The link certainly reflects my own undergraduate experience, where these skills were not the focus of teaching.
It sounds like the sort of thing covered in "Software Carpentry" workshops -- practical skills around unix, git, and a scripting language. These are generally aimed at graduate-level students who now suddenly need these skills. The name "carpentry" is very deliberate. These aren't fancy skills that can only be be taught at a university, but it also seems to mean they aren't taught at university.
For when you really need a less purely functional language,
when you want your data to mutate, and your code not to.
When the possibility any function might be a macro is too frightening, but the possibility any function might mangle its inputs is fine.
If I can pick out a somewhat abstract question: Can we believe that something exists without knowing its cause?
Yes. We believe in electromagnetism, for example. We've characterized it, it has reliable properties, we therefore believe it exists.
The recent Institute of Medicine report giving diagnostic algorithm for CFS/ME (and proposing changing the name to SEID) is similar. There is a cluster of symptoms that occur together, we can give it a name, characterize it more accurately, and search for treatments.
Hopefully we will find a cause, it is very good fortune that many diseases have simple causes but it isn't a given. It looks like a lot of genetic diseases don't have simple causes, for example (hence GWAS has been disappointing).
This seems to be the wrangling Bruce Sterling is recently talking about[1]. John Carmack is brilliant, but a lot of what he's doing here is using his reputation and technical skill to get people and companies all pulling in the same direction. This isn't something a start-up in a garage could do.
It sounds like the sort of thing covered in "Software Carpentry" workshops -- practical skills around unix, git, and a scripting language. These are generally aimed at graduate-level students who now suddenly need these skills. The name "carpentry" is very deliberate. These aren't fancy skills that can only be be taught at a university, but it also seems to mean they aren't taught at university.