Darwinian Software and Intelligent Design

On Open Enterprise blog.

"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.

Scrying an Oracle

This story has so many interesting elements in it that it's just got to be true.

According to Business Week, Oracle is poised to snap up no less than three open source companies: JBoss, Zend and Sleepycat Software. JBoss - which calls itself the "professional open source company", making everyone else unprofessional, I suppose - is one of the highest-profile players in this sector. Not least because its founder, the Frenchman Marc Fleury, has a tongue as sharp as his mind (you can sample his blog with this fab riff on genomics, Intelligent Design and much else).

His controversial remarks and claims in the past have not always endeared him to others in the free software world. Take, for example, the "disruptive Professional Open Source model" he proudly professes, "which combines the best of the open source and proprietary software worlds to make open source a safe choice for the enterprise and give CIOs peace of mind." Hmm, I wonder what Richard Stallman has to say about that.

JBoss has been highly successful in the middleware market: if you believe the market research, JBoss is the leader in the Java application server sector. Oracle's acquisition would make a lot of sense, since databases on their own aren't much fun these days: you need middleware to hook them up to the Internet, and JBoss fits the bill nicely. It should certainly bolster Oracle in its battle against IBM and Microsoft in the fiercely-fought database sector.

While many might regard the swallowing up of an ambivalent JBoss by the proprietary behemoth Oracle as just desserts of some kind, few will be happy to see Zend suffer the same fate. Zend is the company behind the PHP scripting language - one of the most successful examples of free software. (If you're wondering, PHP stands for "PHP: Hypertext Preprocessor" - employing your standard hacker recursive acronym naming convention).

Where JBoss is mostly key for companies running e-commerce Web sites, say, PHP is a core technology of the entire open source movement. Its centrality is indicated by the fact that it is one of the options for the ubiquitous LAMP software stack: Linux/Apache/MySQL/PHP or Perl or Python. The fact that Oracle will own the engine that powers PHP will be worrying for many in the free software world.

About Sleepycat, I can only say: er, who? - but that's just ignorance on my part. This article explains that Sleepycat's product, Berkeley DB, is actually the "B" in LAMP. Got that? The Sleepycat blog may throw some more light on this strange state of affairs - or maybe not.

Whatever the reason that Oracle wants to get its mitts on Sleepycat as well as Zend and JBoss, one thing is abundantly clear if these rumours prove true: Oracle is getting very serious about open source.

In the past, the company has had just about the most tortuous relationship with open source of any of the big software houses. As I wrote in Rebel Code, in early July 1998, an Oracle representative said "we're not seeing a big demand from our customer that we support it" - "it" being GNU/Linux. And yet just two weeks later, Oracle announced that it was porting Oracle8 to precisely that platform. This was one of the key milestones in the acceptance of free software by business: no less a person than Eric Raymond told me that "the Oracle port announcement...made the open source concept unkillable by mere PR" - PR from a certain company being a big threat in the early days of corporate adoption.

Open source has come on by leaps and bounds since then, and these moves by Oracle are not nearly so momentous - at least for free software. But I wonder whether the otherwise canny Larry Ellison really knows what he's getting into.

Until now, Oracle has mainly interacted with open source through GNU/Linux - that is, at arm's length. If it takes these three companies on board - especially if it acquires Zend - it will find itself thrown into the maelstrom of open source culture. Here's a hint for Mr Ellison: you don't get to assimilate that culture, whatever you might be thinking of doing with the companies. You either work with it, or it simply routes around you.

Yes, I'm talking about forks here: if Oracle misplays this, and tries to impose itself on the PHP or JBoss communities, I think it will be in for a rude surprise. To its credit, IBM really got this, which is why its embrace of open source has been so successful. Whether Oracle can follow in its footsteps, only time will tell.

But the rumoured acquisitions, if they go ahead, will have one other extremely significant effect. They will instantly add credibility, viability and desirability to a host of other second-generation open source companies that have grown up in the last few years. Free software will gain an immediate boost, and hackers will suddenly find themselves in great demand again.

Given the astonishing lift-off of Google's share price, and the palpable excitement surrounding Web 2.0 technologies (and the start-ups that are working on them), the hefty price-tags on open source companies being bandied around in the context of Oracle have a feeling of déjà-vu all over again: didn't we go through all this with Red Hat and VA Linux a few years back?

You don't have to be clairvoyant - or an oracle - to see that if these deals go through, the stage is well and truly set for Dotcom Delirium 2.0.

Open Access vs. Intelligent Design

Michael Eisen, a co-founder of the wonderful Public Library of Science project - a series of journals that make all of their content freely available - and one of the keenest exponents of open access, points out that a good way of combatting the pseudo-science of Intelligent Design is to make more of the real stuff available through open access.

The piece forms Eisen's first posting to his Open Science blog, which should be well-worth following.

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.