Virtual Organisms: The Startling World of Artificial Lifeby Mark Ward
Harmless artificial life forms are on the loose on the Internet. Computer viruses and even robots are now able to evolve like their biological counterparts. Telecommunications companies are sending small packets of software to go forth and multiply to cope with ever-increasing telephone traffic. Protein-based computers are on the agenda, and a team in Japan is
Harmless artificial life forms are on the loose on the Internet. Computer viruses and even robots are now able to evolve like their biological counterparts. Telecommunications companies are sending small packets of software to go forth and multiply to cope with ever-increasing telephone traffic. Protein-based computers are on the agenda, and a team in Japan is building an organic brain as clever as a kitten. Welcome to the startling world of Artificial Life.
Artificial Life scientists are taking inanimate materials such as computer software and robots and making them behave just like living organisms. In the process they are discovering much about what drives evolution and just what it means to say that something is alive. Virtual Organisms traces the origins of this field from the days when it was practiced by a few maverick scientists to the present and the current boom in Alife research.
Leading technology correspondent Mark Ward presents a fascinating survey of current ideas about the origins of life and the engines of evolution. Through interviews with leading developers of Artificial Life, and through his own compelling research, Ward shows how the convergence of technology with biology has enormous implications.
In an accessible, entertaining manner, Virtual Organisms reveals an unexplored avenue in predicting the future of Artificial Life, and whether new forms of Alife may be evolving beyond their designer's control.
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The Startling World of Artificial Life
By Mark Ward
St. Martin's PressCopyright © 1999 Mark Ward
All rights reserved.
During evolution there was great selection pressure for immediate action: crucial to our survival is the instant distinction of predator from prey and kin from foe, and the recognition of a potential mate. We cannot afford the delay of conscious thought or debate in the committees of the mind. We must compute the imperatives of recognition at the fastest speed and, therefore, in the earliest-evolved and unconscious recesses of the mind. This is why we all know intuitively what life is. It is edible, lovable or lethal.
The Ages of Gaia, James Lovelock
Physicists are among the luckiest of scientists because they can see almost to the edge of creation. In contrast the view that biologists have of their own big bang, the origins of life, is much muddier and indistinct.
Theories about events during the first moments of the Universe start a mere 10-43 seconds after the Big Bang. The difference between zero and 10-43 seconds later might not sound like enough to matter. In fact its very nearly nothing at all, although the moment 10-43 seconds after the Big Bang has a name, the Planck time. The early Universe managed to get a lot done in a tiny amount of time. It went from being infinitely hot to a temperature of only 1028Celsius by 10-35 seconds after the Big Bang. It has cooled down a lot since then. Today the average temperature of space is a chilly -270°C. In a tiny fraction of a second the Universe expanded from nearly nothing into something as big as a pea. A very heavy, very hot pea.
Physicists are not entirely sure what was happening before 10-43 seconds but they have their suspicions. They think that before this time all the familiar forces of today (electromagnetic, gravity, the weak and strong nuclear forces) were united into one superforce. Gravity dropped out at 10-43 seconds and by 10-35 seconds the others had separated out as well. The interplay of these forces sets the Universe into the form we see it today by restricting the ways that subatomic particles can interact. But 15 billion years ago they were only just getting started as the Universe cooled and expanded enough for them to separate out. Testable theories about when and how three of the forces mix and match are well established, but it is proving difficult for physicists to work out how gravity fits in with the others. Fitting it in and getting closer to the Big Bang requires a quantum theory of gravity, something that has so far proved elusive.
So if you want to look the creator, or creation, in the face, become a physicist, not a biologist. In comparison to the pin-sharp hindsight of physicists, biologists are cursed with myopia. When they look back they see only shapes and suggestions in soil and rocks not certainties written across the skies. Biologists have yet to agree when and how life got going, let alone plot the order of events since.
Earth is around 4.6 billion years old, over a quarter of the age of the Universe. This is an unimaginably huge span of time and one that is hard to get to grips with. My mental ready reckoner can cope with life spans of about a hundred years and histories of civilizations a couple of thousand years old but it cuts off well before ten thousand years, never mind one hundred thousand times as long as that.
An analogy may make it slightly easier to appreciate. If we take a mile to represent a million years and you were to drive at a steady 60 mph, it would take three days, four hours and 36 minutes of non-stop driving to journey from the Earth's beginning to the present day. Four thousand six hundred miles is roughly the distance by road between Lisbon in Portugal and Athens, Greece. It's a little further than the distance by air between London and Anchorage, Alaska.
It's not just you and I that have problems handling these great swathes of time. To make them easier to deal with scientists who work with geological time scales on a daily basis have divided up the span of time between then and now into a series of eons, eras, periods and epochs. The eons are the largest divisions and the others are sub-divisions within these.
At first glance this division seems arbitrary and devoid of sense. There is no set span of time between eons, they do not fall regularly every billion years as any sensible dating system would have them do. Instead the earliest eon – the Hadean – lasted 600 million years but that which followed it – the Archaean – lasted over twice as long. The Hadean encompasses the time from the formation of the Earth to the age of the oldest rocks.
Memorizing this table is a formidable task. Harvard geology and zoology professor Stephen Jay Gould used to lighten the load by turning the task into a mnemonics contest. He says that the 'all-time champion' turned the list of eras and periods into a review of a pornographic movie called Cheap Meat.
But there is a subtle intelligence at work in this chronology. The divisions are not arbitrary, they reflect the sequence in which the rocks of the Earth were laid down, changes in fossil forms and even great events that affected living organisms. The boundaries between the two most recent eras mark great extinctions, one of which did for the dinosaurs. The break between the Proterozoic and Palaeozoic eras around 570 million years ago marks the great blooming of life known as the Cambrian Explosion. Using the 1 mile:1 million years scale this is roughly the distance between London and Aberdeen. However, Athens, Anchorage and the origins of life lie much further afield.
Hell on Earth
The earliest eon of Earth's history is known as the Hadean and it is aptly named because the early Earth was a hellish place. Hades is the name for the Greek kingdom of the dead and the description fits because at this time Earth was devoid of life. It was little more than an intensely radioactive molten-lava fireball. There was no land, lakes or seas, but the planet was brimming with the chemicals that would soon spring into life.
While there is agreement about the state of the planet during the early centuries of the Hadean eon, there is no such accord about what happened next. The Hadean was the place that life started and it has proved just as fertile a ground for theories about the origins of life. Every stage in the story of life is fiercely contested. Arguments rage about what chemicals were present and in what concentrations, what reactions they might have taken part in and the energy sources they might have tapped. There is even dispute over where these chemicals might have come from in the first place.
There are two reasons why the origins of life are so hotly disputed. Firstly there is no hard evidence to study, no fossils to point at and poke, and secondly no one has worked out how exactly you get from a seething chemical broth to self-replicating, stable chemical forms to cells and then on to you and me.
There are no fossils because any dead proto-cells that were around at this time would have been destroyed by geological processes over 4 billion years or so since they came into being. The oldest recognizable microfossils are around 3.5 billion years old, but life itself is thought to be older, perhaps half a billion years older.
Palaeobiologists are not on a wild goose chase when they go looking for these traces. There was definitely something living all those years ago, there is more than enough secondhand evidence for that. You might think that a slowly cooling fireball the size of the Earth would make it difficult, if not impossible, for life to begin. Yet this is exactly what happened. In fact life is thought to have got started several times only to be snuffed out by the impact of a large meteor, comet or moonlet.
Rock of Ages
The Isua rocks of western Greenland and those from the nearby Akilia island are the most ancient rocks on Earth at around 3.8 billion years old. They mark the end of the Hadean eon and they bear the unmistakable stamp of life.
In 1988 Manfred Schidlowski and his colleagues reported their discovery that the ratio of carbon-12 and carbon-13 isotopes in the Isua rocks was not as it should be. Usually these isotopes are found in rocks in roughly the same proportions. Yet in the Isua rocks the carbon-12 isotope predominates. The only process that uses the slightly lighter carbon-12 and therefore might lead to it being found in greater quantities in very old sedimentary rocks is photosynthesis – the process of using light energy to make carbohydrates.
The Akilia rocks bear different signs of the same process. These rocks contain patterns of minerals known as banded iron formations (BIFs). The thin bands in these formations are made up of iron oxides – haematite and magnatite – formed when oxygen combined with iron ions in the early oceans. The atmosphere of Earth in this eon was dominated by carbon dioxide so it has been claimed that the mineral layers formed because of the waste oxygen gases given off by photosynthetic bacteria.
If you were driving that car through history, you would do well to keep the windows rolled up when passing through this eon. There is no breathable oxygen in the atmosphere, instead it is made up of carbon dioxide, formaldehyde and hydrogen cyanide. Until 1994 this last gas was used by some US States in executions. The only other things in the atmosphere are ammonia, hydrogen sulphide and methane. All of which are superheated by the volcanic and nuclear activity of the newborn planet.
The picture is emerging that a mere 600 million years after the Earth was born life had taken hold. It got started nearly as soon as the Earth had cooled enough to produce a cracked crust riddled with niches for life to live in. The only question that remains to be answered now is: How?
Embarrassingly for biologists their success at explaining evolution and the transmission of genetic characteristics has not been matched by a similar level of success regarding theories about the origins of life. As ALife researcher Walter Fontana puts it: 'Biology has claim to two theories unto itself: Darwin's natural selection and Mendel's transmission rules. Both are correct, their joint operation can be nicely formalized, and together they are insufficient to account for the history of life as we know it.'
The problem is that these theories deal with living organisms, but they make no suggestions about how these organisms may have arisen in the first place. Many, many theories have been put forward to explain the origins of life. Some are more plausible than others. The most respectable start with the seething stew of chemicals that was present on the surface of the Earth a little over four billion years ago.
As the Hadean eon ended and gave way to the Archaean the planet began to cool. The water vapour that until then was kept in the upper atmosphere by the heat of the Earth's surface fell, condensed and became rain. The rain fell for centuries. There was so much rain that warm shallow seas were created. The falling water eroded the young rocks and the run-off formed chemical-rich rivers and streams that mixed vital nutrients and delivered them to the new seas.
Soon the seas were swimming with chemicals. The cycle of light and dark, heat and cold, evaporation and inundation turned the world into a vast vat, providing energy and opportunity for compounds to mix and match. As this global mixing went on, the key chemical trends of self-reference and auto-catalysis became established. These are important because they help chemical structures maintain themselves in self-sustaining cycles. Catalysts are like spanners and can be used again and again without themselves being changed, they facilitate a reaction but are not changed by it and are free to do the same thing again and again. A short description of a living being might be a self-sustaining entity. This could apply to a man, a mouse, an amoeba or a mass of chemicals in a tidal pool. Lynn Margulis, one of the most respected researchers into early life, says: 'Today, although all of the chemicals in our bodies are continually replaced, we do not change our names or think of ourselves as different because of it. Our organization is preserved, or rather it preserves itself.' Margulis sees common forces at work at every level. She claims that molecular complexes that arise spontaneously are doing the same thing as clusters of RNA that collaborate to create amino acids and other biogenic chemicals. Both of these share characteristics with crude cells that replenish themselves from their surroundings. In this commonality of action she says: '... we begin to see the winding road that self-organizing structures travelled on their journey toward the living cell.'
Artificial Life researchers are helping to show that getting started on this journey is relatively straightforward. Theoretical biologist Stuart Kauffman, who works at the Santa Fe Institute, has built computer models of what happens when lots of simple polymers are mixed together. Polymers, such as DNA, are long chain molecules with many repeating sub-units. Kauffman started with soups of short polymers and gave them the ability to take part in different catalytic reactions, including those that make more of the short chains. The molecules and compounds bump around making and breaking chains and forming new longer polymers as well as more of the ones that were there first. There comes a point when all of the catalysts needed to maintain the different polymers are present and the system becomes self-sustaining. Out of the random and chaotic mixing of chemicals emerges order and self-maintaining systems. The sparks of life.
It should be stressed that Kauffman's chemistry is, initially at least, all about self-maintenance rather than self-replication. It tries to show how stable compounds can arise rather than how they can reproduce. However, self-maintenance is clearly a long way down the path of self-replication and it may have been that out of a stable population of such chemicals self-replication emerged.
Kauffman claims that these 'auto-catalytic sets' as he calls them show that emergent order is fundamental and arises essentially for free. We do not need to appeal to luck and probability to explain how a sea of blindly reacting chemicals gave rise to life. Which is just as well, because as Sir Fred Hoyle said, there is more chance that a hurricane passing through a scrapyard will assemble a working 747 aircraft than random collisions in the early oceans would eventually produce you and me. Or as planetary biologist James Lovelock has put it: '... life is characterized by an omnipresence of improbability that would make winning a sweepstake every day for a year seem trivial by comparison.'
But once you admit that certain collections of chemicals can boot-strap themselves into ordered self-sustaining states the emergence of life becomes less problematic. As Kauffman says: 'Spontaneous order has been as potent as natural selection in the creation of the living world.'
This does not mean that the problems have been solved. Showing how it can be done is no substitute for finding out how it is done. Kauffman's work, though suggestive, has all been with computer models, but now he is starting to mix chemicals to see what emerges and whether auto-catalytic structures emerge.
Kauffman was not the first to advance the idea that some populations of chemicals are self-sustaining. Over twenty-five years ago Humberto Maturana and Francisco Varela introduced the idea of autopoiesis in an attempt to capture the self-preserving properties of living systems. Autopoietic systems are self-sustaining, they take the materials they need from the world around them and turn them to their own purposes. As an epithet it can be applied to everything from the first cells right up to the largest animals. Typically though it is used to describe basic organisms such as prokaryotic bacteria. This is because those interested in autopoiesis prefer to study it raw, free of the complications that studying a larger animal would bring.
Maturana and Varela were among the first to test their ideas using a computer model. In 1997 Barry McMullin, an ALife researcher from Dublin City University, revisited their work and created an artificial chemistry to test their theories. McMullin did this partly for historical reasons and partly so that other ALife researchers could play with the earlier system or use it as a test bed to try out their own theories.
His artificial chemistry was very simple and had only substrates, catalysts and links. Using these few elements McMullin wanted to see if any kind of autopoietic system could arise, if order would emerge spontaneously. In any one run of the system McMullin seeded a space with a few of his chemicals and let it run. When he reported his first results McMullin had not had much success but he was persevering and had come tantalisingly close on a couple of occasions to seeing an enclosed cell spontaneously form. His work continues.
Excerpted from Virtual Organisms by Mark Ward. Copyright © 1999 Mark Ward. Excerpted by permission of St. Martin's Press.
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Meet the Author
Mark Ward has managed to make a career out of writing about technology. He is the technology correspondent for the Daily Telegraph and he has been a reporter for Computer Weekly magazine and New Scientist. He lives in England.
Mark Ward, author of Virtual Organisms, is an Associate Professor of Statistics at Purdue University. He has held visiting faculty positions at The George Washington University, the University of Maryland, the University of Paris 13, and a lecturer position at the University of Pennsylvania. He received his Ph.D. from Purdue University in Mathematics with Specialization in Computational Science (2005), M.S. in Applied Mathematics Science from the University of Wisconsin, Madison (2003), and B.S. in Mathematics and Computer Science from Denison University (1999). His research interests include probabilistic, combinatorial, and analytical techniques for the analysis of algorithms and data structures. Since 2008, he has been the Undergraduate Chair in Statistics at Purdue, and the Associate Director for Actuarial Science. Dr. Ward is currently the Principal Investigator for two NSF grants, "MCTP: Sophomore Transitions: Bridges into a Statistics Major and Big Data Research Experiences via Learning Communities" (NSF-DMS #1246818, 2013-2018), and "Science of Information: Bringing Many Disciplines Together" (NSF-DUE #1140489, 2012-2014). He is also Associate Director of the Center for Science of Information (NSF-CCF #0939370, 2010-2015).
He and his wife homeschool their four children.
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