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Having read about molecular biology and so forth, I would love to be
able to simulate this kind of thing in a computer. With real organisms,
you have to guess what happened from the evidence that is left today.
With a computer simulation, you could potentially record the entire
history of the whole system.
There's a couple of problems with that though.
One problem is chemistry. In real life, the amino acid sequence of a
protein dictates the way it folds up to make a functional molecule, and
the folded shape dictates what the molecule actually does. But
currently, predicting the way that one single small protein will fold is
a computational problem so crushing that it brings state-of-the-art
supercomputers to their knees. The largest computer cluster in the
world, folding@home, exists to simulate *simplified* protein folding
experiments.
If it takes that much computer power just to calculate the shape of one
single protein, then simulating an entire living cell, consisting of
many hundred trillion protein and other molecules is obviously vastly
infeasible. Simulating a multicellular organism such as a tiny ant is
laughably impossible.
The next problem is the size of a typical genome. According to
Wikipedia, the various genomes that have been sequenced vary from 10 MB
to 10 GB of data. Now, evolution usually happens in populations of
thousands if not millions of individuals. If each individual has a 10 GB
genome and you've got a million individuals, that's 10 petabytes of
data, right there. And if you want to keep a complete record of the
genome of every single organism that has ever lived... we're easily
talking about exabytes of data here.
And then of course, there's the sheer implausibility of /creating/ life
in the first place. You might have to wait a *long* time for your
randomly mixing chemicals to do anything even remotely interesting.
Come to think of it, evolution is very, very slow anyway. To get
anything interesting, you would have to have vast environments of varied
types to inhabit, and you would have to wait a very long time.
In all, simulating life as it exists on Earth is infeasible. All the
computers on Earth couldn't handle a few microbes, never mind anything
that could be called an ecosystem.
Most artificial life simulations don't do this, of course. They simulate
a small data set, apply some kind of arbitrary "fitness" function to it,
and keep all the individuals with fitness above some arbitrary cutoff
value. They then do some kind of duplication / mutation process, and repeat.
The thing is, usually the way the fitness function is set up, there is
exactly one possible solution, and the system is so simple that there's
only a handful of ways to achieve that solution. And the whole machinery
of the system is very simple. Usually only one tiny component of it can
change.
In real living systems, on the other hand, *everything* can potentially
be modified. For example, an organism can evolve a brand new amino acid.
Not just theoretically; this has actually happened. But a computer
program that just copies a set of codes according to hard-coded rules
can't ever do something like that.
Real systems have other interesting properties. Organisms can actually
alter their environment. (E.g., Earth's atmosphere didn't originally
contain oxygen. Plants invented that.) And organisms don't just die if
their fitness is less than X, otherwise live forever. They live or die
depending on how favourable the conditions are. There are predators and
prey. There is competition for space, food and materials. All this
richness that the computer simulations almost never include.
On the other hand, I'm still at a loss for how to include all this
interesting stuff without the simulation slowing down to the point where
it's slower than *actual* evolution...
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