Here’s another post on my long and winding attempt to crack the code of genetic programming.  Genetic programming, or the evolution of computer programs, will revolutionize the speed and effectiveness of solving hard problems, and it will be something that we can plug into systems like Assembla to spit out useful subroutines.  First, we must get over some obstacles.  After 17 years of research and 10,000 times the computing power, our ability to make complex software has not measurably improved.  It appears that there are a lot of things that we don’t know about how evolution works.  I will crack the code yet.  However, it will take a while.  On the way, I hope to learn a lot of amazing things about evolution and it’s anthropic twin, innovation.

Saturday I went to see real genetic geneticists at a “Future of Life” event at Harvard and got to see amazingly smart researchers say something about their latest work.  

Craig Venter gave an overview of his recent work – collecting and sequencing 20M genes from ocean bacteria, approaches to growing biofuels, and experiments in building a bacteria from a naturally-inspired but minimum-sized synthetic genome.

George Church showed some even more recent work, including his hot-off-the-press in-vitro ribosome (a ribosome builds proteins and is extremely useful if you want to, for instance, generate a lot of different proteins and see what they do) which can be constructed outside the cell with 158 genes.  He also had very interesting things to say about biofuels.  He likes the idea of using algae for making biofuels because they can make exactly the fuel you want – typically clean-burning diesel oil.  He has worked out some clever ways to get them to emit the oil, so in theory the oil can be skimmed off the top of the pond, rather than pressed out with great waste.

He taunted me for my interest in evolvable software, observing that future bio-reactors should be able to test 20 trillion combinations in a batch, a scale that software will never match.  Venter has his 20M marine genes to sort through.  Church has a machine, a chip, that can spit out genes with many slight variations.  So, once they crank up the synthesis machinery, they will have a lot of raw material.  And, they have moved far beyond drug discovery in the search for new fuels and materials.

However, as they described their struggles to build a complete organism, and I contrast it with the relative ease of manipulating gene variants, it seems to me that they are running up against the same problem that we ran up against with genetic programming.  They can make simple things, and select for them, but not complex things.  There is a missing link in this artificial evolution, too.

Even so, I would never bet against these guys.  They are using machinery that is getting exponentially more powerful, at rates much faster than Moore’s law.  I would bet on algae as a fuel source even though the VC are pulling back (probably a good sign for returns) – 

Yesterday I had a chance to talk to one of my heroes, Stuart Kauffman.  As I am one of the six people to actually finish his amazing book Origins of Order, we had a lot to talk about.  He’s moved up to “Reinventing the Sacred” and doing a stint at Harvard Divinity School.  His basic point,  as he explained it (I haven’t read the book) is that the deterministic world of Laplace doesn’t have any room for innovation.  In a mechanical, predictable universe, everything that can be is prefigured and can be precomputed by its initial conditions.  The mathematics of chaos makes this unlikely, however, and the emergence of new kinds of life is unexpected.  My interpretation of his theory is that innovation is real, that new things come from life, things that didn’t exist before, and that progress exists in the universe.  I agree with that.

What’s so great about The Origins of Order?  It was one of the first things that I read which acknowledged that natural selection is actually a weak force compared with the innate order in genetic machinery.  That’s one of the things we need to realize about artificial evolution.  The genetic machinery is just as important as the selection machinery.

Kauffman agreed that most of the a-life experimenters he talked to have discussed the same issue – the difficulty of making anything beyond a certain level of complexity.

I proposed to him that our current emphasis on selecting the best item out of a genetic algorithm is like trying to build a house by selecting good bricks.  You keep pulling apart the house to find the best brick.  To build the house, you need to let the bricks fit together.  You need collaboration, co-evolution, and symbiosis.  The trick to determining the brick size and relationships might be found in his N-K network theory.  We’re going to get together to think about that.

One of the interesting things that I learned is that climate change can be very extreme.  For example, our oxygen-rich atmosphere is chemically unstable and is maintained only because we are surrounded by plants that emit oxygen.  The early earth had an atmosphere that was “anoxic”.  What I didn’t know is that scientists believe that earth went through about a billion years of a highly sulfuric atmosphere.  I had previously heard that eventually, when a lot of continents moved to the equator and started reflecting sunlight, the earth went into a super ice-age called “snowball earth” in which the oceans froze one mile thick.  These ice ages were interspersed with periods of scalding heat and acid rain.  Various kinds of bacteria happily lived through these various conditions, and contributed to the Permian explosion of multicellular life after the snowball earth thawed.  So, be happy with today’s weather.