Monthly Archives: December 2011

Dorkins Speaks!

After months of emails, instant messages, not-so-instant messages, and dammit-downright-slow messages attempting to get his attention, Genotopia has finally secured an interview with Dick Dorkins, the professional cynic, atheist, and genomics enthusiast. Genotopia readers first met Dorkins when he commented on the discovery of a gene for thalassophilia. Best known for his work with SPITTOON, the Society for the Prevention of Intelligent-design, Theology, or Other Nonsense, Dorkins is also an outspoken advocate for personal genomics, which he champions as the true path to spiritual enlightenment. In this first part of our interview, he tells about “Project Dick,” his effort to sequence his own genome, and the breakthrough technique that has made it possible.

 

GT: Thanks for taking the time to sit down with us.

DD: Don’t be an ass. I’m just banging out ex cathedra ripostes in between doing things that matter.

GT: What matters?

DD: Well I do, for starters. But I’m not doing myself at the moment, if that’s what you’re implying.

GT: What are you doing then?

DD: If you must know, I’m looking at myself.

GT: In the mirror? Doesn’t that make it confusing to type?

DD: Don’t be an ass. Not my image. My self. My true self. My genome.

GT: Ah, your DNA sequence. But wait—your genome famously refused to be sequenced.

DD: That’s right, it did. But I kicked its nucleic butt and now it’s as docile as a retriever.

GT: How did you do that?

DD: Through a breakthrough technology called “nuclear sequencing.” Not as in the cell nucleus. As in Hiro-fucking-shima. You’ve heard of shotgun sequencing?

GT: Sure. Craig Venter’s technique of “blasting” the entire genome into smithereens of DNA, sequencing the fragments with high-powered automated sequencers, and stitching the pieces together using massive computing power. It’s how the Human Genome Project finished early.

DD: You’re not as dumb as you type. Well, as you know, I’ve formed a company to sequence my own genome. We call it “Project Dick.”

GT: Catchy. I like the ambiguity.

DD: I came up with it myself. Anyway, as you say, my genome was impervious to shotgun sequencing. It squinted down the barrel of Venter’s biggest ABI machine, tossed back its head and gave a bitter, defiant laugh: “Hahahaha.” There might even have been an evil “Bwa” at the beginning. We hit it with everything we had and when the smoke cleared my genome was still just sitting there smirking.

GT: Tough. What did you do?

DD: We invented machine-gun sequencing. But still, nothing. My genome wears kevlar nucleus armor. It drives an Armored Personnel Carrier. Not so surprising really, when you consider the individual it encodes. So this brilliant chap we’re collaborating with out at Stanfoo University, Will B. Rich, upped the ante, so to speak, and invented the atom bomb of DNA sequencing.

GT: How does it work?

DD: It literally destroys my DNA, atom by atom, and then reassembles it. The processing power this requires is staggering.

GT: My God.

DD: Not quite. Google.

GT: You hired Google to sequence your DNA?

DD: Hired? Don’t be an ass. Like God, Google is everywhere. We have written code that borrows computing cycles one at a time from every desktop and mobile device on the planet and uses them to assemble the sequence of my genome. In between the “A” and the question mark of your last question, your Android contributed one tiny piece of my genome. Your device is sequencing me. You are sequencing me.

GT: You’re welcome. So in a sense, Google already has all this information—about you, and, theoretically, anyone else—and you are simply tapping in and extracting it? Should we be concerned about this?

DD: Google knows. Google cares.

GT: Dick! What you’re suggesting is the exploitation for personal gain of a giant omniscient, omnipresent, celestial intelligence, privy to our every move and capable of probing into the deepest recesses of our genetic structure–and that moreover, it is in a sense voluntarily created by our desire for communication with our fellow man and our desire for really cool apps! Explain, please!

DD: Can’t. Later, at my leisure, I will try to explain it to you slowly. But it’s time for my cup of special Punjabi aceyjee tea. It has telomere-lengthening properties, don’t you know. So ciao for now.

(Check back later for Part II of our interview!)

 

Science of the tattoo-obsessed

Scientists are nerds. They are passionate about something most people can’t care about, dig deeper into it than most people have patience for, and are easily bored by subjects they are not obsessed with. Nerds can be fun, in the way that autoclave spaghetti and midnight races with experimental sea slugs are fun. But what nerds aren’t, therefore, is cool.

Tattoos are cool. It hurts to get one, they evoke sailors and bikers and punks and other naughty people. And damn, man, that thing’s permanent, what are you going to tell your mom, and how the hell do you think you’re going to get a job? The problem with tattoos is that most of them suck. They are done by slacker punk kids with no talent, they are flash designs of butterflies or hearts or anchors or swallows. Employing my favorite technique of rectally deriving my statistics, fully 90% of tattoos are clichés, and 90% of those are badly placed and badly executed. And with them, the wearer usually proclaims, “I’m part of a group!” Historically, most ink signifies membership in some (usually seedy) club.

IMG 1661 225x300 Science of the tattoo obsessed

Brachyhypopomus (originally, Hypopomus) pinnicaudatus, a Venezuelan electric fish

One of the all-time great Reese’s Peanut Butter Cup moments in recent cultural history, therefore, is the advent of science tattoos. Nerdy tattoos. Unique images chosen out of passion for one’s calling, designed lovingly late at night over strong coffee and weak beer, collaboratively modeled to sculpt the body region best suited to it, meticulously needled by artisanal craftsmen charging upward of $200 an hour, and worn proudly as a badge of individuality rather than uniformity. (Tattoo aficionadoes are chagrined, and sometimes furious, when they see “their” image on someone else.) Beautiful, sexy tattoos that you can wake up in the morning, stone sober, and look at in the mirror and be glad you got. And do the same 40 years later.

Me, I have a fish on my back. Brachyhypopomus pinnicaudatus, to be both generic and specific. I discovered it in Venezuela in 1987, during a long and traumatic field season. I wrote the paper describing the new species, I wrote a Master’s thesis on it, and I drew the illustration that accompanied the type specimen. It was a painful experience in many ways. That fish came to symbolize both achievement and failure, as well as my first attempt at synthesizing art and science. I carried that experience for 20 years, until I figured out ways to overcome the guilt, shame, and emotional scarring of those first years in grad school. And so I brought my original drawing to the best tattoo artist I could find, Tom Beasley at Dragon Moon Tattoo, and had him ink it on me. Its electric organ discharge, as visualized on an oscilloscope, plays above it on my neck. This body ornament took about 4 hours and cost $600. While Tom’s needles played over my dorsal tissues, I meditated on that experience. As he worked, I felt the weight lifting. Tom lifted that fish off my back, actually.

That, and my other tattoos, are why I pre-ordered Carl Zimmer’s lavish new book, Science ink: tattoos of the science-obsessed. Though bereft of tattoos himself, Zimmer has remarkable empathy for the inked. He gets why we do this. On his blog he collected stories and photographs of science-related tattoos. Zimmer, who writes for Discover magazine, presents the images along with explanations of the science and symbolism behind them. It’s a trove of science knowledge broken appealingly into Reese’s Pieces-sized chunks, and a big bag of eye candy for ink fetishists. These are tattoos that don’t suck.

Zimmer groups the images by discipline: physics, chemistry, natural history, neuroscience, and so on. The tattoos range from dainty anklets to dramatic full backpieces and sleeves. Zimmer is at his best when he walks us through a large, complicated tattoo with many elements. He describes an “ecological allegory” adorning the hip, side, and back of Maureen Drinkard, who wrote her PhD thesis on the bogs of Ohio. He tells us about the bog ecosystem, then describes the cardinal flower on her ribcage, the skunk cabbage that blooms beneath on her hip, the dragonfly she chose as a reminder to be strong and ferocious, and rat-tailed maggot she considers her future. The “ick” reaction some might have to the unromantic rat-tailed maggot is tempered by the “rainbow sheen” it gives off when plucked from the slimy bog and held in the sunlight. Science tattoos are almost always ultimately about beauty.

They are also about facts, which makes these images a playground for a science writer. “Six hundred million years ago,” Zimmer writes about Anthony Pirulli’s full “evo-devo” sleeve,

“a worm-like creature swimming the Precambrian seas used networks of genes to build its body—networks for determining its head-to-tail anatomy, its front-to-back coordinates, its appendages, its organs. That early worm gave rise to many lineages of new kinds of animals, which are still thriving today. And despite their diversity—from insects to squid to starfish to humans—they still use the same basic gene networks to build their bodies. These networks took on new functions through the evolution of the genetic switches that turned the genes on and off. So in a very deep sense, the heart of a fly is much like our own heart. Ever since, Firulli has been studying the functions of some of those genes.”

That’s nice writing. It captures the current understanding of systems biology and embeds it in its evolutionary context, without relying on technical jargon or the dry scientific passive voice. Zimmer gets the science right and expresses it in language a bar-brawling biker can understand.

The book is richly, even extravagantly produced. Though the pages are matte, the photos are mostly high-quality. The cover is in two colors of cloth and has molecular cut-outs, through which neurons, DNA, and microbes peek out. I’m not crazy about the gothic type on the headers, which, I suppose, is meant to evoke 19thcentury German scientific papers. It seems a bit over the top. The text is carefully edited, although in one case a bird is re-classified as a mammal when the South American motmot is listed as a “marmot.” The index is brief but effective; it thoughtfully includes the illustrated organisms and mathematical variables, as well as the names of the doctoral canvases that bear the imagery. Nerds can look up their friends, whether they be researchers or the researched.

IMG 1698 1 300x214 Science of the tattoo obsessed

Phi, the golden ratio (1.618...)

I was simultaneously proud and a little dismayed that my other science-related tattoo (so far) merits an entry. Phi, the so-called “golden ratio,” is the first irrational number; a constant that, like the more familiar pi (3.1416…), can be carried out to an infinite number of decimal places and thus must always be approximated, its precision foiled by that tantalizing ellipsis. The golden ratio occurs frequently in nature, from the spiral of the chambered nautilus to the whorls of pine cones, sunflowers, and spiral galaxies. Fortunately, none of the four phi tattoos Zimmer presents are just like mine—or as beautiful, in my view. My tattoo has several layers of meaning for me, because I am a nerd, but one of them is as a reminder that mathematics, often called the language of nature, has limitations.

Sometimes natural truth lies not in the number but in the image. Now that’s cool.