Spore and artificial life

Spore, the latest game from Sims/SimCity creator Will Wright, comes out this Friday. The Creature Creator for the game has been out for a couple months, and over three million creatures have been created (one of mine is here). Today's NY Times science section has an article about the game that nicely summarizes Will Wright's creative intention - to make a fun game loosely based on evolutionary principles - while correctly pointing out some of the scientific caveats. Wright spent a lot of time talking with scientists to really understand how the diversity of life arises from simple systems. It looks like a lot of fun, I'm happy it will be available for my Mac.

Some Spore creatures interacting


The article points out another interesting video-game like application of evolutionary principles, this one much more useful for research. Scientists often use computer simulations to model population dynamics - how large groups of a species interact, mate, survive, and spread their genes. Avida is a software program developed by researchers at Caltech and Michigan State that imposes a digital version of natural selection (the mechanism of evolution) on a collection computer programs designed to behave like simple organisms. Each little program has it's own virtual CPU and isolated memory, allowing it to run at different speeds. The programs can mate, mutate, replicate, compete for digital resources and, over time, evolve into slightly new programs, with slightly different code (analogous to mutations and changes in DNA that correspond to the evolution of real organisms).

The simulations are totally computer based, so it's possible to examine evolution at extremely large time scales. This offers great insight into how simple organisms behave and evolve over time, and it allows scientists to test real-life events (such as mass extinctions, the introduction of new species, etc) that would normally only play out over millions of years. They can also test various mating and survival strategies and a whole slew of other interesting questions. This article entitled "Digital Evolution" offers a lot more information about simulating evolution in a computer, and one of this group's original scientific papers can be found here.

Thinking more about this, how much research is going to be conducted as a simulation in 50 years? There are limitations now, of course, we are nowhere near adequate simulation of complex organisms - that still requires grunt work out in meatspace - but if one day you could build a computer and run software over the weekend to collect data instead of observing some natural phenomenon for several years, that's going to be a game-changer.
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Check out this brain book

I'm reading Soul Made Flesh: The Discovery of the Brain--and How it Changed the World (buy it from Amazon), by Carl Zimmer. Zimmer is a science journalist and author, featured often in the New York Times and other newspapers, Discover, Scientific American, and other publications. He also has a blog, The Loom, and has written several books on eclectic science topics.

Soul Made Flesh is an account of the conceptual developments and discoveries of the past 2,000 years that led to our current understanding of the brain and nervous system, presented within their political and cultural context. From the start the focus is on Aristotle and the Four Humors, then Galen and Descartes. The meat of the book dwells on the Oxford circle in 17th century Britain. This group of natural philosophers included Robert Hooke, Christopher Wren, Robert Boyle, and Thomas Willis, with influences from Thomas Hobbes, among others. In the midst of English civil war, the fall of the monarchy at the hands of Oliver Cromwell, the eventual Restoration of royal rule, and many religious feuds, Oxford remained a bastion of scientific pursuit. Willis and the others performed countless dissections and experiments on the corpses of criminals (and dogs), leading to a detailed account of the anatomy of the nervous system and the first basic understanding of where human perception, thought, emotion, and intelligence reside. For nearly 1500 years before their discoveries, most people thought the heart was the center of human sensation and the soul was it's rational intellect. Aristotle's dogma loomed large over the Catholic church of Europe, and criticism of his Humors was serious business.



Most of the men of the Oxford group are known today for other work (e.g., Boyle, of Boyle's Law fame. Remember high-school chemistry?), or not known at all, but they are largely responsible for giving brain science (and in some ways, science in general) a systematic framework. It's true, though, that most were polymaths, dabbling in alchemy/chemistry, medicine, physics, astronomy, and other fields. Willis, the unofficial leader of the group, specifically published detailed drawings of the nerves, muscles, and brain, and is partly responsible for the idea of blood circulation. He was also the first psychiatrist, unknowingly diagnosing disorders like bipolar, depression, schizophrenia, and Alzheimer's centuries before they were fully understood. Most of this seems to be forgotten today. You might have heard of Boyle, or Hooke and Hobbes, but you probably don't know Willis. Ask any medical or neuroscience graduate student, however, and they will be able to credit Willis with at least one thing: the Circle of Willis.

The Circle of Willis is a ring of blood vessels that runs along the underside of the brain and brainstem, supplying it with blood. Oh, how many times I drew this picture during neuroanatomy last Spring. This is all that Willis gets, his name associated with a few (very important) blood vessels. It's a raw deal, if you ask me.

I'm two-thirds into this book at the moment - still in the 17th century - so I've yet to get to the more modern work of 19th century anatomists and the rise of the neuron in the 20th century - topics I'm more familiar with. So far this is a very nice account of the conceptual revolution underlying the shift away from a dualist perspective on the brain/mind that dates back to the ancient Greeks. The Oxford circle, though deeply religious themselves, moved understanding of human consciousness away from the sort of mystical soul-talk of the Middle Ages, and into the head. The cultural significance of this shift was huge, and Zimmer spends a lot of time discussing the persistent ideological struggles in Britain and elsewhere.

This obviously isn't just a neuroscience book. If you are interested in understanding how radical ideas develop within a cultural and political context, this offers an interesting perspective. Other late Renaissance philosophers and scientists, like Galileo, revolutionized their fields amidst similar tumult. There are also plenty of good bits on England early in it's colonial period, something most history classes seem to gloss over. Sometimes in the middle of the book, which I just read through, the chapters meander, and you're not sure who's book this is, who Zimmer is focusing on. I think that underscores the point, however, that big changes in the way people view themselves and their world, like the shift from a metaphysical mind to one made of matter, require a lot of time and a lot of people working to drive that change.

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