DrugMonkey asks "Is the NIH trying to get rid of smaller laboratories?" Before I get to my take on the answer, what I'll be talking about is based on private conversations, so I won't be attributing some things to specific people (sorry Ed!). Take this for what it's worth...
I don't think NIH is specifically trying to tank smaller labs. Instead, NIH seems to be reacting to frustration, both within and outside NIH, about the pace (or lack thereof) of translational research. Without viewing the funding situation for independent PI-driven labs in the context of larger NIH-wide moves towards 'big science', we get into arguments about trying to purge the excess labs and so on. Simply put, I don't think NIH cares very much about that, one way or the other.
Let's break this down some more.
First, there is legitimate frustration: we've spent a lot of money and haven't made that much progress in some key areas. We can talk about the importance of basic research--and it is absolutely critical--but, at some point, there's the expectation that NIH research should be more productive and lead to treatments. That's why we saw a couple of prominent mainstream science reporters bash basic research last year (note: I criticized them for this).
But, having spent some time in public health, the incremental approach can be frustrating, especially when confronted with big problems:
So onto an antibiotic resistance example. A while ago, I wrote about some excellent work by ScienceBlogling Tara Smith, and that was written up in The NY Times by Nicholas Kristof. Basically, Tara established that a clone of MRSA, ST398, which spread throughout Europe's farming system, and is now entering Dutch hospitals, and has established itself as a commensal in the human population, is found at really high levels in two Iowa farm systems (covering ~20 facilities). Now, under our current system, the next step would be that Tara applies for a grant--and Tara's very smart so she would probably get it--to look at more farming systems over a longer period of time (An aside: Having been a weird hybrid of federally funded researcher/policy wonk, I have some experience in what typically gets funded in this field). This is about what an R01-like grant with several years of funding could accomplish. And if Tara does go down this route, I wish her best of luck--she certainly has earned it.
But that's not ideally how the question should be addressed (and I've actually testified in front of federal committees about this--I'm not just ranting). To address the question of the introgression of resistance genes and resistant organisms from the farm to the clinic, you would need to do work on a scale that simply can not be funded by the R01 mechanism. You would need to collect tens of thousands (if not more) of isolates from farms, abattoirs, retail meat, fecal lagoons, farm workers, human commensal isolates (both in farming communities and distant from pig farms), pigs, and clinical isolates. These isolates would need to be systematically stored, screened for resistance, and genotyped (including sequencing, plasmid profiling, virulence factor typing (PCR and hybridization). There should also be a genomic component for a subset of the strains, both gene array and genomic sequencing. Then, of course, you need the informatics to store all of these data. And this is a multi-year project, and probably should be expanded to a couple of other critical organisms.
There is, of course, a potential problem:
This is expensive. Really expensive. That means if this fails, it's very risky.
Add to this a growing belief at NIH that many independent PIs are not really concerned with the health objectives of the institutes, and are parochially concerned with only their specific sub-sub-fields:
But the primary goal should be moving the science forward, not providing tenure milestones for universities.
So I think we're going to see an emphasis on 'big science.' In other words, identify an important question and get all Manhattan Project on its ass (and do this multiple times).
We can argue over whether this is a good idea (I'm sure it will happen in the comments and I'll probably have to revisit previous posts about this), but it's coming whether we like it or not.
it's coming whether we like it or not
For those of us who deal with NASA, it's already here. Astrophysics has recently completed a decadal survey, and the Heliophysics people are currently working on one. Resources are limited and space flight hardware is expensive. So certain questions get high priority at the expense of others. There is still a place for small departments, but they have to find a niche that's aligned with funding priorities. Even NSF has some programs along these lines.
I don't know whether NIH is as explicitly programmatic as NASA is, but they are throwing big piles of money around and need to make sure they are getting something for it. It will probably be better if the community gets behind something like a decadal survey before the head of NIH does.
At Dept of the Army, this is exactly the model being used for antimicrobial resistance in the health care system. It is funded under 'performance improvement' and not research at all. We have the 'program' collaborate with researchers when there is a need for new technologies, strategies, or analytical techniques. As infection control, it can be put on the 5 year government ppbe (programming, planning, budgeting, evaluation) cycle, with a multi-million per year budget. It can also publish a little technical bulletin (grey literature, in a way) that is meant to inform but isn't research publication. There are other efforts in the military which cover other organisms and scopes in a similar vein.
Funding public health through R01 grants is not appropriate, really. Once a project shows that surveillance is useful, actually doing the surveillance is no longer research - 'big science' or 'small science' is no longer the question.
If you don't do the "basic science" projects, then somebody else will. And those that do are those that end up with the patent rights in the specific field. Patent rights you'll need to acquire to translate your results into actual medical practice. So you'll end up paying for the basic research one way or another no matter what.
This is not a bad thing, mind you; both the small-scale research and the big practical projects get done and everybody is better off for it. But it won't necessarily translate to faster or cheaper health care-related results.