Read the graphs. We increased funding 50% in real (i.e. "constant FY 2012") dollars, in nominal dollars it increased marginally more (inflation wasn't that important). The bulk of the increase was in the NIH - look at the second graph which breaks it out by agency.
Defense R&D includes a lot of basic science, I have no idea where you get the idea it doesn't. For example, this paper of mine (http://arxiv.org/pdf/0708.0635.pdf) has support from the Air Force. A lot of work in computational electromagnetism and operations research (to name two fields I know moderately well) is funded by the military.
You mean from 1976(/1996) to present? Yeah, I got that. My original comment was about why that's a pointlessly superficial way of looking at the data.
"Defense R&D includes a lot of basic science....for example, this paper of mine..."
...was mostly funded by the NSF, if the footnote is to be believed. That's not defense money.
In any case, I never said that defense research doesn't involve any science, I just said that most of it goes to defense contractors. I hate to break it to you, but the government didn't double defense R&D after 9/11 in order to increase the number of papers being written on antenna theory. Most of that money went toward things like airport bomb-sniffers and futuristic weapons systems. I'm sure you can find some pure-science papers that were written with that money, but that wasn't the point of the funding.
From about 2000 to 2010 it went from $100B to $150B and dropped to $140B after the "bloodletting".
Your "more nuanced interpretation" that "training of new scientists starting (~1996), and when they needed funding to really get their labs started (~2000), we stranded them" is simply wrong.
Yes, that's why I said "in real terms". The situation is worse in inflated dollars -- even if we'd held the budgets steady in real dollars, we'd be losing to inflation.
"Funding rose about 50% in the early 2000's and leveled off after that."
Non-defense R&D climbed from 1996-2003, then declined. Defense R&D increased from 2001-2003 (thanks mainly to 9/11), held steady for most of the decade, and began to decline in 2010. Defense R&D is not spending on "science" by any conventional definition (most of that money goes to the defense industry), but it does employ some scientists, so we count it.
"I'm not sure what political point you think I'm trying to make."
You were arguing that the data doesn't support the thesis of the story, and implied that those who supported the thesis were making "political points" (at the time of your comment, almost all of the other comments were in support of the thesis).