Monday, December 28, 2015

Why aren't research grants centralized?

A recent question on Academia StackExchange asked something that looked simple to me at first, but turned out to be much deeper and more subtle that I had expected as I thought about it more.  The question is, in essence: "Why aren't research grants centralized?"  

In other words, why do countries generally have messy and complicated research funding systems like we do in the United States, where there are a bazillion different independent agencies and mechanisms for funding research, each with its own peculiar mechanisms and application rules? Wouldn't it make more sense to have some sort of unified science system where all of the science people can go and ask to get their science things funded?  

I enjoyed thinking about and exploring this question, and so I wish to share my answer with you here as well:

First, let us consider why there are many organizations that fund research, rather than a single research-funding organization. This is a matter of evolutionary organizational structure. In most countries, research has a non-trivial budget and applies to many different concerns of government. That means there has to be some (probably largely hierarchical) structure for organizing it. Now, let's consider two prototypical organizational structures for government-funded research. First, we might have a general research agency, which contains subdivisions addressing the research needs of various other governmental tasks: 

Alternatively, each government department might have its own research agency: 

Almost everywhere, we see organizations more like the second structure than the first---there might well be some countries in the world where research is so small or so controlled that is it organized in the first way, but if so, I am not aware of them. Why might that be?

Consider what happens if you are a leader in the department of agriculture, and you want to expand your agency's research work. Unless strong regulation prevents you from doing so, it's much easier to create or expand a research organization within the agriculture department than it is to get an independent research department to do it for you. A research sub-department within agriculture is also more likely to serve the peculiar needs, time scale, market structure, etc. as relates to agriculture. It's also easier and more rewarding to go to government leadership and fight to get resources for your own organization, where you can explain exactly how you plan to utilize them, than to fight to give them to somebody else.

Since both government structure and research needs evolve over time, we may thus expect research organizations to multiply, both across the government as a whole and also within individual sub-organizations. They are, in fact, occasionally reorganized and combined with the goal of making them simpler and more efficient to interact with, just as other government agencies are, but that will typically not reduce the number down to one, just to a smaller "many." Moreover, we've only discussed government funding, not industry funding or funding by foundations and NGOs, which all have their own separate needs and desires and further complicate the funding landscape.

Now, to the second aspect of the question: why is there no central database for applications? Sometimes there are, at least partially. For example, in the United States all government requests for proposals go through FedBizOpps. Most research solicitations can thus be found there (though not all, due to the diversity of mechanisms), along with requests for things like security guards for the US Embassy in Costa Rica. As you might guess, however, the sheer breadth means this often isn't a terribly efficient method of searching.

Likewise, every agency has different sorts of information it's looking for in research proposals. Again, taking the US as an example, the NSF really wants to know how its funds will support graduate student and postdoc education, since that's a key part of its mandate. AFRL, on the other hand, usually doesn't care much about supporting students, and has a mandate instead focusing on how its funds will affect current military concerns. As a result, a "universal" proposal would likely be quite cumbersome even if the bureaucracies were somehow reconciled.

Bottom line: "research" is too complex and pervasive a set of needs to readily stay contained within a single unified organization.

Sunday, December 06, 2015

A Publication Sea Change?

Now, in the closing of the year, is a time to start taking stock of my scientific progress over the last twelve months.  What in my professional life is going well, what things need care and focus, what things have changed on me a bit at a time without me noticing all of the accumulation?

As I've been looking back over my publications of the last year, I've noticed something that is unexpected: apparently, 2015 is the year my publications moved to journals.  During graduate school, I barely published in journals at all, being both a less mature writer and in the deepest depths of computer science workshop/conference culture.  By the time I graduated and came to BBN, my work was starting to mature and I began putting extended versions of my conference papers in journals, to a tune of about two journal papers per year, still only a fraction of my scholastic output.

This year is is different: this year I have twelve journal articles stamped with an official publication date of 2015 and three more that have appeared in "online early" editions.

In large part, this reflects the growth of the synthetic biology side of my research.  Synthetic biologists typically publish in journals rather than conferences, and so what might have been conference publications in computer science go to journals instead in synthetic biology.  I've been working seriously in synthetic biology for several years now, but my collaborations have been growing and maturing, and some of those articles reflect projects multiple years in the works that have had long and hard roads to publication.  There are also some that in practice were published online last year, but have only this year been officially assigned to a theoretical paper issue that no-one really reads that way any more.

Five of my publications, however, are from the aggregate programming / spatial computing side of my world, and that also reflects a major increase in activity.  Here, though, the time to publication is often a very much longer road indeed.  I have noticed that computer science journals are often much more comfortable with lengthy times in review and revision than biology journals are.  Once of my articles that's just come out, for example, was first submitted in February of 2014; another article was submitted in March of 2014 and should appear in mid-2016.  I think that this may be because of the conference culture in computer science: a journal can afford to be quite slow and dozy in review because the editors assume that everyone has already got access to the prior version of the paper, and the journal issue will simply be the extended remix.  I do not know if that's the case, but my experience has certainly showed a stark difference in the urgency that attends each culture's publications.

In fact, then, my surge of journal publications does not actually reflect a surge of writing in this year, but rather a more gradual increase over the last few years, first picking up on my computer science side, then rising on the biology side as well.  The slower computer science and faster biology waves then happen to coincide in 2015, creating this prominent spike in journal publications.

In fact, the rate at which I am writing publications does not appear to have changed all that much.  The actual numbers of publications that I am an author on that have been initiated in these last few years is:

  • 2012: 17 publications initiated
  • 2013: 17 publications initiated
  • 2014: 16 publications initiated
  • 2015: 20 publications initiated

The quality and intensity of those publications has risen, though, as has the degree of collaboration, which also no doubt leads to more publications per unit effort on my part.

So, what does this all mean?  In short: this means that I seem to be saying things that others are interested in scientifically, and working with more people to say more things more clearly, and overall I think that's good.

Saturday, December 05, 2015

SBOL Visual

We have just published what I believe is a very important paper, "SBOL Visual: A Graphical Language for Genetic Designs."  You can read it online for free, from PLOS Biology.  This is the culmination of a long and slow process (as most standards work tends to be) of looking at the different ways that people make diagrams explaining genetic designs and trying to boil it all down into a simple common language for communicating.

Diagram languages for communicating designs are practically universal, in any area of human endeavor where we need to talk about making complicated things.  Whether you're building electronic circuits or houses, writing software or maintaining a sewer system, sewing from patterns or folding origami, there are standard ways of drawing diagrams in order to communicate ideas and minimize confusion.  So of course we need them for engineering biological organisms as well, and thus, SBOL Visual.

The basic idea is quite simple, and can be captured in a simple image of genetic constructs organized along a DNA or RNA sequence "backbone":

The current set of icons covers a lot of the constructs that people engineer, though by no means all.  If you've got another thing to put on a diagram, you can use any icon you want, as long as it doesn't conflict with an existing SBOL Visual icon. To let SBOL Visual expand and become more universal, however, there's an open community process for adding more icons, with a number of icons slowly working their way through the process.
Current SBOL visual icons
Finally, although we provide "standard" icons, there is actually a great deal of flexibility in how you can style them, which makes it easy to use these icons in anything from scribbling on a whiteboard to computerized design software to figures in scientific publications.
All of these diagrams follow the SBOL visual standard.
In some ways, this is a very simple thing.  It is, however, extremely important to get these simple thing right, in order to reduce the amount of friction, frustration, and mistakes we make when we work together and communicate about the things we do.  SBOL Visual is an important step in getting that "less wrong" in the engineering of biology, and I'm glad that it's officially become published now as well.