Wow, this is an interesting article and I agree with much of it. I've had my PhD for about 2 years now (neurobiology) and I agree that academia is eating..itself. The inefficiency, politics, hostility are some of the things, but much like any other governmental thing, it's just run poorly...and that trickles down to the PIs, students, departments etc.
[edit] this got really long, I'm going to create a blog post on this instead and host it at another time [/edit]
Here is an example:I applied to a training grant (t32) that will pay my salary and help me through my PhD. It was not funded initially because my PI's funding was running out in a year. I was applying for funds to continue my education so my PI wouldn't have to pay me (so we could use that money for my research), but they wouldn't fund me because my PI was running out of funds...to fund me.
I resubmitted the exact same grant, with zero changes, but I included a letter staying that I'd be covered if my PI ran out of money. Then I got funded. Total time? 1 Year! It took a year for a paragraph to propagate through the granting agency, as I had to resubmit the grant again and wait 6 months to get a vague answer (priority score).
This is one of many examples I have that are consistent with the OPs article, the system is broken.
And this is a wide spread problem that is going to require all of science to really make a change happen. I'm intending on doing so with my startup (just applied to YC) to bring transparency, efficiency, and opportunity to scientists. My goal is to bring the semantic web to academic science to start linking data sets between fields. Positive, negative and pilot data all available in one spot so I can run meta analysis on these data and create preliminary data for a grant or future studies. (there is more to it, but this isn't the place to plug my site)
What I'm most concerned about isn't the technology, it's the people using the technology. I recently got this comment, "Wow, that is a brilliant idea....but good luck getting scientists to use it." The dinosaurs are scared of change, and their fear(ignorance?) is by far the hardest thing I'm going up against. It's also one of the biggest problems we are going to have in science.
Still gotta try though:)