This post over at Daily Kos is a real indicator of a problem, but not the way darkside uses it.
The problem is the second chart which shows the "Percentage of NIH R01 Applications Funded" dropping sharply in ~2003. The reason is not underfunding. NIH is actually fairly well funded. The reason is drift. Because the NIH's research funding budget increased dramatically in the 90's, they were, at first, able to fund more applicants. NSF funding was supposed to be increased as well, but that never happened.
Over the next ~10 years, science depts and universities came to realize that the promised funding would not arrive, and they began a real shift. They pushed hard to expand departments that could capitalize on the NIH funding, and in those areas where NIH funding was traditionally less important (chemistry, physics) there was a drive to shift emphasis in such a way as to qualify for the ample funding, and to hire people whose research goals were better aligned with the new funding reality.
The result was that applications for NIH money soared, and so the modest (inflation type) changes to their money subsequently were not enough to offset the increased number of applicants. So the percent funded started dropping.
The problem is not that the NIH is underfunded, it may be that, but the real problem is that the NSF is severely underfunded. It has caused a shift in fundamental science research in this country...away from things that would lead to advances in energy, for example, and towards health research. This is the real problem, and while simply increasing the NSF budget will fix this, the chart does tell us that the shift back will take ~10 years.
Non-health science research has been hurting in this country, and it won't get better in a hurry. Universities have been hiring health related researchers to take advantage of the existing funding dynamic.
Fuel cells, photovoltaics, battery technology--those very things that would have the best hope
at helping with energy problems--have had the short end of the stick, and the problem started in the 90's. It was exacerbated by the Bush administration, but they were not the cause. Blame it on Clinton (Bill) or the Republican congress that thought taking him out was more important than actually governing, but they caused the disparity that has resulted in the chart darkside shows...and the real problem in science funding.