specific way (A with T and C with G) to form the double helix structure Watson and Crick were all aflutter about back in the 1950s. They also found that certain strings of bases affected the physical shape of the DNA molecule, making bends, kinks and folds in the structure. With a few careful adjustments, they thought, bits of DNA could become their personal nanoscale genetic-coded Lego set.

So they built some stuff. DNA origami isn’t quite a full-on Lego kit — you can’t make a Millennium Falcon or model Taj Mahal out of genetic material, yet — but the early attempts were still pretty impressive. In 2006, a group managed to assemble DNA triangles, smiley faces, tiny maps, banners, snowflakes and more. So if DNA origami wasn’t exactly DNA Lego then, maybe at least it was DNA Play-Doh.

Since then, the technology has advanced a bit further — and scientists aren’t playing around any more. They’ve got CAD (computer-assisted design) software to design their shapes and calculate molecular bend angles. They’ve also ramped up to try some pretty useful applications. Many of these involve using folded-up DNA structures to deliver drugs like cancer treatments directly into malignant cells. Or basically, using DNA origami as nano-teeny FedEx drivers.

(Assuming FedEx drivers are in the habit of delivering poison to disreputable households.

Which maybe they do. But that sounds like more of a UPS thing.)

There’s still more to do with DNA origami, though. By using long strands of sequence along with complementary base-pairing “staple” strands to reshape, twist and build bigger structures, much more may soon be possible. Last fall, researchers built the largest DNA origami structure yet, roughly seven times larger than anything previously designed — and it mostly self-assembles. DNA-based nanocomputers — and even nanorobots — are also in the works, and may be next.

And that’s all great and everything. DNA origami is cool. I just want somebody to teach me how to fold one of those stupid napkin swans.

Actual Science:
Popular Mechanics – How DNA origami creates supermaterials
Wall Street Journal – Gene expression: origami at the molecular level
Phys.org – Researchers use DNA strands to create nanobot computer inside living animal
The Scientist – Giant DNA origami
io9 – Researchers turn DNA into robotic “transformers”

Image sources: DVice (shiny happy smiley DNA faces), FireHOW (swanny towel), DavidGiuffre.com (“Lego Falcon, yeeeeeah!”), CBS News and ProSportStickers (United *Poison* Service driver)

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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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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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Ubiquitin


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

Ubiquitin: It's everywhere you want to be (and several places you don't).
“Ubiquitin: It’s everywhere you want to be (and several places you don’t).”

This is one of those times where you can learn about science by knowing a little English. Like how you figure out the dinosaur brachiosaurus was made out of grandma candy, or that the element proactinium will cure your acne, probably.

Sorry. This time will be better. I promise.

The protein “ubiquitin” was so named, back when it was discovered in the 1970s, because it was ubiquitous — in other words, everywhere. Every tissue scientists studied, every microscope they looked in, ubiquitin was there. Probably with enormous lapels and feathered hair, humming Jim Croce ballads. But it was there. Ubiquitously.

But what is it, exactly? Ubiquitin is a small protein that’s now been found in nearly every eukaryote — that is, most anything more evolved than a bacterium. It’s in most every type of tissue, and its job is to be glommed onto other proteins as a sort of targeted messaging system. Think of ubiquitin as the “Kick Me” sign of the cellular schoolyard.

Basically, it works like this: special proteins produced in our cells latch onto ubiquitin proteins and activate them — like writing the message on the sign. Then the ubiqiutin is hooked onto a different specialized protein in a process called “conjugation”. This gets it ready for the final step, like attaching a piece of tape to the top of the sign.

(Hey, genetics was invented before we had Post-It notes, all right? If you wanted to stick a sign to something back in the old days, attaching the tape was a separate step.

And yes, we walked uphill in the snow to do it, and we liked it. Shaddup.)

The final step, ligation, sticks the ubiquitin to whatever target protein is supposed to receive the message. Sometimes one ubiquitin is slapped on; sometimes, it’s a whole chain, like a bunch of latched-together plastic monkeys. Depending on which, and exactly how they’re hung on, determines exactly what fate lies in store for the poor unsuspecting tagged protein.

The most well-studied kind of ubiquitination (or ubiquitylation, if you’re really going for the Scrabble words, Einstein) involves a chain of ubiquitins strung together in a certain way, then tagged onto a protein. The result? That tagged protein is doomed to destruction. The message here is “Kick Me, Hard“, and the intracellular bullies are happy to comply.

But ubiquitination isn’t always a Mafia-style kiss of death. Some ubiquitin tags lead to a protein’s activation, or to being transported to a different part of the cell. So “Kick Me On”, or “Kick Me Over There”, if you like. It all depends on the message, and how it gets delivered. Uniquitin’s not bad; sometimes it’s just attached that way.

Ubiquitin thus plays a whole set of important roles in cells — keeping materials moving, cleaning up waste and flipping switches throughout a cell’s development. That makes it crucial for survival, and also something for infectious agents (like the flu virus) to try and exploit.

For figuring out the ubiquitin signalling pathway leading to protein degradation, three scientists were awarded the 2004 Nobel Prize in Chemistry. Two of them were from Israel, and the third was a researcher from the United States.

Because of course he was, right? Those guys are everywhere.

Actual Science:
WiseGEEK – What is ubiquitin protein?
Baldwin-Wallace University – The ubiquitin system
YouTube / Scottish Enterprise – Ubiquitin proteasome system programme
Bioscience Technology – Applying proteomics to Parkinson’s
Futurity – How the flu gets cells to crack open its shell

Image sources: Osaka University (ubiquitination diagram), Gold Country Girls (Brach’s old people candy), Dates with Kate (“Kick me”), Calvin’s Canadian Cave of Cool (monkeys, monkeys, monkeys!)

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Bioluminescence


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

Bioluminescence: where 'fight or flight' meets light.
“Bioluminescence: where ‘fight or flight’ meets light.”

Have you ever fumbled around in the dark, maybe in an unlit alley or a strange bathroom or in a basement with a burned-out bulb? If so, you should probably stop living your life like an expendable in a horror movie, before something terrifying happens to you.

Seriously. At this rate, you’ll be dead before the slutty girl or the dumb jock boyfriend who brought her out to this isolated cabin built on an Indian burial ground next to the haunted lake infested with vampire sharks. Get a grip, already.

Or you could grow a pair (of extra genes) and make your own light, using the time-tested strategy of bioluminescence. Humans aren’t capable of such things just now, but bacteria, fireflies, deep-ocean critters and some fungi have been doing it for millennia. And no one’s ever chainsaw-massacred them, so it must be doing the trick.

Here’s how it works: bioluminescent organisms produce two chemicals, known as luciferin and luciferase.

Don’t worry; this isn’t a pair of demons coming to get you in that dark alleyway. Chemistry may be many things, but it’s not the debbil.

In this case, the “lucifer” part of the name comes from the Latin word meaning “light-bringer”. And that’s just what these two molecules do. Luciferin undergoes a reaction — typically with oxygen — which produces a new molecule in a chemically excited state.

Because who wouldn’t be thrilled with a fresh batch of oxygen? I get socks for my birthday, and that’s not nearly as exciting.

When this excited molecule settles down (or chemically speaking, decays to its ground state), it emits a photon — in other words, a teeny little speck of light. String enough of these reactions together, and you’ve got yourself a light-up firefly butt. Or glow-in-the-dark mushrooms. Or a vampire squid with flashbulb arms.

(And yes, vampire squid do exist, unlike the vampire sharks I mentioned earlier. Which proves once again that nature is actually way more scary than whatever shit we make up.)

Luciferase catalyzes, or speeds up, this luciferin transformation in cells, so a bioluminescent creature can light up like Las Vegas whenever it likes. This comes in handy for, say, a firefly trying to attract a mate, an anglerfish trying to attract lunch or a mushroom trying to attract… actually, I’m not sure what it is the mushrooms are after. Mario Kart players? Phish fans? The ghost of Jerry Garcia?

At any rate, organisms use bioluminescence for self-protection, camouflage, communication, as a warning and for lighting up some of Mother Nature’s darkest metaphorical alleys, like the bottom of the ocean. Some non-bioluminescent species, like the Hawaiian bobtail squid, even form symbiotic relationships with those that have the “gift” — in this case, a bacterial species whose light helps hide the squid from predators. Basically, when your body parts light up, you can always make a friend. Just ask a certain wrinkly extraterrestrial.

And now that scientists understand the mechanisms of bioluminescence, they’re using it in all sorts of research. Luciferase genes have been cloned into experimental cells, often as a “reporter gene” — or an indicator that other genes cloned in during the same test are present. If the cells light up, everything’s good; if not, it’s back to the drawing board.

Bioluminescent materials have also been used for medical imaging, for exploring “living lighting” in various scenarios, and even as an experimental treatment for cancer.

It’s just too bad you can’t use bioluminescence yet to light up the dark section of those haunted woods. Because it’s a long way back to the cabin. And those footsteps. Are. Right. BEHIND. YOU!

Oh, whew, never mind. It’s just a vampire squid.

AAAAAAAAAAHHHHHHHHH!!

Actual Science:
National Geographic – Bioluminescence
How Stuff Works – How bioluminescence works
HHMI BioInteractive – Symbiotic bioluminescence
RedOrbit – Observing live gene expression in the body
io9 – What kind of demon sorcery created this laser-spitting fish?

Image sources: It’s Okay to Be Smart (bioluminescent [but non-vampire] squid), Bitch Flicks (slutty girl / dumb jock in a cabin), QuickMeme (“Science is the debbil!”), The Abstractionist (E.T.’s glowy finger)

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