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Better Living Through Gaming Nanotech Water Filters Robot Power Plants DECEMBER 2010 Rs 100 / 2005/16515/ . DELENG . o RNI N India Gas from Robot Garbage Power Plants Better Living through Gaming Nanotech Water Filters Anxiety Biophysics Psychedelic Cures Precision Dinosaurs Control of DNA Blood from Stone Nanomotors ON THE COVER India This year’s edition of World Changing Ideas explores Gas from Robot Garbage the leading ways that technology and innovation can Power Plants Better Living through Gaming create a healthier, cleaner, smarter world, from biolog­ ically inspired algorithms to vegetarian robots to a cheap Nanotech W r e t a F ilt e r s nanotech-based water filter. India The DNA Transistor Psychedelic Cures The Universe’s Photograph by Mark Hooper. Hidden Blood from Stone Geometry December 2010 Volume 5 Number 12 34 FEATURES BIOPHYSICS INNOVATION 52 Tuning DNA Strings 16 World Changing Ideas How to precision control molecular engines that read A special report on thoughts, trends and technologies and write DNA. By Anita Goel that have the power to change our lives. INFORMATION SCIENCE PHYSICS 58 Long Live the Web 26 A Geometric Theory of Everything In an exclusive essay, the Web’s inventor argues that Deep down, the particles and forces of the universe are a protecting the Web is critical not merely to the digital manifestation of exquisite geometry. By A. Garrett Lisi revolution but to our continued prosperity—and even and James Owen Weatherall our liberty. By Tim Berners-Lee PALEONTOLOGY LIFE SCIENCE 34 Blood from Stone 64 Jane of the Jungle Mounting evidence from dinosaur bones (such as “Big Primatologist Jane Goodall shares insights from her 50 Mike’s,” shown above) shows that, contrary to common years among the chimpanzees of Gombe. Interview by belief, soft tissue can survive in fossils for millions of Kate Wong years. By Mary H. Schweitzer SPACE EXPLORATION BIOLOGY 66 Jump-Starting the Orbital Economy 42 Life Unseen For the first time in five decades, NASA will soon be out The biological world reveals microscopic landscapes of of the astronaut-launching business. The only way to surprising beauty. By Davide Castelvecchi save manned spaceflight may be to outsource it to pri- vate companies. By David H. Freedman HEALTH 48 Hallucinogens as Medicine ROBOTICS In a matter of hours, mind-altering substances may induce 72 Cyborg Beetles the profound psychological realignments that can take Tiny flying robots that are part machine and part insect decades to achieve on a therapist’s couch. By Ro land R. may one day save lives in wars and disasters. By Michel Photograph by David Liittschwager Photograph Griffiths and Charles S. Grob M. Maharbiz and Hirotaka Sato www.sciam.co.in SCIENTIFIC AMERICAN India 1 By adjusting the mechanical tension applied to DNA molecules the velocity with which a motor enzyme replicates DNA can be precision controlled. XXXXXXXX 52 Scientific American, November 2010 Photograph/Illustration by Artist Name Anita Goel is Chairman of Nanobiosym and a Harvard-MIT physicist and physician. Named as MIT Technology Review’s “World’s Top 35 Science-Technology Innovators,” she has received multiple awards from agencies like DARPA, DOE, DOD, and AFOSR for her work in the emerging field of nanobiophysics. BIOPHYSICS Tuning DNA Strings Precision Control of Nanomotors Tools that can manipulate single molecules make it possible to observe and control the way molecular engines measuring ten billionth of a metre replicate, transcribe, and process information in DNA. By Anita Goel or the most part, throughout the twentieth Erwin Schrödinger, the Austrian father of quantum me- century, biology and physics developed as chanics, charted out a bold roadmap to explore this boundary wholly separate disciplines. Biologists and between biology and physics. After receiving the 1933 Nobel physicists lived in their own reductionistic si- Prize for mathematically describing the evolution of a quantum los, seldom communicating or collaborating system over time, Schrodinger turned his attention to his life- on their respective research. Most physicists long personal quest. This resulted in his 1944 classic work enti- had assumed that our current laws of physics tled What is Life?, where he concluded:“We cannot expect that Fwere essentially complete and biological systems were simply a the ‘laws of physics’ derived … [from the second principle of subset of physical systems; thus there were no new physical thermodynamics and its statistical interpretation] … explain principles needed to explain life or living systems. Yet some of the behavior of living matter… We must be prepared to find a the most prominent physicists of the 20th century questioned new type of physical law prevailing in it.” whether the laws of physics, developed in the context of inani- Schrödinger also wondered whether life, at its most funda- mate matter, could ever fully explain life and living systems. mental level, could somehow be a quantum phenomenon or, at IN BRIEF Nature encodes genetic information for polymerases. nanomachines can also be viewed as in- ics and nanotechnology, we can precision biological systems in DNA and other Such enzymes can be viewed as nano- formation processing machines that re- control how these nanomachines read complex macromolecules. This biological scale bio-motors or molecular engines spond to cues in the environment as they and write DNA, enabling a host of practi- information is replicated, transcribed, or that convert chemical energy stored in replicate a strand of DNA. cal applications and shedding new light otherwise processed by enzymes such as nucleotides into mechanical work. These With the advent of new tools from phys- on fundamental scientific questions. Photo illustration by Kapil Kashyap www.sciam.co.in SCIENTIFIC AMERICAN India 53 OPEN SYSTEMS A Network Model Nanomotors assemble DNA polymers by incorporating nucleotides as building as suggested by x-ray crystallography data. Likewise, the green pentagon denotes blocks into a growing DNA replica strand. Shown here is a simple network model to the exonuclease or error correction cycle in which the nanomotor unzips or describe our nanomachine. Each node of the network represents an internal micro- removes 1 base pair from the double helix for each exonuclease cycle it completes. scopic state of the nanomachine and the topology of this network denotes the This network model provides a powerful conceptual framework for us to mathe- allowed transitions between these internal states. The DNA polymerase (DNAp) matically predict how various parameters or “knobs” in the environment couple into motor replicates one base for every polymerase cycle it completes. The polymerase the dynamics of these nanomachines. These environmental parameters or “knobs” cycle is illustrated here a by a red pentagon, where the nanomotor cycles through in the motor’s environment include temperature, ambient concentrations of nucle- internal states or nodes (3->4->5-> 6->7->3’) of the network to achieve the polym- otides [dNTP] and other biochemical agents [DNAp], [PPi], the amount of mechani- erization of 1 base pair [Goel et al. (PNAS, 2003)]. For instance, nodes 4 and 5 corre- cal tension (f) or torsional stress on the DNA. spond to open and closed conformational states of the polymerase DNA complex —A.G. DNAp Motor Template Strand Single Double Strand Strand Exonuclease Polymerization Domain Domain Laying Down Repairing DNA DNA Tracks Tracks 1 [DNAp] [DNAp] [dNTP] [dNMP] 3 2 4 ? 2’ f 3’ [PPi] f Exonuclease Polymerase Cycle Cycle ? 5 ? States have not been 7 fully observed Environmental Knob ? 6 least, be influenced by quantum effects. Could complex mole- that were operating at or near equilibrium. Any interaction cules somehow store biological information in living organ- with the environment was considered, at best, to be a small per- isms? Although many of these speculations have been dis- turbation to these closed systems. In contrast, living systems, missed by mainstream scientists, Schrödinger’s book did influ- are fundamentally open systems that continuously exchange ence the thinking of an entire generation of physicists delving matter, energy, and information with their environment. De- into biology, including Watson and Crick for their Nobel Prize- spite the advent of thermodynamics, statistical mechanics, and winning discovery of the DNA double-helix. quantum mechanics, physics had not yet developed adequate Still, in some quarters of the physics community, the un- mathematical and conceptual tools to predict the behavior of orthodox idea persisted that physics itself might have to under- non-equilibrium systems that are strongly coupled to their en- go some radical transformations in order to adequately de- vironment. Even Einstein, exasperated with this seeming inad- scribe life and living systems. The physics of the 20th century equacy of modern physics, confessed to Leo Szilard that “One had been formulated in the context of nonliving matter. Its can best appreciate from a study of living things how primitive mathematical language dealt primarily with closed systems physics still is”. 54 SCIENTIFIC AMERICAN India December 2010 www.sciam.co.in SCIENTIFIC AMERICAN India 55 The Russian-Belgian physicist Ilya Prigogine realized that Our framework in DNA. Could cancer-causing in order to describe the dynamics of open, dissipative systems mutations result, in part, from that are far from equilibrium, physics would need new theoret- suggests that the environmental stresses on the ical constructs and a mathematical machinery capable of pre- information motor as it reads DNA? Armed dicting the dynamics of systems where the environment is content or with new experimental tools strongly influencing, if not blatantly driving, its evolution. from nanotechnology and con- Prigogine, a 1977 Nobel Laureate, took issue not only with clas- number of bits ceptual tools from physics, I set sical physics but also with quantum physics (including stored in a DNA- out to elucidate how various Schrödinger’s equation), notably with the idea that fundamen- changes in the environment of a tal processes were reversible and thus predictable.
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