Faster, smaller, and organic

Update Aug 20 2012. Last week, George Church and colleagues have encoded books and images in DNA. Another use of biological material as engineering device. And one that transforms the sequencers described below in organic Kindle!

Less than two weeks ago, at the annual Advances in Genome Biology and Technology  meeting, a small company, Oxford nanopore , presented his new sequencing technology  based on … nanopores. I found that piece of news very exciting, despite working in an environment where I am force-fed next generation sequencing daily (see for instance the 1000 genomes project).

I am first excited about the new technology, because it is based on proteins. An enzyme processes the nucleic acid that is then passed to a proteic pore. The modification of electrical behaviour of the pore identifies the nucleotide. More about nanopore sequencing on Wikipedia. Biological engineering is progressively coming out of the labs where it’s been cooking for the last two decades, but we only start to imagine the effects it will have on the human society. I am a great fan of science-fiction, and science-fiction novelists played a lot with bioengineering. However, I believe they were far too conservative and the reality of the near future will make all imaginary stories pale in comparison. A USB stick size sequencing machine, built using the building blocks of life, able to sequence DNA super-quickly? Really? What next? What can now possibly be the limit? None. Synthetic biology and bioengineering will have in the first half of the XXIst century the effect that electrical engineering had on the XXth (I say first half of the XXIst century, because while I think the singularity of Ray Kurzweil is a lot of tosh, I agree with him than any tentative of prediction past then is just a waste of time). Not only are we synthesising life and producing in vitro tissues, but we will re-use bits and pieces of life for everything. Evolution and selection allow to optimise systems faster and better than engineering design, and as shown by nature around us, there is virtually no limit to what we can do with materials derived from living forms.

But the success of bioengineering is not the only aspect of the story that made my spine shivered. The size of the portable device, the MinION, is also a revolution. True, NGS allowed genome sequencing to get out of large sequencing facilities, to be installed in many research labs, in hospitals etc. But now, we are talking about bringing sequencing to everyone, everywhere, everytime.  Sequence identification and analysis will still require specific software and databases. But with the arrival of 4G, a MnION plus a smarphone will be sufficient to identify a sequence. What applications can we imagine?

  •  Metagenomics, and biodiversity studies: Investigators will be able to analyse the sequences in situ, without the need to bring back samples.
  • Epidemiology: Epidemics will be tracked on real time, allowing a greater reactivity and flexibility in the responses.
  • Immediate identification of persons: Bye bye fingerprints and iris patterns. GATTACA  is here, now.
  • [Place your favourite application here]

What does that means about genome sequence confidentiality etc? Gone down the drain. The same way we have cards identifying our blood type, we will have our genome on our ID card (or NHS card). And of course the insurance companies will have access to that. They have access to your gender as well. There is no point in keeping those aspects of you secret. In our time of social networking, our genome could even be part of our future Facebook profile. We just have to design new legal protections. Instead of saying “nobody can be discriminated based on its gender or skin color”, we should just have a generic “nobody can be discriminated based on its genome”.  There is no way we can stop that. And the earlier we get rid of this holiness of the genome, the less worried we will be.

Scientific research and feudalism

Recently I felt betrayed by someone I believed protected me and to whom I had always been loyal. I have always consider the scientific research as a sort of feudalism. Instead of providing our swords in exchange for land and protection, we provide our scientific research in exchange of support, moral or financial. The entire system relies on the respect of the given word. A supervisor trains and supports a student or post-doc. In exchange, the latter provides brain power and research activity to the supervisor. This relation continues after the departure of the vassal. The supervisor will provide letters of reference and include the young researcher in hi/her scientific network. In exchange, the young research becomes part of the mentor’s “school”. The same relationship holds for a PI and the head of a department or institute, and so on towards the top.

This organisation is parallel to the official structure of research, and its existence would probably be denied in official circles (because of its possible deviances), but I feel that it must be present for the system to work satisfactorily. Its absence would be akin to the absence of friendships between PhD students or post-doc in the same lab. After decade, some of my co-worker friendships still hold, and the same is true of my feudal relationships with past mentors. When someone breaks his/her word, not only I feel sad and betrayed, but I believe the entire system is weakened and becomes inefficient. To perform scientific research requires a thirst for knowledge. But except highly theoretical work pursued lonely in a secluded office, it also requires emulation by the peers, the desire to look good to your boss, and the need to provide for your staff.

But maybe it is just me. What do-you think? Are-we all lords and vassals?

The right to know

In the comments we often see about author-pays vs reader-pays, one parameter is regularly absent: The ability to access science. As demonstrated by the MMR scare or the climate-gate in the UK, the general population sometimes needs to get access to primary scientific literature. And it cannot. With the generalisation of the 23andMe and similar companies, biological research invaded the life of any citizen. When one obtains one’s SNP analysis and is told that one has an accrued risk of x % of getting a disease, the first reflex is to “google” the disease and search for scientific information (at least this is what I’d do,and what I do each time I, or someone close to me, faces a health issue). At best one can get the abstracts of papers. That generally only reports a biased view of the story (or even the opposite of the paper. I have examples of that, including one where the authors changed a conclusion following peer-review but forgot to change the abstract. For years the paper was quoted for the wrong conclusion in the abstract. That says a lot about citations in life sciences by the way …). And finally, this week I reviewed job applications, and was not able to access many of the applicant papers.This certainly did not help the applicants.

But most importantly, the citizen already paid for this research. They should not pay again to access the results. That publishers want to sale nice journals with added values like layout, news and views etc. is all fine. But trying to forbid the deposition of the manuscript, the raw product of the researchers’ activity, in an open repository – like they do with the  Research Work Act – is criminal. It is purely a robbery of the citizen. Note that Nature Publishing Group is very different from let’s say the AAAS and Elsevier in that respect. Authors retain their copyright and can do whatever they want with their own production. Of course all that is not true Open Access Publication.

Update on February 28 Elsevier withdrawn their support to the RWA. However, in the withdrawal statement, they re-state clearly that they will continue the fight and still support the idea behind the act, i.e. the interdiction of mandatory deposition of manuscripts in open repositories.