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).

Secrets of Shipwrecks

My last summer student of the season just finished. For the past eight weeks I've been supervising James Wong and Steve Hooton as they attempted to wrestle with projects entitled "Bacterial Treasure! Secrets of Shipwrecks"...an excellent example of naff titling. They were both looking at different aspects of bacterial diversity in some quite tricky samples - lumps of wood rescued from the wreck of the James Eagen Layne, a Liberty Ship torpedoed on 21st March 1945 on her maiden voyage and currently sat 24 m down in Whitsand Bay. She was carrying US army military cargo, which included tanks parts and pick axes, and a deck cargo of motorboats and timber; it is samples of the timber that we managed to get our hands on.

My dad is an advanced diving instructor and he and some of the other instructors at Fort Bovisand were kind enough to dive down to the JEL and extract some samples of timber. Not as easy a process as it sounds when I demanded as little handling as possible of the samples by the divers to maintain the natural bacterial population of the samples. They added tags to the zip-lok bags that I provided them with and also a method of cleaning the knife used so that, although it wasn't sterile, it wasn't contaminating the samples with grease used to protect the blades of divers' knives - as you can see below:



And this is a piece of wood that was actually sampled (the end was trimmed off one of those loose spars):



And just to prove that there's big stuff down there for those who like their organisms larger: gratuitous dogfish, spider crab and sea-snail shots (all photos taken by my dad!):







Another tricky part of the exercise was actually getting the samples from Plymouth to Liverpool as they needed to be stored in dry ice - with a little help from some friends at the Diving Disease Research Centre and Plymouth Marine Laboratory we were able to purloin some dry ice and get the samples couriered up. Then the fun began!

James was sponsored by the Society for General Microbiology and concentrated on attempting metaproteomics on the samples, looking for cellulases and chitinases. He used protein gels to look at some strains of bacteria that had been isolated from the same area. Steve concentrated on extracting DNA from the wood samples and using DGGE (denaturing gradient gel electrophoresis) to characterise the populations of bacteria in the different samples and was sponsored by the Nuffield Foundation. Both projects were a tall order and both students rose to the challenge. Our major problem was the nature of the samples themselves, the wood wasn't very degraded and there was evidence that it had been treated in some way (a strong smell of bitumen when some of the samples were freeze-dried was a give-away!). There wasn't likely to be much DNA or protein present in the samples, and the presence of co-extracting compounds was likely to foil down-stream analyses. In the end, after many attempts of different methods and James' and Steve's tenacity, it became clear that we weren't going to be able to extract any DNA or protein from the samples. A bit of a shame, but not really the ultimate aim of the projects.

These summer studentships are a great opportunity for undergraduates between their second and final years, to get experience of a working lab and of carrying out a defined piece of research, with all the frustrations that go with that intact. I was lucky enough to do one myself as an undergrad, at the Marine Biological Association with Willie Wilson and it really gives you a taste for research. Plus as the students are new to the subject and the methods and full of enthusiasm, it's good to view things through their eyes when it's easy to become jaded.

We never managed to find any bacterial treasure (or even a scrap of DNA or protein) but hopefully they both enjoyed themselves and they'll certainly get a head-start in their final year research projects. Both my students from last year are now doing PhDs or applying for them and knowing that a summer project may have helped them decide to go ahead with that (or at least not put them off it) is a really satisfying feeling. Hopefully James and Steve enjoyed themselves too!