Has Google Forgotten Celera?

One of the reasons I wrote my book Digital Code of Life was that the battle between the public Human Genome Project and the privately-funded Celera mirrored so closely the battle between free software and Microsoft - with the difference that it was our genome that was at stake, not just a bunch of bits. The fact that Celera ultimately failed in its attempt to sequence and patent vast chunks of our DNA was the happiest of endings.

It seems someone else knows the story:

Celera was the company founded by Craig Venter, and funded by Perkin Elmer, which played a large part in sequencing the human genome and was hoping to make a massively profitable business out of selling subscriptions to genome databases. The business plan unravelled within a year or two of the publication of the first human genome. With hindsight, the opponents of Celera were right. Science is making and will make much greater progress with open data sets.

Here are some rea[s]ons for thinking that Google will be making the same sort of mistake as Celera if it pursues the business model outlined in its pending settlement with the AAP and the Author's Guild....

Thought provoking stuff, well worth a read.

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Saint Johnomics

Sir John Sulston is one of my heroes, right up there with RMS. Indeed, Sulston can reasonably be called the RMS of genomics (or maybe RMS is the Sulston of software). More than anyone else, it was Sulston who fought for and won the free availability of the human genome's digital code. Without him, I suspect that the company that once seemed set to become the Microsoft of molecular biology, Celera, would "own" the human genome, with all the appalling things that this implies.

I mention this because there was short piece by him in the FT recently. It's an edited extract from a talk he gave; the editing and extraction are not very well done, and it certainly doesn't do justice to the man or his ideas. For that, you should read his book The Common Thread - significantly, subtitled "A Story of Science, Ethics and the Human Genome".

Great literature it ain't, but it fair bristles with the same sense of mission and moral imperatives that makes RMS's stuff such fun to read. If RMS is St IGNUcius, perhaps Sulston is St Johnomics.

The World's First Open Source Man

The genome – the totality of DNA found in practically every cell in our body - is a kind of computer program, stored on 23 pairs of biological DVDs, called chromosomes. Within each chromosome, there are thousands of special sub-routines known as genes. Between the genes lie stretches of the main program that calls the subroutines, as well as spacing elements to make the code more legible, and non-functional comments – doubtless deeply cool when they were first written – that have by now lost all their meaning for us.

DNA's digital code – written not in binary, but quaternary (usually represented by the initials of the four chemicals that store it: A, C, G and T) – is run in a wide range of cellular computers, using a central processing unit (known as a ribosome), and with various initial values and time-dependent inputs supplied in a special format, as proteins. The cell computer produces similarly-formatted outputs, which may act on both itself and other cells.

Thanks to a far-sighted agreement known as the Bermuda Principles, the digital code that lies at the heart of life is freely available from three main databases: one each in the US, UK and Japan. As a result, the DNA that was obtained through the Human Genome Project is open source's greatest triumph.

But so far, no human genome can be said to represent any single human being: that of the Human Genome Project is in fact a composite, made up of a couple of dozen anonymous donors. But soon, all that will change; for the first time, the complete genome of a single person will be placed in the public databases for anyone to download and to use, creating in effect the world's first open source man.

His name is Craig Venter, and for nearly two decades he has been simultaneously revered and reviled as one of the most innovative researchers in the world of genomics. He was the person behind the company Celera that sought to sequence the human genome before the public Human Genome Project, with the aim of patenting as much of it as possible. Fortunately, the Human Genome Project managed to stitch together the thousands of DNA fragments it had analysed – not least thanks to some serious hardware running GNU/Linux – and to put its own human genome in the public domain, thus thwarting Celera's plans to make it proprietary.

A nice twist to this story is that it turned out that Celera's DNA sequence was not, as originally claimed, another composite, but came almost entirely from one person: Craig Venter himself. So his latest project is in many ways simply the completion of this earlier attempt to become the first human with a fully-sequenced genome. The difference now, though, it that it will be in the public databases, and hence accessible by anyone.

This will have profound consequences. Aside from placing his DNA fingerprint out in the open – which will certainly be handy for any police forces that wish to investigate Venter – it means that anyone can analyse his DNA for anything. At the very least, scientists will be able to carry out tests for genetic pre-dispositions to all kinds of common and not-so-common diseases.

So it might happen that a laboratory somewhere discovers that Venter is carrying a genetic variant that has potentially serious health implications. Most of us will be able to choose whether to take such tests and hence whether to know the results, which is just as well. In the case of incurable diseases, for example, the knowledge that there is a high probability – perhaps even certainty – that you will succumb at some point in the future is not very useful unless there is a cure or at least a treatment available. Venter no longer has that choice. Whether he wants it or not, others can carry out the test and announce the result; since Venter is a scientific celebrity and a public figure, he is bound to get to hear about it one way or another.

So while his decision to sequence his genome might be seen as the ultimate act of egotism, by choosing to publish the result he will in fact be providing science with a wonderfully rich resource - the complete code of his life - and at some considerable risk, if only psychological, to himself.

Publish and Be Damned!

The wilful misunderstanding of Google Books by traditional publishers is truly sad to see. They continue to propagate the idea that Google is somehow going to make the entire text of their titles available, whereas in fact it simply wants to index that text, and make snippets available in its search results.

As a an author I welcome this; nothing makes me happier than see that a search for the phrase "digital code" at Google Books brings up my own title as the top hit. The fact that anyone can dip into the book can only increase sales (assuming the book is worth reading, at least). Yes, it might be possible for a gang of conspirators to obtain scans of the entire book if they had enough members and enough time to waste doing so. But somehow, I think it would be easier to buy the book.

Of course, what is really going on here is a battle for control - as is always the case with open technologies. The old-style publishers are fighting a losing battle against new technologies (and open content) by being as obstructive as possible. Instead, they should be spending their energies working out new business models that let them harness the Internet and search engines to make their books richer and more available to readers.

They are bound to lose: the Internet will continue to add information until it is "good enough" for any given use. This may take time, and the mechanisms for doing so still need some work (just look at Wikipedia), but the amount of useful information is only going in one direction. Traditional publishers will cling on to the few titles that offer something beyond this, but the general public will have learned to turn increasingly to online information that is freely available. More importantly, they will come to expect that free information will be there as a matter of course, and will unlearn the habit of buying expensive stuff printed on dead trees.

It is this dynamic that is driving all of the "opens" - open source, open access, open genomics. The availability of free stuff that slowly but inexorably gets better means that the paid stuff will always be superseded at some point. It happened with the human genome data, when the material made available by the public consortium matched that of Celera's subscription service, which ultimately became irrelevant. It is happening with open source, as GNU/Linux is being swapped in at every level, replacing expensive Unix and Microsoft Windows systems. And it will happen with open content.