Darwinian Software and Intelligent Design

On Open Enterprise blog.

Open Source Life

Fascinating:

Whatever Carl Woese writes, even in a speculative vein, needs to be taken seriously. In his "New Biology" article, he is postulating a golden age of pre-Darwinian life, when horizontal gene transfer was universal and separate species did not yet exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. Evolution could be rapid, as new chemical devices could be evolved simultaneously by cells of different kinds working in parallel and then reassembled in a single cell by horizontal gene transfer.

But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell, anticipating Bill Gates by three billion years, separated itself from the community and refused to share. Its offspring became the first species of bacteria—and the first species of any kind—reserving their intellectual property for their own private use. With their superior efficiency, the bacteria continued to prosper and to evolve separately, while the rest of the community continued its communal life. Some millions of years later, another cell separated itself from the community and became the ancestor of the archea. Some time after that, a third cell separated itself and became the ancestor of the eukaryotes. And so it went on, until nothing was left of the community and all life was divided into species. The Darwinian interlude had begun.

Of Philip Rosedale, God and Darwinism

Here's an entertaining piece of a biotech writer grappling with and finally grokking Second Life via biological metaphors:

I’m trying to wrap my barely evolved first-life brain around the idea of a virtual organism where I (or, more accurately, my imagination) am a gene (a bundle of code) and where my “second me” was brought to life by Philip Rosedale, who then cast me off to fend for myself, although within a system of rules he launched when the world began. These rules themselves are evolving. For instance, what is to be done about evil? Should people be allowed to hurt and kill others? Rosedale seems to be a benign God, with a baby face and an easy smile in his first life as a human. But can we be sure about this?

"Intelligent" Design

So the ID'ers are stepping up the pressure, here in the UK. They have a shiny new Web site - Truth in Science, no less - that looks jolly impressive in its comprehensiveness. You might think it would require an equal number of pages to counter the arguments put forth there. Fortunately, that is not the case.

It all comes down to the following section:

What is Intelligent Design?

The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

Well, natural selection is not an "undirected process": it is one absolutely directed by a very simple, readily comprehensible mathematical fact: that a system with a greater rate of growth than rival systems will inevitably overtake the latter as time progresses. The graph is steeper, so whatever the starting point, there will come a time when it overtakes every other system's graph. The difference in growth rates is what is known as the "natural selection": in fact, there is no selection, just this gradual but inevitable emergence.

Every change to a system that causes it to grow faster is a change that will be propagated more thoroughly than one that tends to slow down the growth. This means that systems "evolve" - that is, that they change over time in such as way as to maximise their growth (and note that this evolution is not unique or directed at any particular "goal".)

On the other side, the basic fallacy of invoking "intelligent" design to explain "certain features" of the universe, is that it explains nothing. It is a completely circular argument: things are as they are because an "intelligent cause" made them that way.

That is neither explanation nor science, and as such has no place in either schools or universities except as fodder for debating societies who wish to hone their skills in demolishing specious arguments.

Digital Fish Wrap

There is a wonderful evolutionary winnowing process underway within the mainstream media: those that get the Internet are thriving, while those that don't, come up with ideas like this:

Here's my proposal: Newspapers and wire services need to figure out a way, without running afoul of antitrust laws, to agree to embargo their news content from the free Internet for a brief period -- say, 24 hours -- after it is made available to paying customers. The point is not to remove content from the Internet, but to delay its free release in that venue.

A temporary embargo, by depriving the Internet of free, trustworthy news in real-time, would, I believe, quickly establish the true value of that information. Imagine the major Web portals -- Yahoo, Google, AOL and MSN -- with nothing to offer in the category of news except out of date articles from "mainstream" media and blogosphere musings on yesterday's news. Digital fish wrap.

See Darwin run. (Via Techdirt.)

Viral Evolution

As a big fan of the explanatory power of Darwinian evolution - which, for those still concerned about its "theoretical" status, is basically just maths - I have to say I'm impressed by this story:

SpamThru takes the game to a new level, actually using an anti-virus engine against potential rivals.

Of course, this is precisely the same strategy that baby cuckoos use. Self-standing, evolving computer viruses living across the Net are getting ever closer....

The Evolution of Academic Knowledge

The complete works of Charles Darwin are now online. This is certainly an important moment in the evolution of academic knowledge, since it points the way to a future where everything will be accessible in this way - call it the Googleisation of academia.

A pity, though, that the terms of use are so restrictive: not a CC licence in sight. Obviously we're still at the Neanderthal stage as far as copyright evolution is concerned.

Half-Open, Half-Closed

This isn't really open source, but it seems to me that the underlying idea has much in common with the open source development process - call it half-open (or half-closed). Here's TechCrunch's explanation:

Utah-based Logoworks, which just relaunched a major new user interface, has an innovative and inexpensive way of creating corporate and other logos for customers. They outsource the project to interested and pre-approved designers who come up with design concepts. You then pick the concept you like best and iterate from there. Designers are paid bonuses based on having their designs chosen, and so a very efficient and competitive market is created around each logo creation project.

Although TechCrunch frames this in terms of the "competitive market", I prefer to think of it as a Darwinian selection process that is akin to what happens with the larger open source projects. In any case, it's an interesting application of that idea in a general commercial context.

Intelligent Design ... and Bioinformatics

If you are interested in the background to the recent ruling against the teaching of Intelligent Design alongside Darwinian evolution in science classes, you might want to read a fine article on the subject, which also includes the judge's splendidly wise and perceptive remarks.

Of course, it is sad that the case even needed to be made. The idea that Intelligent Design - which essentially asserts that everything is as it is because, er, everything was made that way - can even be mentioned in the same breath as Darwinian evolution is risible. Not because the latter is sancrosanct, and cast-iron truth. But Darwin's theory is a scientific theory, testable and tested. So far, it seems to be a good explanation of the facts. Intelligent Design is simply a restatement of the problem.

Among those facts are the growing number of sequenced genomes. It has always struck me that DNA and bioinformatic analyses of it provide perhaps the strongest evidence for evolution. After all, it is possible to bung a few genomes into a computer, tell it to use some standard mathematical techniques for spotting similarities between abstract data, and out pops what are called phylogenetic trees. These show the likely interrelationships between the genomes. They are not proof of evolution, but the fact that they are generated without direct human intervention (aside from the algorithms employed) is strong evidence in its favour.

One of the most popular ways of producing such trees is to use maximum parsimony. This is essentially an application of Occam's Razor, and prefers simple to complicated solutions.

I'm a big fan of Occam's Razor: it provides another reason why Darwin's theory of natural selection is to be preferred over Intelligent Design. For the former is essentially basic maths applied to organisms: anything that tends to favour the survival of a variant (induced by random variations in the genome) is mathematically more likely to be propagated.

This fact alone overcomes the standard objection that Intelligent Design has to Darwinian evolution: that purely "random" changes could never produce complexity on the time-scales we see. True, but natural selection means that the changes are not purely random: at each stage mathematical laws "pick" those that add to previous advances. In this way, simple light-sensitive cells become eyes, because the advantage of being able to detect light just gets greater the more refined the detection available. Mutations that offer that refinement are preferred, and go forward for further mutations and refinement.

It's the same for Intelligent Design's problem with protein folding. When proteins are produced within the cell from the DNA that codes for them, they are linear strings of amino acids; to become the cellular engines that drive life they must fold up in exactly the right way. It is easy to show that random fluctuations would require far longer than the age of the universe to achieve the correct folding. But the fluctuations are not completely random: at each point there is a move that reduces the overall energy of the protein more than others. Putting together these moves creates a well-defined path towards to folded protein that requires only fractions of a second to traverse.