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 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
What I’ve Learned:

DNA polymerase: come with me if you want to replicate.
“DNA polymerase: come with me if you want to replicate.”

DNA polymerase is an enzyme present in every living cell. Hay cells, jay cells, even George Takei cells. Oh, my.

In these cells, DNA polymerase has one job — just one job — and it’s both the easiest and hardest job on Earth. Biology textbooks would tell you that job is to “replicate” the cell’s genetic material, reading and copying DNA so when the cell splits, both new cells contain a full set of genes.

And that’s true, in the same way it’s true that Tito Jackson recorded twenty Jackson 5 records. He did — but he had a hell of a lot of help.

It’s the same with DNA polymerase. It plays an important role in replicating DNA, sure, but it’s led to the job site by an entourage of support proteins, propped into place, and prompted for its lines. Each bit (or “base”) of DNA to be copied is a cue, and it’s DNA polymerase’s job to add the right complementary base in response. There are four different kinds of bases, so it only has four lines to remember.

This is why DNA polymerase’s job is the easiest in the world. It’s treated like a star. It gets driven to the set, carried to the stage, and it barely has to study a script. It just reads a cue and delivers the right line, out of four choices. It’s the gig of a lifetime.

Actually, I imagine it’s a lot like Arnold Schwarzenegger’s life these days. He probably does the odd public appearance for pocket change, followed around by a gaggle of handlers. They’d behave like the DNA replication helpers — getting him to the podium, making his hair look nice and prompting him for the appropriate line:

If it’s a Terminator convention, he’ll say: “I’ll be back!

At a children’s event: “It’s not a tumah!

At a GOP fundraiser: “I’m the Governator!

For a crowd of Predator fans worried about Anna: “Get to da choppa!

So wherever he goes, a flunky whispers into his ear: “Terminator”, “children”, “GOP” or “Anna”. And Arnold gives the proper response.

(Maybe the flunky even shortens it to one-letter codes: T, C, G and A.

Aw, yeah. You biochemical geneticists see what I did there.)

So DNA polymerase’s job is simple — as easy as a T-800 following a four-path if-then logic loop. Which is to say, it’s easy to do once. Even a few times a week, a la the former-Governator.

But there’s the rub. Human DNA polymerase reads and matches a DNA base about fifty times per second.

(E. coli polymerase is even faster, around one thousand matches per second. If you can picture a bacterial Arnold Schwarzenegger, moving at twenty times the speed. Hasta la nightmare, baby.)

That’s why DNA polymerase has the hardest job in the world. Our genomes are three billion bases long, and in rapidly-dividing cells like skin or hair or stomach lining, the replication never stops. One mismatch could create a mutation that kills the cell, or cause out-of-control growth into cancer. (“Then it IS a tumah!”) Yet our DNA polymerases are extremely accurate, mismatching less than once every ten million bases — and they can even correct their occasional mistakes.

Which is good news for us. It’s no big deal if an aging actor accidentally tells a bunch of six-year-olds to “get to da choppa!“. But our inner Ahhhnolds get their lines right — all the time, nearly every time, and without the help of cue cards. That’s why if it bleeds… we can find DNA polymerase inside it.

Actual Science:
How Stuff WorksDNA replication
The OncologistThe molecular perspective: DNA polymerase
WileyDNA replication
Asian ScientistDemystifying Rule-Defying DNA Polymerases

Image sources: Vanderbilt University (DNA replication), Fanpop / Michael Jackson (Jackson 5), Screening Notes (“Tumah!”), New England Biolabs and TalkBacker (polymerase T-800)

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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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