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, Genetics
What I’ve Learned:

Synthetic genomics: when regular old DNA just won't do.
“Synthetic genomics: when regular old DNA just won’t do.”

Genomics is the study of and the fiddling with (science term) an organism’s DNA. So naturally, you might think that “synthetic genomics” is studying and fiddling with DNA while wearing polyester.

It’s not. From what I’ve seen of most biologists’ wardrobes, the polyester thing is pretty much implied in all of genomics. And most weekend parties.

Instead, synthetic genomics is a particular style of fiddling with DNA that uses components and rules that nature hasn’t gotten around to trying yet.

(Because nature tends to be very busy doing other things. And in her spare time, distracted by all the polyester.)

There’s a big difference between sciences like “genetic modification” or “genetic engineering” and synthetic genomics. All sorts of organisms’ genomes have now been modified in the lab — corn, for instance, and glow-in-the-dark fish, and possibly Jocelyn Wildenstein. But in these cases, the genes engineered into the DNA came from other species in nature, and followed the usual rules for how DNA works.

(Not how faces work, necessarily. But at the DNA level, it’s all textbook. And usually a difference of just one or two genes.)

But synthetic genomics is different. Here, the usual rules go out the window. Recently, a team of scientists used computers to redesign a chromosome found in yeast, synthesized the new sequence and plugged it back into real yeast cells.

Why? I’m not entirely sure. Maybe they’re trying to create glow-in-the-dark beer, or sandwich bread that talks to you while you eat it. Both of which I’m in favor of — preferably in the same meal. But in the meantime, it’s a monumental bioengineering achievement, and could produce more efficient yeast.

No doubt the Pillsbury dough boy and Budweiser Clydesdales are salivating over that.

Another team is trying to modify pig DNA to look more similar to humans. Which, of course, because a real-life Porky Pig is an obvious choice to be the next judge on The Voice. But actually, it’s so pig lungs can be yanked out and transplanted to save humans with terminal lung disease, while eliminating the problem of foreign tissue rejection.

Which just goes to show, everything is better with bacon. Including cross-species thoracic surgery. Mmmmmm, bacon.)

The biggest news to come out of synthetic genomics recently is that the DNA inside every living thing — from bacteria to badgers to Barbara Walters — can be expanded upon. Improved. Turned to eleven.

Announced just this week, scientists at the Scripps Research Institute whipped up a strain of E. coli bacteria that don’t just use the usual four basic building blocks of DNA, but instead use six.

This is big news. It’s like when Columbus turned Europeans on to a whole new continent, or Lewis and Clark followed Sacagawea through the Northwest, or the day you discovered you like actually dark beer. Whole new frontiers open up, full of possibility and hangovers and grizzly bear attacks.

And now, full of semi-synthetic genetically-fiddled-with E. coli., like little microscopic scientists wearing polyester pants. Sometimes the bacteria don’t fall far from the tree.

In practical terms, an expanded DNA alphabet could lead to revolutions in genetics, bioengineering and the ability to mass-produce useful proteins that have never before existed.

Whether that will finally improve biologists’ wardrobes is still up in the air. Science can only do so much.

Image sources: ChemistryWorld (6-base DNA), NBC New York (Jocelyn Wild-n-woolly-stein), Broadway World and Popscreen (Porky and the Voice), Unstable Molecules (unfashionable scientists [Phil and Lem, awww])

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

The punctuated equilibrium of Tatiana Maslany in Orphan Black
“Properly-punctuated equilibrium: Ten million ellipses, then a whole bunch of exclamation points.”

Punctuated equilibrium sounds like something you get when you perforate an eardrum. Like there should be PSAs about it, with scary pictures of death metal bands and Beats headphones with blood on the cans.

Luckily, it’s not that. No one’s coming to tear the Dethklok from your cold, deaf hands.

Instead, punctuated equilibrium is an evolutionary biology concept that made a big splash in the 1970s. It’s been desplashed a little since then, but it’s still pretty important. Plus Stephen Jay Gould helped think it up, and mostly everybody liked him. So there’s that.

The idea is this: in (at least) some cases, the pressure on organisms to evolve and adapt and squirt out a bunch of funky new species isn’t constant over time. When there’s plenty of food and the water is fine and everybody owns their own TiVo, then it doesn’t matter much if your individual set of genes makes you three percent hardier than your neighbor.

Oh, sure, you might get off your deoxyribonucleic ass and mutate up another leg or some gills or an enzyme to digest styrofoam. But let’s face it: you’ve got a pizza coming, and you’re still catching up on last season’s Orphan Black. Who has the time to speciate? And frankly, why bother?

This could go on for millions, or tens of millions of years.

(Well, Orphan Black won’t, of course. Tatiana Maslany is terrific and all, but she’s going to be too old for this thing at some point. I don’t care how many gills she grows.)

Things get interesting, says punctuated equilibrium, when the going gets tough. If the resources dry up, individuals die out. Small groups get separated from others; exploitable niches become more important. The quickest — and perhaps most radical — to adapt will ultimately thrive. Like the guy who brings a flask to the keg party, in case the beer runs out.

Or something less alcoholic. If you must.

It’s during these periods of ecological pressure and isolation that many new species are born. In between, all the old fern and finch and crocodile species sit around getting fat on Cheetos. And often each other.

But introduce a little hardship, and nature blossoms with adaptation to take advantage. That’s why an oceanful of brine shrimp will remain boring dumb brine shrimp forever. They want for nothing; they’re little trust fund crustaceans, born with silver… um, tiny handled eating utensils that rich baby shrimps would use… in their mouths.

(Or gills. Or whatever. Look, there’s no “aquatic face anatomy” tag on this post, all right? You get the idea.)

However! Scoop a small colony of shrimp out of the sea, stuff them in an envelope and shove them in the mail — now that’s an ecological challenge. And it’s enough to turn them into a whole new species: Sea Monkeys, with legs and fingers and brains and disturbingly human lips and what appear to be testicles growing on stalks out the tops of their heads.

And how does it work? Through the science of punctuated equilibrium.

So far as you know, unless you happen to own any of Stephen Jay Gould’s work. Or a freshman biology book. Or Sea Monkeys.

Stupid Sea Monkeys.

Actual Science:
Princeton UniversityPunctuated equilibrium
Evolution 101 / BerkeleyMore on punctuated equilibrium
National Center for Science EducationThe origin of species by punctuated equilibria
Shaking the Tree / Google BooksPunctuated equilibrium comes of age
Astrobiology MagazineLife after catastrophe

Image sources: BioNinja (evolution models), NeatoShop (poorly punctuated), BioNinja, The Mary Sue, io9 and Huffington Post (Tatiana Maslany clone evolution), She’s Fantastic! (Sea Monkeys)

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

Optogenetics: science--invented, laser doge-approved
“With optogenetics, you won’t just ‘see the light’. You’ll feel it.”

The brain is a pain in the ass, scientifically speaking. And scientific-researchly speaking, which is probably a real thing.

Studying the brain is unusually tricky. It’s a complicated organ with billions of cells, electrical signals whizzing everywhere and neurotransmitters getting passed back and forth like the last beer at a tailgate. You want “simple”, go study an appendix. The brain is not for you.

Also, the brain comes not-so-conveniently wrapped in a hard candy shell called a skull. To reach it, you’ve got to drill through bone — and then dig through brain, if the bit you’re after is in the middle. For decades, brain science was like trying to yank grapes out of Grandma’s Jell-O without breaking the mold. As any eight-year-old can tell you, that’s damned near impossible.

Then there’s the scale. Most organs you study with a microscope, or even a camera. Drop a miniature Nikon down (or up) someone’s gut and watch a day in the life of a colon unfold in real time.

Or slower, if your test subject is a big fan of fiber.

But the brain operates at millisecond speed. Blink, and you miss a million firing synapses, lighting up the cerebellum. And the cerebrum. And that other bit — the one for remembering numbers and science facts and what parts of brains are called. Mine doesn’t work, apparently.

How can scientists possibly get around all these problems? Enter optogenetics, which allows neurocowboys a new way to put eyes on the brain. Literally. (Almost.)

The ‘opto-‘ part of the name suggests light (or eye doctors), and refers to light-sensitive proteins — like those in our eyes’ rod and cone cells — found in species like fruit flies, algae and bacteria. These proteins react to specific wavelengths of light; by snipping out the DNA sequences coding them (hence the “-genetics”) and linking them to genes in test animals, scientists can set off signals in those animals’ brains — just by turning on a flashlight.

A very special kind of laboratory flashlight. Very wavelength. Much science. Wow.

Now researchers can trigger — and measure — brain events at the speed of light. They’ve even developed wireless versions of their flashy-light and brain-detect-o-matic devices, allowing them to study animals running free in the lab. Or “free” in a cage. But not attached by the forehead to an industrial science laser. Which is nice.

The techniques are fairly new, but have already changed the neurobiology game. Among other things, scientists have used optogenetic methods to implant false memories (and sexy thoughts) in fruit flies, flip-flop social behavior in mice, relax muscles in worms, break habits in rats and kill pain (again in mice) with a flash of light. Creepy Island of Doctor Moreau vibe aside, this research could someday have important applications in human medicine. Also, with all the flashing lights and artificial mind altering, the lab animals just think they’re at tiny adorable raves.

One final measure of the impact of optogenetics: In 2010, it was named scientific “Method of the Year”. Presumably, it beat out “stash your samples on ice overnight so you can duck out for Happy Hour”. For scientists, that’s a huge upset.

Image Sources: ExtremeTech (lab mouse), Jello Mold Mistress (Jell-O mold), NoodlyTime (laser doge), Redshirt Knitting (mouse rave)

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