Digital Biology : How Nature Is Transforming Our Technology and Our Lives

by Peter J. Bentley

• ISBN13: 9780743204477
• ISBN10: 0743204476
• Format: Hardcover
• Copyright: 2002-02-05
• Publisher: Simon & Schuster

Summary

Imagine a future world where computers can create universes -- digital environments made from binary ones and zeros. Imagine that within these universes there exist biological forms that reproduce, grow, and think. Imagine plantlike forms, ant colonies, immune systems, and brains, all adapting, evolving, and getting better at solving problems. Imagine if our computers became greenhouses for a new kind of nature. Just think what digital biology could do for us. Perhaps it could evolve new designs for us, think up ways to detect fraud using digital neurons, or solve scheduling problems with ants. Perhaps it could detect hackers with immune systems or create music from the patterns of growth of digital seashells. Perhaps it would allow our computers to become creative and inventive. Now stop imagining. digital biology is an intriguing glimpse into the future of technology by one of the most creative thinkers working in computer science today. As Peter J. Bentley explains, the next giant step in computing technology is already under way as computer scientists attempt to create digital universes that replicate the natural world. Within these digital universes, we will evolve solutions to problems, construct digital brains that can learn and think, and use immune systems to trap and destroy computer viruses. The biological world is the model for the next generation of computer software. By adapting the principles of biology, computer scientists will make it possible for computers to function as the natural world does. In practical terms, this will mean that we will soon have "smart" devices, such as houses that will keep the temperature as we like it and automobiles that will start only for drivers they recognize (through voice recognition or other systems) and that will navigate highways safely and with maximum fuel efficiency. Computers will soon be powerful enough and small enough that they can become part of clothing. "Digital agents" will be able to help us find a bank or restaurant in a city that we have never visited before, even as we walk through the airport. Miniature robots may even be incorporated into our bodies to monitor our health. Digital Biology is also an exploration of biology itself from a new perspective. We must understand how nature works in its most intimate detail before we can use these same biological processes inside our computers. Already scientists engaged in this work have gained new insights into the elegant simplicity of the natural universe. This is a visionary book, written in accessible, nontechnical language, that explains how cutting-edge computer science will shape our world in the coming decades.

Author Biography

Peter J. Bentley is an honorary research fellow in computer science at University College London, where he supervises Ph.D. students and runs various research groups. He holds a Ph.D. in evolutionary design and has received international recognition for his work on evolutionary computation. He regularly speaks to audiences ranging from academics to government officials to businesspeople.

Table of Contents

Introduction	9	(7)
Universes	16	(24)
Evolution	40	(25)
Brains	65	(38)
Insects	103	(29)
Plants	132	(29)
Immune Systems	161	(37)
Growth	198	(30)
Answers	228	(26)
Bibliography	254	(3)
Acknowledgments	257	(2)
Index	259

Excerpts

Introduction

Imagine a future world where computers can create universes -- digital environments made from binary ones and zeros. Imagine that within these universes there exist biological forms that reproduce, grow, and think. Imagine plantlike forms, ant colonies, immune systems, and brains, all adapting, evolving, and getting better at solving problems. Imagine if our computers became greenhouses for a new kind of nature. Just think what digital biology could do for us. Perhaps it could evolve new designs for us, think up ways to detect fraud using digital neurons, or solve scheduling problems with ants. Perhaps it could detect hackers with immune systems or create music from the patterns of growth of digital seashells. Perhaps it would allow our computers to become creative and inventive.

Now stop imagining.

We are all becoming blasé about computers. The whirring, chittering box sitting on (or underneath) your table is probably no longer an off-putting device for you. More likely, you regard it as a necessary evil. When working, it becomes part of the furniture, and when not working, it becomes something to hurl abuse at. You cannot even escape it when leaving your office. Everywhere you go, you hear people talking in a new language of e-mails, dot-com domain names, and template files. What existed only in the laboratories of computer scientists ten years ago now forms part of everyday conversation for the least computer literate of us. Computers and computer software are everywhere, and yet, except for a few of the "nerdy types," they are largely ignored or taken for granted by us. Somehow this seems unfair. When some of the most exciting and inspiring new developments of our technology are happening inside the minds of these benign cream-colored boxes, to disregard them is to ignore something wonderful. So I shall not ignore them. I shall do the opposite: I will focus on them. By doing so, I will change the way you think about computers.

Follow me into a different universe -- the digital universe of our computers. I will show you the marvels that inhabit this strange new environment. You'll find them familiar, but different. Alike, but diverse. The digital entities I want you to meet are not incomprehensible collections of numbers or equations. They are just the same as you and the natural world that surrounds you. They may live and die within digital domains, but they are every bit as biological as you. Together, they comprise digital biology.

To make this journey, we must abandon our physical forms and don digital bodies, for we cannot exist in a digital universe as we are. Ready? Here we go.

Through the Looking Screen

The journey from our universe to the digital universe is instantaneous. We open our digital eyes and see...trees. But these trees are not static. As we watch, we see them grow -- from a small seedling to a vast, towering pine. The immense and beautiful complexity of the branches develops before our eyes; leaves form in symmetrical patterns; stems thicken into trunks. A forest grows up around us, the trees all trying to outreach their neighbors in the quest for the sunlight. At our feet are other plants -- ivy sending out tendrils to the trees and then swarming up them like leafy snakes. Ferns unfurl themselves, and we see their intricate fractal-like forms spread wide to catch the low level of light at the forest floor. We move through the forest and spot some seashells on the ground. Again, they grow before our eyes, the spirals and patterns emerging like ripples on water. When you pick up one of the shells and put it to your ear, instead of hearing the sea, you hear the pattern of the growing shell, transformed into music. These are not ordinary plants and shells. They are not made from atoms and molecules, and they are not growing in our universe. They are digital plants, made from the flow of electrons within the digital universe of a computer.

Let me slow down time in this digital universe. The growth of the trees and plants slows and stops. Now other movement becomes evident. On the ground we see insects scurrying along. A long line of ants marches forward, each following the pheromone trails left by its companions ahead of it. As we watch, the first few ants reach a specific point on the ground and turn, heading toward a new location, with the ants behind them following like an over-ambitious conga line. As we stand back, we can see that the ants are tracing out a complex and zigzagging route across the ground. Looking up, we see the sky filled with a flock of birds, flying in astonishing formations. They circle around each other, dive up and down, and suddenly all change direction at the same time -- yet never does a single bird collide with another. But there are still many more digital marvels in this universe for me to show you. Let me adjust our size.

We shrink rapidly, until the ants tower above us, as high as skyscrapers. Suddenly everything becomes dark. We have been swallowed by some digital creature. Don't be alarmed -- I arranged for this to happen. I would like to show you around inside.

We watch the flow of cells from within the veins of the creature. Most are completely normal, but once in a while, we spot a cluster of cells stuck together. In the center of the cluster is a virus or some other unwanted intruder into this creature. It is surrounded by large, colorless cells, which are attacking it. These are the leukocytes -- the white blood cells of our digital creature that detect anything that is not regarded as "normal." We move into the bone marrow of the creature. It is here that new white blood cells are constructed. Using the patterns laid down in the DNA of this creature, new cells are created constantly, each configured to attack a different invader. As we watch, a new cell is created and released into the bloodstream. If this cell finds an intruder, it will immediately clone itself, increasing the number of cells designed to attack this particular type of unwanted guest. Throughout the network of veins, an ever-changing police force of white blood cells patrols the creature, ensuring that immunity to all types of attacker is maintained at all times.

We move again inside the digital creature and find ourselves in the brain. Around us is a dazzling electrical storm of activity. Interconnected neurons fire electrical signals at each other in a vastly complicated network, informing their companions to stop or start firing themselves. In parallel, chemical signals are constantly emitted from the cells, and new connections between cells are grown or lost. The unceasing activity around us embraces electrical signals generated by the creature's senses and emits a never-ending stream of signals to the muscles and organs of the creature, causing it to react to its environment and learn, plan, and predict things in its world.

I shrink us again in the digital universe. We are now so small that we are within a single cell of the creature. In fact, we can see molecules within the cell. One vast spiraling molecule dominates the view -- a strand of digital DNA held within the nucleus of every cell of the creature. The DNA defines how the creature is grown from a single cell. It also specifies how the creature should mature and controls the production of cells for the immune system. The separate genes in the DNA are rules, designed to turn on and off the production of proteins. The proteins trigger new cells to grow, cause them to differentiate into different types of cell, and even tell cells to die. The DNA of this creature defines a complex recipe of actions and counteractions, safeguards and repair mechanisms.

I grow us back to our original size; the creature we were in shuffles away. Again trees, ants, and birds surround us. Digital DNA is held within all of these aspects of digital biology, defining the growth and behavior of everything we see. But to show you how the genes of the digital DNA are created, I must speed up time in this digital universe.

As the movement of the birds and insects disappears in a blur of activity, once again we see the trees and plants growing around us. I continue to speed up the passage of time, until even the growth of trees becomes too fast to see properly. Now all we can see is a nebulous landscape of digital biology, with forms appearing and disappearing as their lives are lived in split seconds. And as these biological forms live, as they find their partners and reproduce, they form part of an ever-changing environment. Whether tree or ant, if the offspring inherit some genes that allow them to perform a little better in the digital universe, then they will survive a little longer and on average will have a few more offspring than the others. So the more useful genes become more numerous in the populations, resulting in more successful creatures. This continuous process of change is known as evolution, and it shapes digital biology in the digital universes of our computers just as it shapes the natural world in our own universe. Indeed, as we watch, new types of tree form, changing generation by generation. New types of ant, with subtly different behaviors, emerge, more complex brains develop, more efficient immune systems grow. But our time grows short, so we must depart from the digital universe and return to more familiar surroundings.

Natural Technologies

Now that we have left the digital universe, I must come clean. Digital biology does not exist in a single universe, in a single computer. All of the aspects of digital biology I have just described exist in different, isolated digital universes. The digital ants will never meet the flock of birds, nor will they crawl on the ferns in the digital forest. Even the immune system and brain of the creature that swallowed us do not coexist in the same digital universe. But the fact that they do exist is undeniable.

I am one of hundreds of scientists who spend their time understanding the processes of nature and enabling those same processes to happen in computers. To achieve this, we create simple digital universes in computers, using laws of physics laid down in our software. Within these digital universes, we grow a new type of nature. We have harnessed the power of natural processes such as evolution and growth. Digital embryos grow from digital DNA, digital plants evolve, ant colonies swarm, neural network brains learn. We use such digital biology to evolve solutions to problems, such as methods for detecting fraud. We explore how immune systems can be created within computer networks and used to attack hackers. We discover how to use colonies of computational ants to search for better solutions to scheduling problems. We examine how architectural designs can be grown from a set of digital genes into adult form. We find out how to use digital neural networks to detect the difference between benign and malignant cancer cells. We learn how to develop colonies of digital cells that have the behavior of fire. By using the natural processes responsible for life within computer software, we are overturning all preconceptions of what computers can and cannot do.

Through our work, we find new and highly efficient ways of solving today's problems. We also learn about the techniques we have borrowed from nature. We find out more about our own origins, about the mechanisms behind evolution and embryology. We learn how plants grow, how animals develop, how our immune systems work, and even how we think.

These new techniques will form the next generation of our technology. By understanding the solutions of nature and using them to solve our own problems, we have found a whole new class of computation, a whole new way of using computers. Digital biology will allow us to survive in the modern world. It will guide us through the ever-growing complexity of our global, interactive, fast- paced, modern lives. These new software techniques will provide us with invaluable assistance from their digital universes. They will find us information, detect crime for us, identify faults, and even repair themselves. They will design new products for us, create art, and compose music. They will have originality, creativity, and the ability to think for themselves. How do I know that these things will happen? Because they already have. Using the methods of digital biology, we have achieved all of these feats.

And in the future? Who knows? But it seems almost certain that the first forms of alien life we see will be not through telescopes but through the windows of our computer screens into digital universes. The first person to hold a conversation with an alien intelligence will not be an astronaut, it will be a computer scientist or computational neuroscientist, talking to an evolved digital neural network. The first glimpses of nonhuman cultures and technologies will occur in our research labs, where the digital biology grows more complex day by day.

Perhaps these grandiose visions will be a long time in coming. But the next time you hear your cream-colored box whirring and clicking to itself, just stop and think what type of digital biology might be blooming inside.

What This Book Is About

Think I'm kidding? Or exaggerating? Well, read on. The whole point of this book is to explain, for the first time, how biology and computers have become so closely entwined. Chapter by chapter, I describe how the processes of nature work, to the best of current scientific knowledge. I'll include the voices of the biologists who have discovered and investigated aspects of biology. I'll also tell you how computer scientists, designers, engineers, artists, and many other people make use of the same processes with their computers. You'll read how they have used biology to improve our technology, enabling remarkable new advances in all fields. You'll also read how our use of biology within digital universes is expanding our knowledge of life, the universe, and everything. This new breed of scientist, whom I shall call the digital biologist, creates digital universes, genes, evolution, brains, insect swarms, plants, immune systems, and growth. In doing so, digital biologists learn how these processes work.

My aim in this book is to promote understanding. I hope that when you have read it, you will know the reason that so many of us devote our time, energy, and skills to the development of various aspects of digital biology. It is because of the compelling and overwhelming excitement we feel as we uncover some of the fundamental truths of nature.

The book is organized into seven major chapters that explore natural and digital biology: Universes, Evolution, Brains, Insects, Plants, Immune Systems, and Growth. Each chapter is designed to stand alone with its own distinctive identity. However, if you truly wish to follow the processes of biology that this book describes, you should read each chapter in order. You should then discover, as I have, how all biological processes are aspects of a single, fundamental process, as described in the final chapter: "Answers."

Our first step is the beginning of a theme that I shall continue throughout this book: natural and digital biology follow the same processes, just in different universes. Before you can really understand either, you should understand what a universe is.

Excerpted from Digital Biology by Peter J. Bentley. Copyright © 2001 by Peter J. Bentley. Excerpted by permission. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.