Biofactories and cowborgs

Clean energy is going to save us. Oh no, wait! Clean energy is going down the tubes. Maybe nuclear energy ia the next big thing after all. Oh, right, except for the earthquake that vaporized all political support for nuclear power. But maybe thorium fission is the magic we’ve been looking for. Or maybe not.

I tell you, these hype cycles are exhausting. It’s enough to make you pretend you don’t care and hope for the best.

When sorting out the hope from the hype, I like to find technically trained people with clear voices, people like Rob Carlson and Tom Murphy. Carlson is on the leading edge of biotechnology and has some encouraging things to say. I enjoyed this piece on The new biofactories. Biotech is promising because it’s granular, scalable, and distributed. Granular, in that it can work in sizes from the humble test tube to a 1000 liter stainless steel brewing tank. So you don’t need a hundred billion dollars just to see if it will work (cough, fusion!). And biotech is scalable in the sense that if it works, you make a lot of product. The fact that it can be distributed means you can make stuff close to where you use it. So not only can you avoid going to the most dangerous part of the world for what you need, you also get to avoid the long trip home from Godforsakenville.

Clearly it would be foolish to say that biotechnology is going to solve our problems, energy-related or otherwise, but it’s coming faster than you think. Read Carlson’s essay and see if you can picture his image of cowborgs mildly sucking on sewage as we milk them for butanol.

Who knows where it’s all headed, but that’s the hype that I’m buying this week.

What malaria looks like

Drew Berry is an animator, and what he animates is something that can’t be seen. He takes the latest research on molecular biology and turns it into movies about how life works. His protagonists, the molecules that constitute our cells, are smaller than the wavelength of the light we use to see. But in a broader and more figurative sense, scientific advances are shining a bright light on vast previously unknown landscapes of biology, and the view is absolutely breathtaking. So while we cannot see the molecules drive us, we do know what they look like.

I’ve collected and admired Berry’s videos for some time, so I was delighted to come across a TED talk in which he discusses and showcases his work. I was surprised to learn that he was originally inspired by none other than David Goodsell, the other guru of biological visualization, and another hero of mine. What’s great about these guys is that they keep up with the science so you know what you’re getting is not a watered-down version. Everybody knows the basics of DNA, but Berry is going to show you the weird whiplash mechanics required to replicate the strand of DNA that’s moving in the “wrong” direction (3:50 in the video below). Every biology student has seen the blobby diagrams that correspond to the phases of mitosis, but Berry is going to show you the teeming construction site view of the microtubule scaffolding that attaches to the chromosomes. Watch those dyneins and kinesins zipping up and down the microtubules like trams in a train yard (8:20 in the video). Finally, you may have some understanding of the life cycle of malaria, but Berry will bring it to life in disturbing detail. Watch as the nasty little parasite smashes the window on a red blood cell, crawls inside, and turns it into a clotted crawling nest of writhing plasmodium babies (12:40 in the video).

I’ll close with Berry’s own words. This is from an article describing his MacArthur Grant award.

My approach is the opposite tack to simplifying the science. Rather than dumbing it down, I set out to show the audience exactly what the scientists are talking about. By building accurate visualisations founded on real scientific data, the animations come alive of their own accord, engage the audience, and go a long way towards explaining what the science is about. The science is rich, detailed and fascinating, and if you can watch it in action you will intuitively get to know how it works.

UPDATE: I just noticed that Apple is featuring Berry’s animations prominently in their recent iBooks textbooks announcement.

Kickstarter, the possibility engine

Kickstarter precipitates novelty and weirdness from the web.

Kickstarter is a site that helps people who need a little capital to reach out to the world and ask for it. It’s a clever idea, but they’ve executed on it so well that it has become a remarkably successful platform for launching small companies. By asking people to support ideas that haven’t been funded yet (like windowfarms or hamburger wrapping paper), Kickstarter builds “pre-communities” for their products. This helps in multiple ways: builders get money, early customers, and word-of-mouth marketers. Consider the alternative. You beg a bank for some money, then make a product, and only then try to market and sell it. It’s all the wrong way around. The bank wants its money back before you even start to attract enough customers.

Kickstarter thus has an alchemical effect, reducing the energy required to start selling niche products, which means products get nichier and weirder. They did a nice review of 2011 featuring some of their favorite videos. If you’re wondering why I keep using the word weird, take a look at the Freaker. They’re not all weird, but this one is. In a good way.

Play this game: you are a banker. Zach walks into your office and asks you for $48,500 to support his great new idea, the Freaker. Do you give it to him? In a bland and demanding world, Kickstarter is your friend. Gold is everywhere if we can be bothered to see it.

Spit and adenosine triphosphate

How is it you can drink saliva all day long and never run out of the stuff?

Sorry to put the image of spit-drinking in your mind, but you’re doing it right now, am I right? And the more you think about it, the more you do it. Before today is over, you’ll have swallowed more than one vice-president of the stuff. Here’s how I figure it: a healthy human (that’s you) consumes something like a liter of spit per day. That would fill up a typical pitcher, and John Nance Garner, who was vice president under Franklin Roosevelt, once remarked that his job was “not worth a pitcher of warm spit.” So the vice-president, as a unit of saliva volume, is therefore less than your daily output. This reminds me of the names of champagne bottle sizes. The larger sizes are named after rulers of Israel and Babylon. So a double magnum, or three liters of champagne, is known as a Jeroboam (the first king of northern Israel). By extension we might measure salivary volume in terms various legislative occupations. How much is a Speaker of spit? Or a House Minority Whip of spit?

But I digress.

My point is that your body is a collection of remarkably dynamic processes that give the illusion of stasis. And the thing that got me started on this line of thought was this sentence:

In order to provide energy to sustain our lives, every day, each one us produces a quantity of ATP by this mechanism that is approximately equal to our body weights.

Yikes! That’s an astonishing amount of flux for one single molecule. Do you want to see how (most of) this ATP is made? Look at this.

The quote and the image come to us courtesy of the Mitochondrial Biology Unit at Cambridge University. We’ve known for a long time where the ATP was being synthesized. But now we know the shape of all the insane molecules that do that work. The ATP mill you’re looking at here isn’t something exotic. Your body has enough of them to pump out a pound of ATP every ten minutes or so, one molecule at a time. And that is a spitload of ATP.