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I can't speak for biomedicine, but speaking as an academic in CS the claim that "close to nothing of what makes science actually work is published as text on th

I can't speak for biomedicine, but speaking as an academic in CS the claim that "close to nothing of what makes science actually work is published as text on the web" looks like a huge hyperbole to me. It's true that the so-called "folk knowledge", knowledge that exists in the community but no one bothers to publish in the form of papers, is a real problem, but at least in my field, it's by no means the majority of knowledge. As someone from a peripheral university where you can't just drive a few miles and talk to the best in your field, I have successfully started in new subfields of study (getting to the level of writing research papers in top-tier venues) by reading the literature. While this essay provides a very interesting point of view, I suspect it's heavily colored by the authors' failure to monetize the technology (which is related to the fact that people doing most of the grunt research work, who would benefit the most for this, are PhD students and postdocs who have no money to pay for it - in the text, the author hints at this). I wouldn't take it as an accurate description of academia.

viewfromafar 5y ago
Also CS, my interpretation of "what makes science work" is a little different and I would argue that - despite a lot of foundations and techniques being shared in research papers - this field more than any other is constraining the free circulation and application of knowledge. The equivalent to those biomedical industry players are the big tech who develop closed source and push the edge in some area. They will publish but that does not mean you can replicate any of it. Software is also fragmented, crippled by IP lawsuits, patent trolls and so on. This does inhibit ability of society to benefit from software since it depends on the private sector to sort things out. The PhDs go and build businesses to "make the science work" in that sense. The ideal of detached pursuit of knowledge is not a complete fiction (despite the hyperbole), but it does remain an ideal that can only be approximated.
- Al-Khwarizmi 5y ago
  As an academic, all my papers from the last 5 or so years have associated github repos where all the code is accessible under free licenses. Most of my peers in academia do the same. Documentation quality is admittedly quite hit-and-miss, because we aren't paid for that and we need to jump to the next paper, but all the code is there and everything can be replicated even if it takes some effort due to rushed code or suboptimal documentation. Industry is a different world, and indeed there are plenty of opaque industry papers that aren't replicable at all because much of the model is essentially a trade secret, and the paper is more an avenue for bragging than for developing new knowledge together with the rest of the community. To be honest, I would just outright disallow that kind of papers. But that's not a popular opinion, and taking into account that big tech companies sponsor our conferences and provide grants, I can't blame those who think otherwise.

viewfromafar 5y ago

Also CS, my interpretation of "what makes science work" is a little different and I would argue that - despite a lot of foundations and techniques being shared in research papers - this field more than any other is constraining the free circulation and application of knowledge. The equivalent to those biomedical industry players are the big tech who develop closed source and push the edge in some area. They will publish but that does not mean you can replicate any of it. Software is also fragmented, crippled by IP lawsuits, patent trolls and so on. This does inhibit ability of society to benefit from software since it depends on the private sector to sort things out. The PhDs go and build businesses to "make the science work" in that sense. The ideal of detached pursuit of knowledge is not a complete fiction (despite the hyperbole), but it does remain an ideal that can only be approximated.

Al-Khwarizmi 5y ago
As an academic, all my papers from the last 5 or so years have associated github repos where all the code is accessible under free licenses. Most of my peers in academia do the same. Documentation quality is admittedly quite hit-and-miss, because we aren't paid for that and we need to jump to the next paper, but all the code is there and everything can be replicated even if it takes some effort due to rushed code or suboptimal documentation. Industry is a different world, and indeed there are plenty of opaque industry papers that aren't replicable at all because much of the model is essentially a trade secret, and the paper is more an avenue for bragging than for developing new knowledge together with the rest of the community. To be honest, I would just outright disallow that kind of papers. But that's not a popular opinion, and taking into account that big tech companies sponsor our conferences and provide grants, I can't blame those who think otherwise.