Collected Essays (32 page)

In computer A-Life, we often allow both of the newly mated genomes to survive. In fact, the most common form of computer A-Life reproduction is to replace the two original parent programs by the two new crossed-over programs. That is to say, two A-Life parents often “breed in place.”

In a world where several species exist, it can even sometimes happen that one species genome can incorporate some information from the genome of a creature from another species! This phenomenon is called “exogamy”. Although rare, exogamy does seem to occur in the real world. It is said that snippets of our DNA are identical to bits of modern cat DNA. Gag me with a hairball!

Mutation, Transposition and Zapping

The fourth sex topic involves
random changes to the genome.

Mating is a major source of genetic diversity in living things, but genomes can also have their information changed by such randomizing methods as mutation, transposition, and zapping. While mating acts on pairs of genomes, randomization methods act on one genome at a time.

For familiar wetware life forms like ourselves, mutations are caused by things like poisons and cosmic rays. Some mutations are lethal, but many of them make no visible difference at all. Now and then a particular mutation or accumulation of mutations will cause the phenome to suddenly show a drastically new kind of appearance and behavior. Perhaps genius, perhaps a harelip, perhaps beauty, perhaps idiocy.

In the A-Life context, where we typically think of the genome as a sequence of zeroes and ones, a mutation amounts to picking a site and flipping the bit: from zero to one, or from one to zero.

Besides mutation, there are several other forms of genome randomization, some of which are still being discovered in the real world and are as yet poorly understood.

One interesting genome changer is known as
transposition
. In transposition, two swatches of some genomes are swapped.

Another genome randomizer that we sometimes use in A-Life programs is
zapping
, whereby every now and then
all
of some single creature’s genome bits are randomized. In the real world, zapping is not a viable method of genetic variation, as it will almost certainly produce a creature that dies instantly. But in the more forgiving arena of A-Life, zapping can be useful.

In the natural world, species typically have very large populations and big genomes. Here the effects of mating—sexual reproduction—are the primary main source of genetic diversity. But in the small populations and short genomes of A-Life experiments, it is dangerously easy for all the creatures to end up with the same genome. And if you crossover two identical genomes, the offspring are identical to the parents, and no diversity arises! As a practical matter, random genome variation is quite important for Artificial Life simulations.

Death

What would life like if there were no death? Very crowded or very stagnant. In imagining a counterfactual situation like
no death
, it’s always a challenge to keep a consistent mental scenario. But I’m a science fiction writer, so I’m glad to try. Let’s suppose that Death forgot about Earth starting in the Age of the Dinosaurs. What would today’s Earth be like?

There would still be lots of dinosaurs around, which is nice. But if they had been reproducing for all of this time, the dinosaurs and their contemporaries would be piled many hundreds of meters deep all over Earth’s surface, in fact they would fill all known space. Twisted and deformed dinosaur mutations would be plentiful as well. One might expect that they the dinos have eaten all the plants up, but of course there would be no death for plants either, so there would be a huge jungle of plants under the mounds of dinosaurs, all of the dinos taking turns squirming down to get a bite. The oceans would be gill to gill with sea life, and then some. I think of the Earth before Noah’s flood.

Would mammals and humans have evolved in such a world? Probably not. Although there would be many of the oddball creatures around that were our precursors, in the vast welter of life there would be no way for them to select themselves out, get together, and tighten up their genomes.

An alternative vision of a death-free Earth is a world in which birth stops as well. What kind of world would that lead to? Totally boring. It would be nothing but the same old creatures stomping the same old environment forever. Like how the job market looks to a young person starting out!

Meaningless proliferation or utter stagnancy are the only alternatives to death. Although death is individually terrible, it is wonderful for the evolution of new kinds of life.

Evolution is possible whenever one has (1) reproduction, (2) genome variation, and (3) natural selection. We’ve already talked about reproduction and the way in which mating and mutation cause genome variation—so that children are not necessarily just like their parents. Natural selection is where death comes in: not every creature is in fact able to reproduce itself before it dies. The creatures which do reproduce have genomes which are selected by the natural process of competing to stay alive and to bear children which survive.

What this means in terms of computer A-Life is that one ordinarily has some maximum number of memory slots for creatures’ genomes. One lets the phenomes of the creatures compete for a while and then uses some kind of fitness function to decide which creatures are the most successful. The most successful creatures are reproduced onto the existing memory slots, and the genomes of the least successful creatures are erased.

Nature has a very simple way of determining a creature’s fitness: it manages to reproduce before death or it doesn’t. Assigning a fitness level to competing A-Life phenomes is a more artificial process. Various kinds of fitness functions can be chosen on the basis of what kinds of creatures one wants to see evolve. In most of the experiments I’ve worked on, the fitness is based on the creatures’ ability to find and eat food cells, as well as to avoid “predators” and to get near “prey”.

So far in this essay we’ve talked about life in terms of three general concepts: gnarl, sex, and death. Computer A-Life research involves trying to find computer programs which are gnarly, which breed, and which compete to stay alive. Now let’s look at some non-computer approaches to Artificial Life.

Biological A-Life

In this section, we first talk about Frankenstein, and then we talk about modern biochemistry.

Frankenstein

The most popular fictional character who tries to create life is Viktor Frankenstein, the protagonist of Mary Shelley’s 1818 novel, Frankenstein or, The Modern Prometheus.

Most of us know about Frankenstein from the movie versions of the story. In the movie version, Dr. Frankenstein creates a living man by sewing together parts of dead bodies and galvanizing the result with electricity from a thunderstorm. The original version is quite different.

In Mary Shelley’s novel, Baron Viktor Frankenstein is a student with a deep interest in chemistry. He becomes curious about what causes life, and he pursues this question by closely examining how things die and decay—the idea being that if you can understand how life leaves matter, you can understand how to put it back in. Viktor spends days and nights in “vaults and charnel-houses,” until finally he believes he has learned how to bring dead flesh back to life. He sets to work building the Frankenstein monster:

In a solitary chamber…I kept my workshop of filthy creation: my eyeballs were starting from their sockets in attending to the details of my employment. The dissecting room and the slaughter-house furnished many of my materials; and often did my human nature turn with loathing from my occupation…Who shall conceive the horrors of my secret toil, as I dabbled among the unhallowed damps of the grave, or tortured the living animal to animate the lifeless clay?

Finally Dr. Frankenstein reaches his goal:

It was on a dreary night of November, that I beheld the accomplishment of my toils. With an anxiety that almost amounted to agony, I collected the instruments of life around me, that I might infuse a spark of being into the lifeless thing that lay at my feet. It was already one in the morning; the rain pattered dismally against the panes, and my candle was nearly burnt out, when, by the glimmer of the half-extinguished light, I saw the dull yellow eye of the creature open; it breathed hard, and a convulsive motion agitated its limbs…The beauty of the dream vanished, and breathless horror and disgust filled my heart.

The creepy, slithery aspect of Frankenstein stems from the fact that Mary Shelley situated Viktor Frankenstein’s A-Life researches at the tail-end of life, at the part where a living creature life dissolves back into a random mush of chemicals. In point of fact, this is really not a good way to understand life—the processes of decay are not readily reversible.

Biochemistry

Contemporary A-Life biochemists focus on the way in which life keeps itself going. Organic life is a process, a skein of biochemical reactions that is in some ways like a parallel three-dimensional computation. The computation being carried out by a living body stops when the body dies, and the component parts of the body immediately begin decomposing. Unless you’re Viktor Frankenstein, there is no way to kick-start the reaction back into viability. It’s as if turning off a computer would make its chips fall apart.

The amazing part about real life that it keeps itself going on its own. If anyone could build a tiny, self-guiding, flying robot he or she would a hero of science. But a fly can build flies just by eating garbage. Biological life is a self-organizing process, an endless round that’s been chorusing along for hundreds of millions of years.

Is there any hope of scientists being able to assemble and start up a living biological system?

Chemists have studied complicated systems of reactions that tend to perpetuate themselves. These kinds of reaction are called
autocatalytic
or
self-exciting
. Once an autocatalytic reaction gets started up, it produces by-products which pull more and more molecules into the reaction. Often such a reaction will have a cyclical nature, in that it goes through the same sequence of steps over and over.

The cycle of photosynthesis is a very complicated example of an autocatalytic reaction. One of the simpler examples of an autocatalytic chemical reaction is known as the
Belusov-Zhabotinsky reaction
in honor of the two Soviet scientists who discovered it. In the Belusov-Zhabotinsky reaction a certain acidic solution is placed into a flat glass dish with a sprinkling of palladium crystals. The active ingredient of litmus paper is added so that it is possible to see which regions of the solution are more or less acidic. In a few minutes, the dish fills with scroll-shaped waves of color which spiral around and around in a regular, but not quite predictable, manner.

A Belusov-Zhabotinsky pattern in a cellular automaton.

There seems to be something universal about the Belusov-Zhabotinsky reaction, in that there are many other systems which behave in a similar way: generating endlessly spiraling scrolls. It is in fact fairly easy to set up a cellular-automaton-based computer simulation that shows something like the Belusov-Zhabotinsky reaction—Zhabotinsky scrolls are something that CAs like to “do.”

As well as trying to understand the chemical reactions that take place in living things, biochemists have investigated ways of creating the chemicals used by life. In the famous 1952 Miller-Urey experiment, two scientists sealed a glass retort filled with such simple chemicals as water, methane and hydrogen. The sealed vessel was equipped with electrodes that repeatedly fired off sparks—the vessel was intended to be a kind of simulation of primeval Earth with its lightning storms. After a week, it was found that a variety of amino acids had spontaneously formed inside the vessel. Amino acids are the building blocks of protein and of DNA—of our phenomes and of our genomes, so the Miller-Urey experiment represented an impressive first step towards understanding how life on Earth emerged.

Biochemists have pushed this kind of thing much further in the last decades. It is now possible to design artificial strands of RNA which are capable of self-replicating themselves when placed into a solution of amino acids; and one can even set a kind of RNA evolution into motion. In one recent experiment, a solution was filled with a random assortment of self-replicating RNA along with amino acids for the RNA to build with. Some of the molecules tended to stick to the sides of the beaker. The solution was then poured out, with the molecules that stuck to the sides of the vessel being retained. A fresh food-supply of amino acids was added and the cycle was repeated numerous times. The evolutionary result? RNA that adheres very firmly to the sides of the beaker.

The RNA evolution experiment is described in Gerald Joyce, “Directed Molecular Evolution,”
Scientific American
, December, 1992. A good quote about wetware appears in
Mondo 2000: A User’s Guide to the New Edge
, edited by R. U. Sirius, Queen Mu and me for HarperCollins, 1992. The quote is from the bioengineer Max Yukawa: