Showing posts with label genes. Show all posts
Showing posts with label genes. Show all posts

01 June 2007

Maybe Genomics is Getting a Little Too Personal

So Jim Watson's genome will soon be made public. But not all of it:

the only deliberate omission from Watson's sequence is that of a gene linked to Alzheimer's disease, which Watson, who is now 79, asked not to know about because it is incurable and claimed one of his grandmothers.

The trouble is, the better our bioinformatics gets, the more genes we will be able to analyse usefully, and the better our ability to make statistical predictions from them. Which means that more and more people will be snipping bits out of their public genomes in this way. And which also means that many of us will never put any of our genome online.

27 May 2007

Googling the Genome, Part III

Good to see some others concerned by the imminent arrival of personal genomics:

In addition, many scientists fear cheap genome sequencing could have other, worrying consequences. Professor Steve Jones of University College London, said: 'If you make your genome public, you are not just revealing information about yourself and what diseases you might be susceptible to, you are also giving away crucial data about the kind of illnesses your children might be prone to. Each of your children gets half your genes, after all. They might not want the world to know about the risks they face and become very unhappy in later life that you went public. Your other relatives might equally be displeased.'

And by its implications for civil liberties:

However, there are other concerns, as Professor Ashburner points out. 'Anyone who commits relatively minor offences can have their DNA taken and analysed. At present, the main use of this process is to create a DNA fingerprint that can be used to identify that individual. But soon we will be able to create an entire genome sequence of that individual from a swab or blood sample. We will end up knowing everything about their genes. In the end, we could have millions of people on a database and know every single genetic secret of each person. That has to be a very worrying prospect.'

02 February 2007

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?

17 January 2007

Gene Geni

This is quite clever - although it's a pity it uses Flash. You start to build your family tree on-screen, adding emails to the names where available. These are then sent info about the site, and obviously encouraged to add their own local knowledge of the tree. So the system is viral, and is based on two networks: that of family connections, and that of the Internet.

It's easy to foresee the day when we know all our public genealogical connections in this way - a stage before our genomes are used to show all the private ones, too.... (Via TechCrunch.)

18 July 2006

The Mega-Important MicroRNAs

Yesterday, when I was writing about the structures found in DNA, I said

Between the genes lie stretches of the main program that calls the subroutines

This is, of course, a gross over-simplification. One of the most interesting discoveries of recent years is that between your common or garden genes there are other structures that do not code for proteins, but for strings of RNA. It turns out that the latter play crucial roles in many biological processes, for example development. Indeed, they are fast emerging as one of genomics' superstars.

So it is only right that Nature Genetics should devote an entire issue to the subject; even better, it's freely available until August 2006. So get downloading now. Admittedly, microRNAs aren't the lightest of subject-matters, but they're mega-important.

17 July 2006

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.

13 July 2006

Open Source Evolution

Carl Zimmer is one of the best science writers around today. He manages to combine technical accuracy with a writing style that never gets in the way of his argument. So I was delighted to see this piece on his blog, entitled: "In the Beginning Was Linux?", which includes the following section:

Biologists have long recognized some striking parallels between genes and software. Genes stored information in a language of DNA, with the four nucleotides serving as its alphabet. A genetic code allowed cells to translate the information in genes into the separate language of proteins, which used an alphabet of twenty amino acids. From one generation to the next, mutations introduced slight tweaks to the software. Sex combined different versions of subroutines. If the software performed better--in the sense that an organism had more reproductive success--the changes might become incorporated into the genome across an entire species.

Now, this is amusingly close to the opening chapter (and central idea) of Digital Code of Life, but Zimmer goes further by drawing on the theories of Carl Woese, one of the most original thinkers about how life might have evolved in the earliest stages. It would take too long to explain the details to non-biologists, so I won't attempt it here - not least because Zimmer has already done with customary clarity in his post. Do read it.

19 April 2006

The Euston Manifesto

After the right espousing open source and related open goodness yesterday, today we have the left. More specifically, we have something called The Euston Manifesto (via Compromiso Social por la Ciencia). This may sound a bit like an Ealing Comedy, but it includes the following rather surprising paragraph:

14) Open source.
As part of the free exchange of ideas and in the interests of encouraging joint intellectual endeavour, we support the open development of software and other creative works and oppose the patenting of genes, algorithms and facts of nature. We oppose the retrospective extension of intellectual property laws in the financial interests of corporate copyright holders. The open source model is collective and competitive, collaborative and meritocratic. It is not a theoretical ideal, but a tested reality that has created common goods whose power and robustness have been proved over decades. Indeed, the best collegiate ideals of the scientific research community that gave rise to open source collaboration have served human progress for centuries.

09 April 2006

(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.