This commentary I missed previously on the "research parasites" fiasco

Disproving a claim using the same data is what reproducibility is all about, and this is one of the most important reasons that data needs to be shared. After all, if someone has distorted their data in order to reach a conclusion that isn't really justified, we need someone else–someone not invested in proving the same result–to re-analyze the data using independent methods. This is how science corrects itself.

This post on open educational resources (OER)

Anderson goes on to critique OER:

“A big issue for the open source movement has been its sustainability. And that’s one of the reasons you’re seeing a lot of legislation about it because they are looking basically to the taxpayer,” he said.

I hope to hear more of this criticism of OER from publishers and AAP in the future. Why? The US PIRG’s recent report Covering the Cost estimates that each year approximately $3B – that’s $3,000,000,000US – of financial aid dollars are spent by undergraduates on textbooks and other proprietary educational materials. In other words, under the existing commercial textbook model students are simply valves through which taxpayer dollars flow to publishers. I would love the opportunity to get this number in front of more people.

This HowTo on Python string formatting

Python has had awesome string formatters for many years but the documentation on them is far too theoretic and technical. With this site we try to show you the most common use-cases covered by the old and new style string formatting API with practical examples.

This post suggesting we fund science by lottery

I’m very confident in a peer review to detect the difference between psuedo-science and real science, or complete hype and realistic improvement. But I’m much less confident in the ability of peer review to accurately distinguish “important” from “not important” research. So I think we should consider seriously the lottery for these grants.

Each year all eligible scientists who meet some minimum entry requirements submit proposals for what they’d like to do scientifically. Each year those proposals are reviewed to make sure they meet the very minimum bar (are they scientific? do they have relevant training at all?). Among all the (very large) class of people who pass that bar we hold a lottery. We take the number of research dollars and divide it up to give the maximum number of these grants possible. These grants might be pretty small - just enough to fund the person’s salary and maybe one or two students/postdocs. To make this works for labs that required equipment there would have to be cooperative arrangements between multiple independent indviduals to fund/sustain equipment they needed. Renewal of these grants would happen as long as you were posting your code/data online, you were meeting peer review requirements, and responding to inquires about your work.

These posts on Sci-Hub and open access to research

  • This post claiming that Sci-Hub has brought much-needed attention to an important issue, but that it is not a long-term solution.
  • This response to the original post, from the Sci-Hub founder, which comes across as pretty reactionary and defensive.
  • This post which doesn't (ostensibly) take any sides on the debate, but describes Sci-Hub as necessary civil disobedience and (in my opinion) highlights the good from both previous arguments.

These threads on compiling GCC with OpenMP support on OS X.

I was having trouble installing CD-HIT this week with Homebrew. These two StackOverflow threads (here and here) led me to the solution.

brew reinstall gcc --without-multilib
brew install --build-from-source cd-hit