(Patently) Right

Paul Graham is a master stylist - indeed, one of the best writers on technology around. Reading his latest essay, "Are Software Patents Evil?" is like floating in linguistic cream. And that's the problem. His prose is so seductive that it is too easy to be hypnotised by his gently-rhythmic cadences, too pleasurable to be lulled into a complaisant state, until you find yourself nodding mechanically in agreement - even with ideas that are, alas, fundamentally wrong.

Take his point in this recent essay about algorithms, where he tries to argue that software patents are OK, even when they are essentially algorithms, because hardware is really only an instantiation of an algorithm.

If you allow patents on algorithms, you block anyone from using what is just a mathematical technique. If you allow patents on algorithms of any kind, then you can patent mathematics and its representations of physics (what we loosely call the Laws of Physics are in fact just algorithms for calculating reality).

But let's look at the objection he raises, that hardware is really just an algorithm made physical. Maybe they are; but the point is you have to work out how to make that algorithm physical - and that's what the patent is for, not for the algorithm itself. Note that such a patent does not block anyone else from coming up with different physical manifestations of it. They are simply stopped from copying your particular idea.

It's instructive to look at another area where patents are being hugely abused: in the field of genes. Thanks to a ruling in 1980 that DNA could be patented, there has been a flood of completely insane patent applications, some of which have been granted (mostly in the US, of course). Generally, these concern genes - DNA that codes for particular proteins. The argument is that these proteins do useful things, so the DNA that codes for them can therefore be patented.

The problem is that there is no way of coming up with an alternative to that gene: it is "the" gene for some particular biological function. So the patent on it blocks everyone using that genomic information, for whatever purpose. What should be patentable - because, let me be clear here, patents do serve a useful purpose when granted appropriately - is the particular use of the protein - not the DNA - the physical instantiation of what is effectively a genomic algorithm.

Allowing patents on a particular industrial use for a protein - not a patent on its function in nature - leaves the door open for others to find other chemicals that can do the same job for the industrial application. It also leaves the DNA as information/algorithm, outside the realm of patents.

This test of whether a patent allows alternative implementations of the underlying idea can be applied fruitfully to the equally-vexed questions of business methods. Amazon's famous "one-click" method of online making purchases is clearly total codswallop as a patent. It is a patent on an idea, and blocks everyone else from implementing that (obvious) idea.

The same can be said about an earlier patent that Oracle applied for, which apparently involved the conversion of one markup language into another. As any programmer will tell you, this is essentially trivial, in the mathematical sense that you can define a set of rules - an algorithm - and the whole drops out automatically. And if you apply the test above - does it block other implementations? - this clearly does, since if such a patent were granted, it would stop everyone else coming up with algorithms for conversions. Worse, there would be no other way to do it, since the process is simply a restatement of the problem.

I was heartened to see that a blog posting on this case by John Lambert, a lawyer specialising in intellectual property, called forth a whole series of comments that explored the ideas I've sketched out above. I urge you to read it. What's striking is that the posts - rather like this one - are lacking the polish and poise of Graham's writing, but they more than make up for it in the passion they display, and the fact that they are (patently) right.

"I Am Not a Number - I Am a Free Man!"

Tagging objects with unique, artificial DNA sequences that act as a barcode is not new; but I had no idea that it had progressed to the point where it was almost routine, as in this collectibles tagging service. It works by marking the object with an invisible ink containing small quantities of a synthetic DNA tag.

Although the collectibles story mentions using lasers and fluorescence to authenticate the tag, a more scalable approach would be to read the DNA directly: that requires fast, cheap DNA sequencers, and there's plenty of those under development.

As the cost of DNA synthesis and sequencing plummets, so this kind of barcoding is likely to become common. It's easy to apply, does not disfigure the object as a conventional barcode does (to say nothing of an RFID chip), and so does not need to be removed when the customer takes the item home.

But there is a dangerous downside to this ingenious approach. It will make the idea of DNA tagging uncomfortably mundane. And once people are used to the practice in their daily lives, it's only a short step for companies and governments to move on to identifying people by some very special sequences of DNA - their own.

The big advantage is that you don't even need to apply the invisible ink: practically every cell in our body already has the DNA tag. That tag is unique (modulo the odd identical twin), and you can't change your underlying genomic sequence (local mutations aside). In effect, this DNA forms your very own permanent identification number - written in the quaternary digits A, C, G and T - that is ideal for key documents like passports, driving licences and health cards. What government could pass up the opportunity to adopt such a logical approach?

Moreover, because the number never changes, you leave behind in your life a continuous trail of DNA tags - in the form of discarded cells (hair, skin, saliva, blood) - that forms a complete record of where you went. Put another way, for any given event, governments will be able confidently to assign names to most of the people who were involved, as well as to innocent witnesses - sorting out which is which is merely a forensic detail - on the basis of the genomic calling-cards they inevitably leave behind.

So much for freedom, Number 6.

Open Access and Earwax

Nicholas Wade in the New York Times has an interesting article about earwax. It seems that there are two types, wet and dry:

The wet form predominates in Africa and Europe, where 97 percent or more of the people have it, and the dry form among East Asians, while populations of Southern and Central Asia are roughly half and half. By comparing the DNA of Japanese with each type, the researchers were able to identify the gene that controls which type a person has.

Of course, this makes you want to get the full details - not least because it turns out that this is "the first example of DNA polymorphism determining a visible genetic trait." That is, for the first time, researchers have pinpointed a single letter change in the DNA (out of 3 billion), from a G to an A (the "polymorphism"), that alters something directly observable (the "visible genetic trait") - earwax consistency.

You can read the abstract, but - guess what? - only subscribers get to see the all the gory/waxy details. Surely, when it comes to something as quintessentially human as earwax, we have a right to open access?

Personal Genomics...but Not Yet

A new X-prize, this time for exploring inner rather than outer space, has been announced. To win the prize money, all you have to do is sequence the DNA of a 100 or more people in a few weeks. That may sound a little vague, but it is many orders of magnitude faster than we can do it now (and remember, the first human genome took about 15 years and three billion dollars).

Why bother? Well, it will open up the world of personal genomics: where the particular details of your genome - not the human genome in general - will be used to aid diagnosis and help doctors make decisions about treatment.

The X-prize announcement is really tantamount to recognising that all those breathless predictions of imminent personal genomes, made by some at the time of the Human Genome Project, were rather optimistic.

I have to say that I, for one, am not too sad. Much as I'd like to Google my genome, being able to do so will also raise considerable ethical dilemmas, as I discussed in my book Digital Code of Life.

As St. Augustine nearly said: "Give me genotypability - but not yet...."

A Mammoth Open Genome Project

Open genomics just goes from strength to strength. As this press release reports, there are now over 100,000,000,000 bases (DNA letters) in public databases, all of which may be freely downloaded.

This represents sequences from some 165,000 different organisms. Nearly all of these are living today, but there is an interesting move to sequence extinct animals too. The secret is to find enough ancient DNA, sufficiently well-preserved, that it can be sequenced.

Recently, an important breakthrough in this area was achieved by sequencing nearly 30 million bases of a woolly mammoth. As the relevant paper reports, the sequence identity between this set and the DNA of today's African elephant is a remarkable 98.55%. This means that we are not so far from being able to reconstruct most of the mammoth genome, using the African elephant DNA as a kind of scaffolding. The obvious next step would be cloning a mammoth, using modern-day elephants as egg donors and surrogate mothers.

Do not try this at home.

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.