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!

· Categories: Biology
What I’ve Learned:

Zinc finger: When you're a protein, it's good to get the finger.
“Zinc finger: When you’re a protein, it’s good to get the finger.”

Frogs have given us many things over the years. There’s Kermit the Frog. And… uh, frog legs. And Froggy, from the Little Rascals.

So, three things. Frogs have given us three things. But it turns out there’s a fourth: frogs have also given us the finger. Which is nice.

That’s because the finger in question is something called a “zinc finger”, an important motif in many useful proteins, and it was first identified in a species of African clawed frog that scientists often study when they get tired of squinting at lab mice and fruit flies.

But what is a zinc finger, exactly? In frogs — and most everywhere else, including in people — it’s a set of different regions in a protein that fold together into a finger-like protrusion, which is held in place by various separate bits binding to a single zinc ion. This keeps the “finger” rigid, and the structure stable. The zinc is like the hair scrunchie holding bits of ponytail together, or the plastic doohickey on top of a six-pack.

That’s the classical zinc finger setup, anyway. Since the first, researchers have found other ion-binding interesting structures, including the zinc ribbon, the treble clef and the gag knuckle, which sounds like something out of Fifty Shades of X-Ray Crystallography. They all look a bit different, but have a more or less similar function.

And that function is to reach out and grab onto other things, as fingers are wont to do. Many zinc finger proteins bind to DNA, where they perform (or help other proteins perform) helpful functions like replicating DNA, transcribing DNA into RNA and regulating cell growth, function and hairstyle.

Wait, no. The scrunchy does the hairstyle. But the zinc fingers do all the other stuff.

It’s not just DNA these zinc fingers wrap their sticky selves around, though. Some of them grab onto RNA, others onto specific proteins, and still others grab small molecules of various kinds that float around living cells. Without the zinc fingers, these proteins couldn’t hold on to any of these bits. And if they couldn’t hold on — and there were no microscopic six-pack holders handy to replace them — then our cells wouldn’t get much of anywhere. And we wouldn’t be around to make unsettling science-based Fifty Shades jokes.

Clearly, it would be a world diminished.

If you’re a fan of zinc fingers — and by now, you must be — then you’ll be happy to know that scientists are now able to put them to good use in the lab. With a bit of molecular fiddling, researchers can vary the specificity of zinc fingers for DNA or proteins, to enable new (or limit old) functionality. And they can snip the zinc finger-coding portions out of genes and glom them onto other genes, creating new proteins that can bind and cut specific DNA sequences, for instance. Scientists then use these fingered-up proteins to silence or activate genes and study the effects on cells.

That’s very clever — like taking one of those six-pack rings and making them into, I don’t know, a dress. Only the dress can’t do science. We hope.

So the next time your DNA or protein does something useful, remember the zinc finger proteins and all we’ve discovered about them. And be happy that once upon a time, frogs gave science the finger. Those little rascals.

Actual Science:
RCSB PDB-101Zinc fingers
Zinc Finger ConsortiumScientific background
Virology BlogHIV gets the zinc finger
ScienceBlogsThe knock-out punch: zinc finger nucleases
HDBuzzGiving Huntington’s disease the finger?

Image sources: StudyBlue (zinc finger), Animal New York (fingering frog), Img Arcade (scrunchie Deb), Sue Woodall (six-pack fashion)

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· Categories: Biology
What I’ve Learned:

Kleptoplasty: the five-fingered photosynthetic discount.
“Kleptoplasty: the five-fingered photosynthetic discount.”

They say humans are what we eat. It seems to be at least figuratively true, as there are an awful lot of people who resemble walking stacks of lunch meat.

In the past, some cultures have decided to take the phrase more literally. Warrior tribesmen might eat the heart or brain of fallen foes to gain their power, strength and knowledge.

(Which frankly doesn’t seem particularly efficient. I mean, if those enemies had been smarter, stronger or more powerful, maybe they wouldn’t be the ones being served as appetizers.

I’m just saying, cannibals — maybe eat a dictionary instead. Or a rhinoceros. Think it through.)

These strategies never worked out so well for humans. But a handful of organisms actually can pick up desired traits — as opposed to love handles — from their food. These little critters basically cheat off someone else’s evolutionary paper, in a process called kleptoplasty.

Imagine for a moment you’re a lowly algal cell. Like most algae, you’re not much to look at, just a single-celled blob of schmutz bobbing in a scummy pond. Walking bologna? You wish you were walking bologna.

But you do have a couple things going for you. You’ve got a nucleus, for one. You might be able to swim around, or grow in filaments. Maybe you play a mean accordion; hey, I don’t know what sorts of hobbies algae have. But best of all, you have chloroplasts.

For those who slept through freshman plant biology — i.e., everyone — chloroplasts are little sacks of cellular goop that contain chlorophyll, which lets plants (and most algae) perform photosynthesis, or turning sunshine into energy. You and I don’t have chloroplasts, and we can’t photosynthesize, no matter how many bits of vanquished lettuce or seaweed or single-celled schmutzy algae we eat.

But a select few algae-eaters can.

Most of these chlorophyll filchers are single-celled creatures themselves, like certain dinoflagellates and ciliates. They manage to overwhelm an alga cell and break it down for energy, but they leave the chloroplasts intact. Sort of how we eat corn, and at the end of the digestive process, there’s still… corn.

But unlike corn poops, which are really only good for gross-out third grade homeroom jokes, saving those chloroplasts actually has a purpose. These swiped organelles are still functional inside the new cell, which means — for days, weeks or more — the conquering cell can now perform photosynthesis on its own. And that’s the magic of kleptoplasty.

The most complex known kleptoplastic organisms are Saccoglossan sea slugs, which are not exactly apex predators, but when you’re a smudge of algae, pretty much anything will eat you. The slugs go the extra mile and suck the algae’s chloroplasts out, storing them in digestive tract cells like a chipmunk stuffing its’ cheeks full of nuts.

So if you’re considering “practical cannibalism”, let this be a lesson: kleptoplasty is the way to go. Forget eating your enemies’ hearts or brains or gall bladders. And ditto for corn. All that stuff will get you nowhere.

What you want is to start a war with photosynthesizing pond scum, and eat all the algae you can get your hands on. If you’re lucky, maybe you’ll pick up kleptoplasty and take advantage of photosynthesis yourself. But probably, you’ll just get really, really sick.

Hey, it’s still better than eating bologna.

Image sources: Solar Sea Slug Blog (kleptoplasty), Google Image Search (walking bologna), Someecards / kantinore (“Manana, maize!”), Daily Mail UK (nutty chipmunk)

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· Categories: Biology
What I’ve Learned:

Tumor suppressor: I'm no hero; I'm just doing my job.
“Tumor suppressor: I’m no hero; I’m just doing my job.”

Fighting evil isn’t all it’s cracked up to be.

First of all, it’s hard. Evil is basically everywhere outside of Walt Disney World, so there’s always another battle on hand. Also, evil is fiendishly creative. Just when you think you have it in check, it’ll pop up behind you, tenting its fingers and snarling, “Excellent.”

But the worst part about fighting evil is that you’ll never be recognized for anything else. That must get old for heroes. Sure, Captain America gets medals for thwarting villains — but maybe he writes poetry, too. Nobody talks about that. What if Superman is a great baker? Or Wonder Woman is a two-handicap golfer? Who would even know?

That’s how it is for so-called tumor suppressor genes. These are genes that have perfectly useful functions in normal cells, merrily toiling along, getting their jobs done. But nobody cares about those jobs — outside geneticists, who nose around everything a cell does. Instead, most people focus on one thing:

If these genes are knocked out of a cell — silenced by mutation or deletion or runaway genetic regulation — then the cell may turn cancerous. With tumor suppressors around, no cancer. Without them — watch out.

The thing is, these genes don’t exist to prevent cancer, exactly; the very name “tumor suppressor” is misleading. In their mild-mannered day jobs, these genes get translated into proteins, and those proteins mostly control whether the cell they live in should grow or not. If it’s not time yet, don’t grow. If the cell is damaged, don’t grow. If it’s badly damaged, try and fix it. And if it can’t be fixed, smash it to bits and storm off in a huff of cytoplasm.

(So basically, tumor suppressors are like eight year old children building a Lego set. “Evil fighters”, my ass.)

The “smash it to bits” part is kind of important. If certain tumor suppressors are working properly — but the rest of the cell isn’t, the bum — they can trigger a process called programmed cell death, also known as apoptosis. This is pretty much what it sounds like — slapping a proverbial “KILL ME!” sign on the wall of the cell, and letting the body rip it limb from limb.

Gruesome, maybe — but better than having a mutated cell grow out of control, and eventually form a tumor. Any good horror movie will tell you: better to off yourself in an emergency than to join the mutant zombie horde. All that shambling around is exhausting, and who wants brain stuck between their teeth?

Anyway, tumor suppressors are very important genes; they’re just not named especially well. Fighting evil — or tumors — gets so much attention that the real everyday jobs these genes naturally do barely gets recognized. Instead, they’re known for a function they serve almost by default.

It’s like labeling a butt plug a “poop suppressor”; technically true, but not really what the thing is actually used for. Which, as any Parisian can tell you, is a giant Christmas tree.

I bet that thing would suppress the shit out of some tumors. Ho ho ho.

Image sources: CISN (crash into cancer!), Government Executive (Burns, tenting), Sparkles and Crumbs (sweet-tooth Superman), HugeLOL (apoptosis, post mortem), BoingBoing (Parisian Christmas tree art, aka “O Pluggenbaum”)

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· 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.

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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· Categories: Biology
What I’ve Learned:

Prions: Teaching new proteins fold tricks.
“Prions: Teaching new proteins fold tricks.”

Any neat freak with a hint of OCD can tell you that folding is important. If you two-fold your towels, then a tri-folded one clearly won’t do. If you’re a T-shirt sleeve tucker-underer, then a sideways-folded-over one is just going to make you twitch. And don’t even get me started on socks. I’m pretty sure the Crimean War was started over the improper folding of a pair of tube socks. You can look it up.

What most people don’t realize, though, is that folding is pretty important in other areas, too. Take protein folding, for instance. It’s easy to take protein folding for granted. You probably figure if one of your cells managed to make a protein properly — without any mutations in the gene, or DNA transcription errors, or messenger RNA misreads, or a thousand other pitfalls that can hork a protein entirely — then the hard part is over. But no. That protein still has to fold itself properly, like some tiny automated scrap of origami, to be of any use.

And what happens when the protein doesn’t fold the right way, and helix B wraps around sheet C, instead of sheet A like it’s supposed to? If it’s a specific type of protein found in humans, other mammals, some fungi and possibly elsewhere, then it becomes something called a prion. And that’s very bad.

(Worse than a pair of khakis folded away from the crease? Ay, chihuahua!)

The “common” (or “cellular”) version of the potential-prion protein is found throughout the bodies of humans and animals, in many different kinds of cells. This version is folded correctly, is anchored to the outer membranes of cells, and is thought to be involved in interactions between cells, including intercellular communication like signals passing through neurons in the brain. And as long as it’s pretzeled up the way it should be, there aren’t any problems.

But under certain conditions, this protein doesn’t fold quite right, and that leads to a snowballing set of problems. First, the misfolded prion can interact with “good” versions of the protein, and rejigger them in its image — namely, as bent-out-of-shape kinked-up beasts, ready to wreak havoc all around. Think of the self-replicating Smiths from those Matrix movies that weren’t as good as the first one, only with a hunchback or double-jointed knees or something.

The bigger problem is that these refolded prions can then link together in chains called fibrils, gradually forming huge structures called amyloid aggregates. These aggregates grow larger and larger, until they eventually disrupt cells and tissues — often in the brain. I’m no fancy neuroscientator person, but even I know that having an ever-growing Lego set inside your skull is probably not a good thing.

In fact, it’s an incredibly bad thing. Active prions lead to diseases known as spongiform encephalopathies, where “encephalopathies” means “brain diseases” and “spongiform” means “looking like a sponge”. Brain sponge disease. So the term isn’t as complicated as it sounds — but it’s several million times more frightening.

In sheep, prions cause a nasty-sounding disease called scrapie, and in cows, bovine spongiform encephalopathy, better known as mad cow disease. Humans get the misleadingly innocuously-named kuru, and then some diseases named more appropriately for a horror that turns your brain to Swiss cheese: Creutzfeldt-Jakob disease and Gerstmass-Straussler-Scheinker syndrome, for two.

Sadly, prion diseases are currently untreatable, and universally fatal. On the bright side, if you can manage not to eat the diseased brain of a sheep, cow or sworn enemy that has the disease, you’re pretty unlikely to get it yourself. But just to be safe, whether it’s laundry or proteins — pay attention to your folding. You can’t be too careful.

Image sources: Currents in Biology (prion), MacGyverisms (wrong socks, WRONG!), Twilight Language (“Hello, Mr. Smiths!”), Sargento (Swiss cheese)

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