Sunday, July 23, 2006

Opening up the scientific process

During my stay at the EMBL, for the past couple of years, it already happened more than once that people I know have been scooped. This simple means that all the hard work that they have been doing was already done by someone else that manage to publish it a bit sooner and therefore limited severely the usefulness of their discoveries. Very few journals are interested in publishing research that merely confirms other published results.

From talking to other people, I have come to accept that scooping is a part of science. There is no other possible conclusion from this but to accept that the scientific process is very flawed. We should not be wasting resources literally racing with each other to be the first person to discover something. When you try to explain to non-scientist, that it is very common to have 3 or 4 labs doing exactly the same thing they usually have a hard time integrating this with their perception of science as the pursue of knowledge trough collaboration.
I am probably na├»ve given that I am only doing this for a couple of years but I don’t pretend to say that we do not need competition in science. We need to keep each other in check exactly because lack of competition leads to waste of resources. I would argue however that right now the scientific process is creating competition at wrong levels decreasing the potential productivity.

So how do we work and what do we aim to produce? We are in the business of producing manuscripts accepted in peer reviewed journals. To have competition there most be a scarce element. In our case the limited element is the attention of fellow scientist. Given that scientist’s attention is scarce we all compete for the limited number of time that researchers have to read papers every week. So the good news is that the system tends to give credit to high quality manuscripts. This means that research projects and ongoing results should be absolutely confidential and everything should be focused in getting that Science or Nature paper.
I found a beautiful drawing of an iceberg (used here with permission from the author, David Fierstein) that I think illustrates the problem we have today by focusing the competition on the manuscripts. Only a small fraction of the research process is in view.


Wouldn’t it be great if we could find a way to make most of the scientific process public but at the same time guaranty some level of competition? What I think we could do would be to define steps in the process that we could say are independent, which can work as modules. Here I mean module in the sense of a black box with inputs and outputs that we wire together without caring too much on how the internals of the boxes work. I am thinking these days about these modules and here is a first draft of what this could look like:


The data streams would be, as the name suggests, a public view of the data being produced by a group or individual researcher. Blogs are a simple way this could be achieved today (see for example this blog). The manuscripts could be built in wikis by selection of relevant data bits from the streams that fit together to answer an interesting question. This is where I propose that the competition would come in. Only those relevant bits of data that better answer the question would be used. The authors of the manuscript would be all those that contributed data bits or in some other way contributed for the manuscript creation. In this way all the data would be public and still a healthy level of competition would be maintained.
The rest of the process could go on in public view. Versions of the manuscript deemed stable could be deposited in a pre-print server and comments and peer review would commence. Latter there could still be another step of competition to get the paper formally accepted in a journal.

One advantage of this is that it is not a revolution of the scientific process. People could still work in their normal research environment closed within their research groups. This is just a model of how we could extend the system to make it mostly open and public. The technologies are all here: structured blogging for the data streams, wikis for the manuscripts and online communities to drive the research agendas.

I think it is important to view the scientific process as a group of modules also because it allows us latter to think of different ways to wire the modules together. Increasing the modularity should permit us to innovate. For example we can latter think of ways that the data streams are brought together to answer questions, etc.