Dr. Dobb's Journal - September 2008 - (Page 17)

D09LEAD_p1as.qxp 7/15/08 10:47 AM Page 17 is consistent, we’re building a scaffolding out to this problem, and we find no way to bridge the gap”? Is there an answer to these sort of questions as mathematically certain as “1 = 1” or is there a shape to our intellectual approach that just doesn’t mesh with certain kinds of problems? ED: I would say some of both: That mathematics in general are as close as you can come to Truth; but still, you do rely on your set of beliefs and axioms as to what makes physical Truth. Most people, at least modulo [“until you reach the domain of”] quantum computing, believe the Church-Turing Thesis that computers are just Turing machines, and that is the limit of computation. It’s a bit of a philosophical statement, there’s no sense in which you can establish it. You might find the yet-unknown counterexample. DDJ: Pauwels and Bergier in Le Matin des Magiciens pointed with glee at the establishment science press of the 1890s and its assurance that all the big problems were solved and that all that remained was measurement—this a decade before Relativity. ED: I think that’s a different issue. I hope it’s a different issue! There’s a difference between that and showing that a certain problem as formulated cannot be solved. There’s no shortage of problems that can be solved. DDJ: : What are you solving now? ED: We’d like to solve protein folding. That’s a hard one, not purely mathematical, but biological, how nature folds proteins. DDJ: How does nature fold proteins? ED: How? [laughs] No one knows! Biologists will happily tell you lots of theories. We’d like to know how it works. The practical matter is that you can already design proteins and build them. The trouble is that when you build them, they will fold, and you’d like to be able to predict how [they are] going to fold and see if [they] do what you want [them] to do. This is usually in the context of drug design. Does it kill the virus without killing humans? You could tell that if you understood how proteins work, and one piece of that is what it looks like geometrically, which dictates in part how it interacts with other proteins and other structures. How does nature convert DNA into this three-dimensional shape? If you understood that process, then you could create custom drugs that do the things you want. Can we predict it? If I give you a protein sequence, if I give you the corresponding strand of DNA, then using a computer, can you tell me what shape it will make? Is there an algorithm, which explains what happens? Is there a fast algorithm? DDJ: Do they discover that, given a certain protein sequence, it will fold in just this way? ED: Again, it’s not totally certain. There are definitely environmental factors. That’s part of the challenge. You need chaperones to help protein fold in a certain way. But generally it’s pretty consistent, the same protein usually folds in the same way. DDJ: And the behavior of proteins is governed in part by the shape. ED: It’s their shape, and how they fold. They’re usually flexible after Erik Demaine they form their main shape. But they can still wiggle in certain ways and that controls how they interact. But the big challenge is, how does that initial folding happen? And the converse question is reverse engineering. Suppose I want to build a particular 3D shape because it works so well. What DNA should I manufacture that will fold into that shape? So “How?” is a pretty broad question—we know it involves physics, etc. The more practical problems are as I have stated. DDJ: You get paid to ponder these imponderables. Most of us have to do it sitting on our porches on weekends! ED: It’s a pretty awesome position to be able to think about these basic mathematical truths and what’s solvable and not solvable… DDJ: Aside from the Secrets of Life, what else are you working on? Are you a multitasker, or a one-project man? ED: I work on many things at once. I could go on quite a while on different things. Recently, I’ve been working on decoding Khipu, a conjectured Incan writing system that used knots tied in ropes. What do they say? It seems clear they recorded some numerical data. We see numbers that add up in patterns. But there is linguistic information in there, too. They tell stories. That’s the tantalizing thing. DDJ: How does your interest in geometry, folding, and algorithms come into it? ED: The geometry is a bit superficial. The interest is from the computational perspective, there’s information in the knots, it’s fairly September 2008 l www.ddj.com l Dr. Dobb’s Journal 17 Photo courtesy of Donna Coveney/MIT http://www.ddj.com

Table of Contents Feed for the Digital Edition of Dr. Dobb's Journal - September 2008

Dr. Dobb's Journal - September 2008 Contents Friday Night Fish Fry Alia Vox Developer Diaries Developer’s Notebook A Conversation With Erik Demaine Application Lifecycle Management Meets Model-Driven Development Building a Robust Development Environment Real Users Really Matter Matching Wildcards: An Algorithm The Android Mobile Phone Platform Managing Application Thread Use Signalling Integer Overflows in Java .NET Development & the IBM WebSphere Portal Server The Agile Edge Effective Concurrency Swaine’s Flames

Dr. Dobb's Journal - September 2008

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