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!

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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DNA Methylation


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

DNA methylation: it's like a chastity belt for your chromosomes.
“DNA methylation: it’s like a chastity belt for your chromosomes.”

We humans have a lot of genes — twenty or thirty thousand, give or take a chromosome. But we also have a problem. All those genes are packed into the DNA of each and every one of our cells. You’ve got genes for hemoglobin next to genes for neurotransmitters next to liver enzyme genes next to the ones that tell your left foot to grow toenails. The whole caboodle, in every single cell.

You can’t have all those genes turned on at once, in all the cells. It’d be a disaster. Think of your DNA as a big walk-in closet full of clothes. Some things go together, some things clash, and other things you only wear for holidays — or when senile-assed Aunt Clara shows up to see the stupid lop-eared bunny suit she bought you. But you don’t wear everything you own all at once. That would make you a crazy person.

So it goes with your cells. Depending on where they live — in a little row house along the spinal column, maybe, or a brownstone in the colon — they want to fit in with the neighbors and express the right set of genes. When in Rome, do as the Romans. And when in the respiratory system, don’t spew out growth hormones. That’s not your job, bunnybutt.

There are several ways that cells can shut down or “silence” genes, but one of the most common is DNA methylation. It sounds complicated, but it’s actually pretty simple. To make a protein in a cell, a bunch of enzymes have to get at the bit of DNA coding for it. Those enzymes read the code into RNA, and the protein is built from that. “Methylation” means taking a methyl group, a single-carbon molecule similar to methane, and glomming it onto that DNA structure like a wad of used chewing gum.

Slap enough methyl groups onto a stretch of DNA, and those RNA-making enzymes can’t get at it. Any genes in the neighborhood get completely shut down, like a Honda running out of gas or a dudebro wearing Axe cologne. Even better, when the cell divides, the DNA methylation pattern gets passed down the line. So it’s a great way for specialized cells to shut off genes they have no business fiddling with — basically a permanent genetic cock block.

Though critical for development in mammals — pssssst, that’s us — DNA methylation isn’t used in the same way by all species. Fruit flies, for instance, apparently have better things to do with most of their DNA, and yeast haughtily looks down its nose at DNA methylation.

Or would, if yeast had a nose. Or eyes. Or the genes for being haughty.

In other organisms, DNA methylation comes up a lot. Some — humans and tomatoes, for two — use it to silence potentially harmful genes inserted by viruses into the genome. DNA methylation tends to decrease over time, so it can be used as an indicator of aging. And it’s been linked to diseases like cancer, Alzheimer’s and atherosclerosis, and could offer clues about how those conditions develop.

So DNA methylation is pretty important. Without it, all our cells would crap out all the possible human proteins and we’d be big unregulated oozing blobs of cytoplasm. Like a certain amorphously-shaped cartoon character with a distinct lack of impulse control.

And that’s not attractive. I don’t care how cute a bunny suit you slap on it.

Actual Science:
Scitable / Nature – The role of methylation in gene expression
New Scientist – Hints of epigenetic role in Alzheimer’s disease
RedOrbit – Reasons for age-related cancer incidence increase identified
Phys.org – Plants can ‘switch off’ virus DNA
SciTech Daily – Regular exercise induces changes in DNA

Image sources: UIUC TCB Group (DNA methylation), The Berry (Ralphie bunny), GenTwenty (dudebro shutdown), UnderScoopFire! (Homer, unregulated)

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Telomeres


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

Telomeres in a nutshell: the short of it is bad, and the long of it isn't great, either.
“Telomeres in a nutshell: the short of it is bad, and the long of it isn’t great, either.”

Many things tend to get shorter as we age. Patience. Hairstyles. Time between bathroom breaks.

But something else shortens when we get older, and it’s more important than all the others. Except maybe the haircuts. Nobody likes a geriatric hippie.

This “something else” is a telomere, and it’s a squiggly bit of genetic material stuck on the end of each of our chromosomes, for protection. Sort of like those fiddly plastic things on the ends of shoelaces that stop them from fraying.

(Those are called “aglets”, by the way. That’s not science. I just thought you’d want to know.)

Telomeres play a similar role in our cells — and the cells of most everything else that isn’t a bacterium. When we’re young, the telomeres on the ends of our chromosomes are long. Each time our cells divide, the telomeres get a little shorter, until they’re very small or gone completely. Cells in that state typically don’t divide any more; they’re content to put on a shawl, find a nice rocking chair and wait for the end.

It’s like the aglets on your shoelaces got shorter every time you wore your sneakers, until they finally disintegrated, the laces unraveled and your shoes fell off. Only instead of going barefoot, your hair and skin and brain cells don’t grow back any longer. Which is somewhat more inconvenient, even if you’ve already moved to that shorter hairstyle.

The other more-than-somewhat inconvenient thing about telomere-less chromosomes is that they can lead to cancer. Without those protective bits at the end, genetic material can get chewed away, which is bad. Or chromosomes can link together and loop around, which is also bad. As in, cancer bad. Much worse than frayed shoelaces.

So longer telomeres are better, right? weeeeeell — it depends. In general, yes. Antioxidants in foods like blueberries and kidney beans and artichoke hearts help to lengthen telomeres, and that’s good.

How you get your chromosomes to eat right, I don’t know. Mine are always binging on chips and deoxyribonucleic Oreos.

The thing is, our cells also make an enzyme — called telomerase — that naturally rebuilds telomeres in certain situations. Production of this enzyme is tightly regulated; it’s not normally produced very often or in large quantities. It’s like liquid gold. Or a really good gin and tonic.

In the lab, though, scientists have shown that extending telomeres can reduce signs of aging in mice and worms. Which is great for cowards and lawyers, I suppose — but someday, it could even be applied to humans. That would be sweet.

But there’s a catch. Most of our cells don’t grow constantly. Outside of skin and hair and the insides of our intestines, many cells really shouldn’t be dividing very often. You don’t want lungs the size of life rafts, or a gall bladder you could play volleyball with. Not unless you’re opening a really weird sporting goods store.

So in those cells, if telomerase was always around, the telomeres would keep getting longer. And that might signal the cells that they should divide and divide, out of control. And what are cells dividing willy-nilly, out of control? That’s right: cancer.

So telomeres are tricky. They’re like the Price Is Right showcase game of life: you want as much as you can get, without going over. Because if you do, the consolation prize might be something way worse than Rice-A-Roni.

Actual Science:
University of Utah – Are telomeres the key to aging and cancer?
Nature / Scitable – Telomeres of human chromosomes
Scientific American blog – Aging: too much telomerase can be as bad as too little
NPR – Healthful living may lengthen telomeres and lifespans
The Scientist – Telomeres show signs of early life stress

Image Sources: The Tao of Dana (chromosome telomeres), Heavy (old hippies), Creative Homeschool (aglets), LEXpert (The Price Is Cancer)

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Electric Bacteria


· Categories: Biology
What I’ve Learned:

Electric bacteria: And you thought your 220V plug adapter was impressive.
“Electric bacteria: And you thought your 220V plug adapter was impressive.”

First they came to make our stoves electric, and I said nothing. Because I’m a terrible cook. I can’t even brown bagels.

Then they came to make our lawnmowers electric, and I said nothing. Because who can afford a yard these days?

Then they came to make our cars electric, and still I said nothing. Because Teslas are sexy, and only occasionally burst into flames.

But now we have electric bacteria, and there’s no one left to speak up. Presumably because they’ve been zapped by electric freaking bacteria. What’s next, nature? Chickenpox with tasers? Athlete’s foot fungus armed with bazookas? Napalm-spewing cooties?

Fear not, science fans. Unlike that Electro dude in the Spider-Man sequel, these “electric bacteria” aren’t out to fry humanity like a trillion tiny bug zappers. They’re just efficient little critters trying to cut out the middle man.

All living organisms need energy. We get ours in the form of coffee or cheese sticks or chicken cacciatore. Likewise, animals and plants ingest nutrients in various forms to get the oomph they need. Eating equals energy.

But once the grub goes down the gullet — or up the rootstalk — things get complicated. Nearly all organisms gain energy by transferring electrons from food molecules onto another molecule called ATP.

(No, not the tennis tour ATP. The only thing stored there is Roger Federer’s six thousand watches.)

ATP stands for adenosine triphosphate, possibly the most important bit of microscopic fluff in living cells, because it can hold onto electrons — and therefore energy — until they’re needed. Organisms spend a ridiculous amount of effort getting these electrons onto and off of ATP, using enzymes and cofactors and quite possibly David Blaine is involved — all because our cells can’t deal with bare electrons directly.

But some cells can.

Scientists have known for a while that certain bacterial species can gather energy from an electrical source — that is, a pool of electrons. No ATP needed; these microbes sip electrons like espresso and use them directly.

Dubbed “electric bacteria”, because they survive on raw current — rather than, say, raw currants — researchers believed they were relatively rare. But new experiments have jammed a proverbial fork into that outlet: electric bacteria aren’t rare; they’re everywhere.

Several new types of electron-munching microbes have been recently discovered. How? By jamming electrodes into the ground, turning on the juice (gently) and seeing what grows. Some bacteria in the lab can thrive on just the juice from a simple battery. No food. No water. No Chicken McCoenzymes. Just pure, unadulterated voltage. They’re like tiny little toasters, only alive and creepy and also terrible at browning bagels.

These weirdo electrical bacteria are interesting in a number of ways. Some live deep underground, slowly slurping electrons off the surrounding rocks. These may give us a hint of what primitive life on other planets might look like. They could also help us figure out the bare minimum energy cells need to survive. And they might be engineered to clean up biowaste or toxic spills, powering themselves with loose electrons as they work.

Some species even have filaments called nanowires that help regulate the electrons flowing in and out. These cells can link together, forming a bacterial bridge to transfer electrons several centimeters away. That’s not lightning shooting out of Jamie Foxx’s hands, maybe. But for teeny-ass microbes, it’s like Zeus firing thunderbolts at a bullseye on the moon.

So even if they won’t tase you, bro, don’t mess with electric bacteria. These crafty critters will shock you.

Actual Science:
New Scientist – Meet the electric life forms that live on pure energy
Astrobiology Magazine – Electric-eating bacteria
Discover – Bacteria unite to form living electric cables that stretch for centimetres
LiveScience – Electric bacteria could be used for bio-battery

Image sources: Real Simple Science (plug-in microbe), Tampa Bay Times and Flickr / Dusty_73 (cootie napalm), Silver Screen Serenade (Electro charging), CityNews Toronto (electric Blaine)

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Micelles


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

Micelles: when the heart wants what the head hates.
“Micelles: when the heart wants what the head hates.”

Contrary to popular belief, a micelle is neither an expensive French pastry nor that nice lady currently living in the White House. Instead, a micelle is a clump of wishy-washy molecules called surfactants that can’t make the simplest decisions and probably never see any good action movies.

I’ll back up.

We have love-hate relationships with all sorts of things. Semi-sweet chocolate. That non-frozen yogurt full of bacteria that tastes like armpits. Tom Cruise.

Consider the Cruise. He makes some good movies — and a lot of okay movies — but by most accounts, he’s kind of a schmuck. Also, I think he worships Alf from that ’80s TV show; I’m not so clear on the details. The point is, your heart and your head — and any other organ you invite to the discussion — can rightfully disagree on how you feel about Tom Cruise. And they’ll disagree often, because he’s everywhere. You can’t swing a dead thetan without smacking some new movie, rerun, interview, gossip rag or ironic T-shirt featuring wee Mr. Cruise. He’s practically ubiquitous.

And that’s how surfactants feel about water, a substance almost as ubiquitous as Tom Cruise — although Waterworld really hurt its career.

(Oh, let’s face it. Water hasn’t done a really good flick since Splash. It’s been treading itself ever since.)

Back to surfactants. These are stringy little molecules with separate “head” and “tail” regions. They’re amphiphilic, which just means that one end is attracted to water (or is “hydrophilic”) and the other is repelled by water (aka, “hydrophobic”). They’re like schizophrenic Frosted Mini-Wheats, minus the wheat. And the frosting. And the talking commercial mascot.

(It’s not a perfect analogy. Breakfast cereals can only teach us so much.)

If you dropped one surfactant molecule into a pool of water, it might well go crazy. The water-hating end would flop around, trying to get away, while the water-loving side would soak it all in. All confuzzled, it might contort or explode or lock itself in its room and write awful goth poetry.

But dump a whole bunch of surfactant molecules into water, and they make a plan. The water-repelled ends huddle up and glom together, drawing the water-attracted ends around them on the outside. The result is a big ball called a micelle, with all the brave hydrophilic bits exposed to the water, and the tender hydrophobic bits safely tucked inside.

(Yes, that’s basically the plot to the second half of 300. I’m telling you, water is really clutching at straws for good ideas these days.)

So why are micelles important? Well, they’re how detergents work, for starters. Soaps can pull dirt and nasty bits that wouldn’t normally dissolve in water into the center of their micelles and carry them away. From Dawn to Tide to Irish Spring, micelles make things cleaner.

More important, micelles are critical for life. There’s a lipid bilayer forming basically a big micelle (though technically a “liposome”) around every living cell; it’s called a cell membrane, and all our important DNA and enzymes and junk would leak out without it. Smaller micelles are formed in cells to push or pull in materials, including several vitamins (A, D, E and K) that we couldn’t process otherwise. And scientists can create artificial micelles to deliver drugs into cells directly.

So the next time you feel torn about some wacko celebrity, don’t let it get to you. Tom Cruise won’t live forever (probably), and if you had the same inner conflict about water, you’d never leave the house. Or bathe. Or make a decent cup of coffee.

But micelles make wishy-washy work. And they’ve never even seen Top Gun. Respect.

Actual Science:
Elmhurst College – Micelles
Frontiers in Pharmacology – Polymeric micelles for drug delivery
Chemistry Explained – Soap
Idaho Milk Products – What is a casein micelle?
Lab Muffin – What is micellar water and how does it work?

Image sources: University Federico II (micelle model), DC Dental (Tom Cruise), Business Insider (weepy Mini-Wheat), Chemistry in Your Cupboard (hot detergent action)

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