The article makes a lot more sense if you think of "science" not as the idealized process, but the actual process as practiced by people at Pfizer, Merck, etc. Read the Hume reference not as a criticism of the scientific method, but rather as a reminder of something we already know (correlation != causation), but that we in practice assume all the time in order to apply science to certain problems.
He's saying not that the method is bad, but that things are getting complex enough, at least in medicine, where we're hitting some limits on how easily we can practice science to the necessary level of rigor and precision.
To nitpick, Pfizer, Merck et. al. don't actually do science. What they do is more akin to spraying buckshot into the bushes and hoping to hit a furry animal hiding somewhere inside.
Not that this is a particularly bad approach. It worked amazingly well for the last few decades and has churned out a lot of blockbuster drugs.
It is, however, starting to fall apart as all the low hanging fruit has been picked. It's time for the big pharma's to start doing science again. The problem is that big pharma is thoroughly infatuated with quarterly stock prices and not developing new drugs. They are cannibalizing themselves in an effort to keep stock prices up and profits growing.
It's better to think of big pharma as remarkably successful marketing engines, not medical science companies.
For instance, I know of many scientists that work for big pharma companies which do not have access to any of the scientific literature (past the freely available abstracts). Management will not allow them to purchase these articles.
Consider that for a moment. The companies producing your drugs are not even remotely up to speed on cutting edge biological knowledge.
*Obligatory "I'm in biology so I'm not making this stuff up" disclaimer.
Let me chime in as a biologist that thinks you've hit it right on the head. This is precisely the way to think about the large pharmaceutical companies: marketing companies. They've fired most of their scientists, instead buying positive research results from smaller companies, and market the hell out of the few compounds that have survived the clinical trial lottery.
More than that, the pharmas are absolutely resistant to embracing technology that can save them; they discard scientists that are driving their respective fields forward, and resist the notion that understanding the cell as an information system can provide better returns on their trials.
There are exceptions, when Genentech was run by Art Levinson (a scientist) he was capable of discerning science from bullshit and was an effective CEO. However, I would sell any stock in a pharmaceutical not run by a scientist; such a company may be able to post short-term returns but they're only doing that by selling off any possibility of future success.
"He's saying not that the method is bad, but that things are getting complex enough, at least in medicine, where we're hitting some limits on how easily we can practice science to the necessary level of rigor and precision."
But we are still doing fine and achieving the "necessary level of rigor and precision". The one main example of the article was the drug that was stopped in trials, which is exactly as the process was supposed to work, and yet then the author tries to paint this as a reason or example of the failure of science in general.
I don't see the author as claiming there is a "failure of science in general" (I didn't read the title of the article literally, however). I think a drug like that getting that far into development, despite targeting an extremely well understood biological pathway, is a decent example of the practice of science in at least some contexts hitting certain limits.
An accurate description of the pharma industry (been there, seen it):
Jeffreys, Diarmuid (August 11, 2005). Aspirin: The Remarkable Story of a Wonder Drug. Bloomsbury USA. p. 73. ISBN 1582346003.
But there is an idea in the article, which does seem to be true: most of our current problems are industrial-technology related (environment, energy etc. consumption, known as "externalities" in economic lies, which is basically abusing Earth -- and therefore ourselves -- in the current "economic" system) and just doing more of the same might not be the way out.
Another "critique": All watched over by machines loving grace and Henrietta Lax by Adam Curtis (BBC documentaries). Adam goes further, with TINA.
He's saying not that the method is bad, but that things are getting complex enough, at least in medicine, where we're hitting some limits on how easily we can practice science to the necessary level of rigor and precision.