You're missing the point. The target demographic for this article is someone who is not a computer scientist. He's someone who doesn't have time to deal with thread libraries and low-level matrix operations. He just needs to crunch his data quickly so that he can publish his valuable research. This person reads the same blog articles that computer scientists do, and comes to the conclusion that "I should learn C++ for my number crunching". That's simply not the case; you can use C++ to get good performance, but the amount of knowledge you need to acquire to do so is an entire field. You aren't going to be the world's best human genome researcher and C++ programmer; the time spent learning C++ could have been used to do research.

The idea is: if you use a tool that lets you describe your problem at a high level and let the computer worry about how to do the calculation efficiently, you'll beat your hand-rolled C++ every time. And, there is now the possibility of hiring a "Real Programmer" to hack your math library (Octave, Mathematica, Python + numpy, whatever), allowing you to delegate work. If every calculation was a brand new C++ program, you'd only be able to improve your application's performance by hacking on your application. Separating the problem description and the solution description allows the solution-finding code to be optimized without knowledge of the specific problem.

I think this approach scales to the work that practicing programmers, too. We don't see it a lot because writing tools is time consuming and we all have deadlines; so we pic k the "worse is better" solution and hard-code our applications in what amounts to glorified machine code.

Just because a practice is common doesn't mean it's a good idea.