Venter at TED

TED2008 finished at the beginning of the month and there's been a flurry of new videos of the talks (generally about 15 minutes in length) to the site. One of the new talks is by Craig Venter, I've posted before about his last TED talk here, and like last time I find his new talk fascinating, but it leaves me in two minds.

The science is very impressive and his delivery is understated so that when he says things like "replacing the entire petrochemical industry" or "producing fuel from sequestered CO₂ within 18 months" it makes it seem more so. On the other hand, does he actually answer the question at the end about using the technology he's creating to produce bioweapons? He gives reasons why it is currently unlikely, but is it actually impossible? That's probably unreasonable of me - you can use all sorts of technologies to make weapons that are also used to produce entirely innocuous and useful products.

And the product he's talking about here is to divert CO₂ waste-streams from manufacturing and make fuel directly from them using synthetically constructed microorganisms. Though this doesn't actually remove CO₂ from the atmosphere, you remove the emission - perhaps permanently if when you burn this new fuel you recycle that CO₂ as well. Climate change undeniably needs radical solutions and this certainly is one.

I'm trying to look past the presentation to the heart of his talk and find out what he's actually saying and what I think about it, meanwhile see for yourself below.

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).

Pipe dreams?

I noticed in my Nature alert today a short letter from James Lovelock and Chris Rapley about a potential mechanism for secreting atmospheric CO₂ in the seas. The plan described is to have large pipes (and they mean large - 100-200 m in length and 10 m in diameter!) floating in the sea vertically, allowing mixing of seawater above and below the thermocline. Phytoplankton (algae) require three main things in order to grow, light, nutrients and CO₂. The thermocline is a divide between the sun warmed surface water, which has sufficient light and CO₂ for growth, but few nutrients, and the cool, deeper water which is obviously too dark, but full of nutrients that have fallen out of the surface layers. There are natural places where the two waters mix called upwellings - here you get blooms of phytoplankton which use up CO₂ as they photosynthesise. The pipes would simulate these upwellings and stimulate the uptake of CO₂ by the phytoplankton. Phytoplankton also produce dimethyl sulphide (DMS - the characteristic "smell of the sea") which can stimulate the formation of clouds - cooling the planet by preventing the suns rays reaching the surface. The story has also been picked up by the BBC here (and the New Scientist and umpteen other places - Nature is quite good at getting its stories published elsewhere before they have themselves! My girlfriend used to tell me all the latest research news from the fee paper Metro before I'd even received the original articles) and has some nice diagrams of the pipes in action.

Atmocean, a US company have been developing such a system themselves and have a suitably dramatic video on youtube (note the use of Clubbed to Death by Rob D, as heard on the soundtrack of The Matrix - it signifies 'bad stuff happening').



It is great that someone is proposing some direct action with some science behind it. The idea is an interesting one, but probably won't work. Bold statement huh? I'll try and justify it.

There are fairly large practical difficulties such as the fact that the Atmocean CEO Phil Kithil in an interview as part of the BBC article says that "134 million pipes could potentially sequester about one-third of the carbon dioxide produced by human activities each year" - it's not clear whether this refers to current levels or not as by the time pipes were in place you'd need a lot more as we'll have chucked a whole lot more into the atmosphere, but anyway, installing that many pipes would be quite a task.

Creating phytoplankton blooms doesn't only increase the level of DMS in the atmosphere above the bloom, it also increases the levels of other gases, including methyl bromide and isoprene (see this paper) . Methyl bromide is a major source of bromide to the upper atmosphere and bromide is better at destroying ozone than the chlorine from CFCs, so this would have the potential to enhance ozone layer destruction. Isoprene has a complex, and not completely understood role in atmospheric chemistry - increasing the levels of these compounds in the atmosphere is likely to have an effect, which may be beneficial or otherwise, but as the roles of these compounds in the atmosphere are less well understood than DMS is stimulating their production wise?

There is also likely to be a massive impact on the biology of the sea; organisms have complex and subtle interrelationships that we are barely starting to understand, particularly at the microbiological level - how this will effect the climate is also unknown.

Charles Rapley points out in the BBC article that his and Lovelock's letter is designed to stimulate discussion about direct action, which I hope it will - international agreements like Kyoto being mired in political torpor, but there is a danger that such dramatic suggestions, that to non-scientists could sound like science fiction madness, only add weight to climate change apathy. It is the style of the solutions that captures the imagination rather than the problem itself (think giant solar reflectors in space and dumping iron filings in the sea).

However, if anyone can truly stimulate action it is Lovelock - his invention of the electron capture detector a sensitive device for measuring tiny amounts of chemicals in the atmosphere, prompted Rachel Carson's novel The Silent Spring, ultimately leading to the genesis of the entire green movement. For further reading James Lovelock's website is here.