Bad economics is the driver of most of these problems. When incentives are set up so that if you fudge results, you're more likely to get funded, then fudging results is going to happen. A lot. Hence the "reproducibility" problem. Twice in a row I've had grants that got pretty good scores on round one only to be killed on round two (after, you know, "fixing" the grant they way they suggest). In my latest run in with the NIH, our scores from two of three reviewers got markedly better on round two, and the third guy gave us all 7s, after more like 4s and 5s on round 1. No explanation necessary. No recourse. That's just NIH for you. Peer review is a scam. I were to get a stab at fixing NIH's funding problem, it would be to do what they did in Nigeria with their entrepreneurship grants. Namely, take the top 50% and put them in a lottery. No more study sections. No more grants only going to people who already have grants. No more fretting about getting another grant the minute you get the first one funded. Just luck of the draw if you meet the basic requirements. Easy.
Being obliged to compete where it would be more fruitful to collaborate is a problem in technology as well. It's easier to make the case with scientists, because while competition is completely counterproductive for technologists it is some small protection from the corporations they work for, but I think the conventional wisdom of competition driving progress is only true of manufacturing and competition is only a motivator for people you don't want working on anything important.
Holy crap I love this article. Long form, in depth, about important topics, talking to key players, and distilling the learnings into comprehensible and actionable items. This is some seriously fine journalism. It seems that economics is the core problem to be addressed in science today. Figure out how to generalize the money pool, remove the perverse incentives, and give scientists the time to do science, rather than apply for grants. I could solve this problem in 10 minutes flat, if I had 4 billion dollars. Sheesh. Now I have to go invent something Google will buy...