Collected Essays (34 page)

A Note On Synthetic Biology

The SynBio approach is onto something big—a new version of nanotechnology, which is the craft of manufacturing things at the molecular scale. SynBio’s plan is to capitalize on the fact that biology is already doing molecular fabrication all the time. What might happen if we repurpose biology to our own ends?

One big worry is what nanotechnologists call the “gray-goo problem.” What’s to stop a particularly virulent SynBio organism from eating everything on earth? My guess is that this could never happen. Every existing plant, animal, fungus and protozoan already aspires to world domination. There’s nothing more ruthless than viruses and bacteria—and they’ve been practicing for a very long time.

The fact that the SynBio organisms are likely to have simplified Tinkertoy DNA doesn’t necessarily mean they’re going to be faster and better. It’s more likely that they’ll be dumber and less adaptable. I have a mental image of germ-size MIT nerds putting on gangsta clothes and venturing into alleys to try some rough stuff. And then they meet up with the homies who’ve been keeping it real for a billion years or so.

Now let’s look at the upside. Donning the funhouse spectacles of science fiction, I envision a wide range of biotech goodies.

Every child is likely to want a pet dinosaur, and this will be easily managed once the online Phido Pet Construction Kit is up and running. Of course, if you prefer something cuddly, you can design a special dog with red polka dots.

Rather than mining for ore, why not let plants use their roots to extract minerals from the ground? Sow a handful of Knife Plant grain over a dumpsite, and before long you’ll have what looks like corn—but with a cob-handled steel knife in each ear.

Why bother building houses when you can get a Giga Gourd seed? The seed is the size of a pizza and grows very fast. Push it into wet, fertile ground and stand back. In a few days you’ll have a big, hollow home with plumbing and wiring grown right into the walls, which come complete with transparent window patches.

Of course, people will want to start tweaking their own bodies. Initially we’ll go for enhanced health, strength and mental stability, perhaps accelerating the pace of evolution in a benign way.

But, feckless creatures that we are, we may cast caution to the winds. Why would starlets settle for breast implants when they can grow supplementary mammaries? Hipsters will install living tattoo colonies of algae under their skin. Punk rockers can get a shocking dog-collar effect by grafting on a spiky necklace of extra fingers with colored nails. Or what about giving one of your fingers a treelike architecture? Work ten two-way branchings into each tapering fingerlet of this special finger, and you’ll have a thousand or so fingertips, with the fine touch of a sea anemone.

It’s easy to imagine grafting an electric eel’s electromagnetic sensitivity into our brains so we can pick up wireless signals. There’d have to be an off switch, of course, but the net effect could be amazing. We’d have true telepathy, and the ability to form group minds.

As the technology of brain-to-brain contact improved, you’d no longer need to send someone every detail of a plan, a memory or a design. Instead you could send something like a mental Web link, allowing those you invite to simply view your thoughts right in your own mind.

The biggest problem with manned spaceflight is the immense mass of the requisite life-support systems and radiation shielding. What if the truly determined astronauts could transform themselves into tough, spindle-shaped pods that could sail endlessly through empty space, nourishing themselves with solar radiation and directing their journey with the exhalations of their ion jets?

One last thought. Suppose it were possible to encode a person’s memory and personality into a single, very large, DNA-like molecule. Now suppose that someone turns himself into a viral disease that other people can catch. If I were you—sneeze—oh, wait, I guess I am. Are we completely agreed?

Note on “A Note on Synthetic Biology”

Written in 2007.

Part of a
Newsweek
article on “Synbio,” May 23, 2007.

This was an odd little assignment where a reporter phoned me up and offered me a nice sum of money for writing a very short article. It’s pretty easy for me to write these kinds of articles, as I have so much material that I can draw snippets from.

Mathematica: A New Golden Age of Calculation

Back in elementary school, we learned procedures, or
algorithms
, for doing arithmetic with pencil and paper. (Remember “borrowing”?) As adults, we tend to not use our painfully wetware-programmed arithmetic algorithms because most of us have ready access to machines that can do the algorithms by themselves. You might occasionally add two or three numbers, but if you have some multiplying or dividing to do, you’re going to search your desk or your desktop for a calculator.

Mathematics doesn’t stop at arithmetic. If you moved further on in school mathematics, you learned more and more algorithms; things like plotting the graph of a straight line, factoring a quadratic equation, and multiplying matrices; maybe you even got to calculus and learned about differentiation and integration. As adults, most of us never need to solve these kinds of problems at all, but if you did have to solve them on a regular basis, what would you do? Chances are you’d get hold of a computer running some kind of computer algebra program.

The oldest such package, called
Macsyma
, was born at MIT in the 1970s. An original impetus for the project was to help physicists work with formulae that were simply too long and complicated for the human mind—things like the hundred thousand algebraic terms in (you should pardon the expression) the Ricci tensor used in the spacetime field equations of Einstein’s General Theory of Relativity. By the 1980s,
Macsyma
was like a potbound plant, limited by its design’s restriction to the use of only one megabyte of RAM. Though
Macsyma
was eventually rewritten, other new computer algebra systems arose to take most of its market. The new programs included
Maple
(also sold as
MathCAD
) and—the most expensive and ambitious of them all—
Mathematica
.

How exactly does one use
Mathematica
? The shrink-wrap contains a seriously fat user’s guide by Wolfram and a CD with a powerful graphically-interfaced program that runs on virtually every computer platform. You type in any mathematical expression you like and, depending on what you ask for,
Mathematica
might respond with an algebraically simplified version of the expression, a calculation of expression’s numerical value, a huge data-base table of numbers, or a graph illustrating the expression’s range of values. The graphs can be colored and three-dimensional. With
Mathematica
and an hour’s practice, a college student can solve any and all the problems in a standard algebra or calculus book.

What makes
Mathematica
even more useful is that everything you enter in a given session becomes integrated into a single document, called a notebook. A
Mathematica
notebook can include text, graphics, and mathematical expressions. You can save it, and if you open it again, all of the formulae are “live”—you can highlight a formula, change some of its numbers or symbols, and see the related parts of the whole notebook change accordingly, just like a spreadsheet. A
Mathematica
notebook fully embodies a once-futuristic concept that the physicist Richard Feynman longingly called “Magic Paper”—an intelligent writing medium, in which you can ask the paper to do your calculations for you.

Thanks to
Mathematica
’s notebook feature, you can watch what happens if the numbers in an equation change, or try out wild and crazy problems that ordinarily would be way too difficult to solve. Problem solving becomes a dynamic, experimental process.

The first time I saw
Mathematica
—this was Version 1, nine years ago—I used it to draw the kind of three-dimensional “Lissajous curves” you get if you had an object oscillating at different rates in each of three mutually perpendicular directions.

A 3-D Lissajous curve.

I’d seen two-dimensional versions in science museums and as drawing toys—a pencil or perhaps a slowly leaking container of sand hangs from a pendulum which is linked to a second, perpendicular pendulum. I’d always wondered what a three-dimensional Lissajous would look like. With
Mathematica
it was surprisingly easy. I typed a few lines of code and saw them.

A “baseball stitch” curve.

Before long, I’d exhausted the novelty of 3-D Lissajous curves, so then I imagined a new kind of curve I called a kappa-tau curve. These curves are defined in terms of their curvature (kappa) and their tendency to twist like a helix (tau). To my mathematical satisfaction, I soon got wonderful gnarly curves, some of them looking like the stitching seam on a baseball, as shown above.
Yaaar
!

But when I started wanting to look at lots and lots of my kappa-tau curves, and to set them to rotating in space,
Mathematica
became too slow. The very fact that it is a general-purpose system means that it is not going to be able to run some specific calculation over and over at the best speed. As I discuss in my essay, “How Flies Fly,” I ended up writing a stand-alone
Windows
program to show my kappa-tau curves. But I never would have gotten around to investigating these curves if I’d had to do it from scratch. You can find a my program and a Mathematica notebook for these curves on my website.

Mathematica
makes research easy—well, easier. That’s one reason why it has sold a million copies to labs and offices around the world, at prices now around $1,000 a copy retail (but much cheaper for students).

The
Mathematica
software is the product of a company founded by Stephen Wolfram. Wolfram is a remarkable figure who helped invent the modern concept of complexity theory. Born in 1959, he got his Ph.D. in physics from Caltech at age 20 and won a MacArthur genius grant at the record-breaking age of 22. The first release of
Mathematica
came out in 1988, the second in 1991, and now, in 1996, Wolfram is out and about promoting Version 3.

What took so long? Wolfram offers two reasons. The first is what you’d expect to hear from any earnest software pitchman: Version 3 is
so much better
than Version 2 that developing it took a long time. The second reason is more intriguing. From 1991 to 1995, Wolfram was busy doing basic science research, concentrating on his book-in-progress, a monumental tome that may finally come out in 1999.

A secretive man, Wolfram is reluctant to give out details on his work, but asserts that, “I have in my sights a way to get a new fundamental theory for physics. My ideas are based on some insights into what it is that simple computer programs typically do.” Intriguingly, he says that he wouldn’t have gotten this far if he hadn’t had
Mathematica
to help him. Wolfram has enough intellectual credibility that one is half-tempted to think of Isaac Newton, who invented calculus and then used his new tool to unravel the secrets of celestial mechanics. It would be nice.

When pressed for more information, Wolfram says something like the following: “For the last three hundred years, people have been trying to use mathematics to model the natural world, but that this doesn’t work well for things like biology and complex systems. Equations are human constructs, but maybe nature follows more general rules than that. Maybe we have to go beyond human mathematics and look at how general computing systems work.”

Wolfram feels that there really
is
a simple fundamental theory and that we’ve been looking for it in the wrong way. He thinks that for the first time in about 50 years, somebody has a real chance to find it. Who? “I’m an ambitious guy, all right? My interest is to find the fundamental theory of the universe.”