Can't make up my mind about Venter

Craig Venter causes me problems. Do I like what he does or not? He is a controversial figure; controversy that I think mainly stems from his intention to patent the human genome sequence produced by his company Celera. In a couple of weeks, on Oct 25^th, he is releasing his autobiography A Life Decoded: My Genome: My Life (suffering from the sort of dreadful title long associated with scientists autobiographies see here) of which two extracts have been published in the Guardian (extract 1, extract 2), the first about the race between the two human genome projects and the second about his time in Vietnam. Coincidentally, this is also the predicted date for his creation of synthetic life. How's that for advertising?

Working in microbial ecology I had heard of Venter and the race to produce the first human genome sequence - incidentally, neither the Celera or Human Genome Consortium versions are actually complete, the assemblies of the separate bits of sequence change relatively regularly and there are repetitive tracts that may be impossible to correctly sequence and assemble (we're currently up to version 36.2 according to the NCBI) - but my research was in an entirely different area of biology. Then came Sorcerer II and attempt to sequence the sea, or at least all the bacteria in it that pass through a 0.8 micron filter, but not a 0.1 micron one. The papers containing the detail of the expedition and some of the initial findings were published in the journal PLoS Biology. This produced a vast dataset of marine bacterial DNA sequence, massively increasing the amount of DNA from these organisms available in the DNA databases. Indeed they had to set up their own database to manage the data (and wouldn't have been very popular had they not).

This is where I start to have problems. The data is an excellent resource for people to see whether their favourite gene is present in the samples, but isn't the work bad science? There is no hypothesis being tested by sequencing in this way other than "we can sequence marine bacteria" (which reminds me of my favourite scientific paper - An Account of a Very Odd Monstrous Calf, by Robert Boyle pdf). On the other hand if you have the money and resources to do this kind of thing, why shouldn't you? It is an expedition rather than an experiment. See? Can't make up my mind. There is a presentation from Venter (on his yacht in a typically tropical part of the trip) available here, please ignore the Roche advert and note that even famous scientists can get a bad case of the "this next slide shows".

I think my problems boil down to motivation. Why does Venter want to sequence and patent the human genome? Why was one of the genomes of his own? And more recently why did the project after that have the aim of creating synthetic life? Is it massive hubris or is that entirely unfair?

Still - his competition to be the first to sequence the human genome certainly accelerated both projects and I find the global ocean sequencing data quite handy, plus he is talking about application of a synthetic bacterium, of which his Mycoplasma laboratorium is likely to be the first (as I understand it, currently there is a synthetic genome that has yet to be stuck in a cell and only then does it become an organism), in removal of atmospheric CO₂ (echoes of Lovelock's call for direct action there).

I'm still undecided, but in case you want to see more of him, below is a TED talk covering some of his efforts. It was given in 2005 and predicted and synthetic bacterium in 2007 followed by a synthetic eukaryote by 2015. One down, one to go.



Incidentally, the TED talks site is a great place to find fascinating talks - my favourite that I've listened to so far being Sir Ken Robinson - his description of academics on the dance-floor is entirely accurate (although I'd add more pogoing).

In Our Time

I've sporadically kept a blog before about an Alternative reality game (Perplex City - now on sabbatical) and found that I really wanted to post about so many more things than purely that. One of the main distractions was microbial ecology and this blog is my attempt to give free rein to that distraction.

Though in this first post I still can't quite escape. Through the blog of one of the creators of Perplex City, Adrian Hon I came across a series of programmes on Radio 4 called In Our Time, hosted by Melvyn Bragg (gratuitous photo of famous bouffant do left).

I don't listen to the radio very much, it's something I associate with being driven to swimming lessons as a child (not that I didn't like swimming) and The Archers omnibus on a Sunday when my mum was doing the ironing (idyllic huh? And who'd have thought that Debbie Aldridge was much better as a comedian?), but these sounded great; panel discussions on all manner of subjects including hell, negative numbers, Jung and the Higgs Boson (I have a prejudiced view of the Higgs Boson that for the moment I will refrain from letting forth).

Being quite cautious when it comes to sampling new things I scrolled down the substantial list of programmes in the archive, all still available to listen to, to find one that I might know something about already (goodbye chaos theory and Wittgenstein) and found Microbiology. I fully expected to get annoyed at inaccuracies, or at the ecological aspects of microbiology being ignored in favour of the grisly, crowd-pleasing medical aspects, but was unable to. It was a lovely potted history of the subject which managed to cover the history of its development, its impact and future potential in only forty minutes, less than your average undergraduate lecture. Culturabilty, phylogenetics and similar were all mentioned

Though some of the anecdotes anyone with a GCSE in science will have come across - Edward Jenner injecting poor James Phipps with pus and coming up with vaccination for example - other parts of the programme were more novel. I'm sure I've always been taught about microbiology's origins via the history of microscopy and that the two were inextricably linked, but one of the panellists, Andrew Mendelsohn pointed to the real beginnings of the subject being in studies of function of microorgansisms - physiology rather than microscopic observation. It's nice to make these little connections that I've failed to fully appreciate and happily function has also been the subject of my own work. Definitely worth a listen.

And in case you get hooked on In Our Time (sorry), Adrian also has a discussion site about the programme, After Our Time.