Excuse me Sir? May I see your papers?

It is approaching that time again. My life is characterised by two years of calm followed by a year of building tension thinking "what the hell am I going to do next?". My contract at Liverpool finishes in March and I'm starting to look for jobs.

My first plan was to apply for NERC and Royal Society fellowships. The advantage of these schemes is that they allow you the autonomy to research what you want (in line with original proposal, otherwise the funding bodies might get grumpy) and once you have fellowship status you can apply for grants as principle investigator. Also, universities are strongly encouraged to make research fellows permanent members of staff after the end of the funding, though this is by no means guaranteed. The downside is that they are very competitive, the NERC fellowship covering all the natural environment disciplines, from counting birds and geology to molecular biology and the RS fellowship open to all scientific disciplines. Applications therefore have to be exquisitely constructed things of intricate and arse-covering beauty.

I had an idea for a proposal, I think it was a good one, and I had people who wanted to collaborate and also thought that it would work or at least be interesting. However, I then sat and thought about my publication record.

As a postdoc, papers are everything. They are the only currency that employers and funders understand, they define your career and symbolise your scientific ability. Whether this should be the case, or they are a fair representation is moot. You have to have publications to prove that you are worth employing and that is that. Speaking to an academic who had been on one of the NERC fellowship review panels he reckoned that he'd hope to see three, first-author papers published in a good quality microbial ecology journal for a NERC fellowship applicant in microbial ecology. 'Good quality journal' gets us into the realm of impact factors. Journals are basically judged by the number of times that the papers in them are cited in other papers. It's like climbing up Google's hit list, but harder and with less reward.

The other critical point is 'first-author paper'. There are two positions you want to be in the list of authors on a biology paper (I'm not sure that this necessarily holds for other disciplines), first, or last. First broadly means that you wrote it and contributed significantly to the scientific content. Last means that you concocted the proposal, got the funding, supervised the work and probably edited the paper. Those positions in between have a sort of sliding scale of worth with slap-bang in the middle being the bottom of the pecking order. Experiments are never as straight-forward as 'Bob did the work and Alice' got it funded so there can be jockeying for position and everything gets political, particularly if more than one group was involved in the research.

Which brings me to my own publication record. Brace yourselves, this is not pretty; it is a Frankensteinian creation of little consistency. I start at the very beginning (I'm told it's a very good place to start):

1. Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel.
Wilson, W. H., Tarran, G. A., Schroeder, D., Cox, M., Oke, J., and Malin, G.
Journal of the Marine Biological Association of the UK, 2002.
PDF

2. Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments.
McDonald, I. R., Kampfer, P., Topp, E., Warner, K. L., Cox, M. J., Connell Hancock, T. L., Miller, L. G., Larkin, M. J., Ducrocq, V., Coulter, C., Harper, D. B., Murrell, J. C., and Oremland, R. S.
International Journal of Systematic and Evolutionary Microbiology 55; pp 1827-1832; 2005. Abstract.

3. Use of DNA-stable isotope probing and functional gene probes to investigate the diversity of methyl chloride-utilizing bacteria in soil.
Borodina, E., Cox, M. J., McDonald, I. R. & Murrell, J. C.
Environmental Microbiology vol 7; pp 1318-1328; 2005
Abstract.

4. Stable-isotope probing implicates Methylophaga spp. and novel Gammaproteobacteria in marine methanol and methylamine metabolism.
Neufeld, J. D., Schafer, H., Cox, M. J., Boden, R., McDonald, I. R., and Murrell, J. C.
The ISME Journal vol 1; pp 480-491; 2007
Abstract.

5. A multi-loci characterization scheme for Shiga-1 toxin encoding bacteriophages.
Smith, D. L., Wareing, B. M., Fogg, P. C. M., Riley, L. M., Spencer, M., Cox, M. J., Saunders, J. R., McCarthy, A. J., and Allison, H. E.
Applied and Environmental Microbiology pp (accepted 08/10/2007)
Abstract.

Those are the ones that are out at the moment, there is one more that is currently going through the submission process that I won't jinx by listing and three more that are in various stages of writing that should, hopefully, all be published at some point.

Now, what's the first thing you notice about those four beauties? Firstly, where are the first and last authorships? In a couple of those papers I do an excellent job of squatting in the perfect centre, the nadir of the author list. I should have at least one first author paper from my PhD, and this is currently in production, but the delay in writing (purely my own fault) has meant that I have a gap between 2005 and 2007. Not good.

Secondly, what's the theme here? Is it immediately apparent that I am a focussed researcher with a consistent and driven career plan in molecular marine microbial ecology? Is it buggery. I start with marine algal viruses (the work I contributed to this paper was actually done as an undergraduate during a summer project in 1999), move on to a couple of soil bacteria, have a mooch about in stable-isotope probing (one soil, one marine, both with work from my PhD) and then leap gleefully into shiga-toxigenic phage (these are the ones that make E.coli 0157 nasty).

Looking at the positive, they are all in quite good journals. Delving into the innards of the Journal Citation Reports and coming out smelling of dust and politics, it is possible to discover that Environmental Microbiology is doing the best with an impact factor of 4.630, Applied and Environmental Microbiology is at 3.532, IJSEM is at 2.662 and Journal of the MBA UK brings up the rear with a factor of 0.778 (though please don't judge it harshly, it's a cute little journal from one of the oldest marine biology societies in the world - I say one of as I think it might be the oldest, but can't find the proof). The ISME Journal was only out this year and you need three years of article count data before an impact factor can be calculated.

So, considering the above and the fact that the deadline for fellowship submissions is 1^st November I decided to wait a year before submitting an application. With no first-author papers, no chance. Which leaves me taking remedial action to boost what publications I've got in order to be able to make convincing applications for a second postdoctoral position. First job, that knotty paper from my PhD thesis that has been dogging me (and I have been dogged about) for some time.

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).