A good initiative against the terrible journal publication system that is ruining science

I would say to read this article and weep, but beyond the tears that you should have in your eyes about the horrible state of scientific publication and the terrible incentives it creates for scientists to always hunt exaggerated, “sexy” results, you can take a little comfort in this group that the article mentions that is trying to fight back. Now, if only senior scientists went along!

How to become better at rational thinking

I recently stumbled upon this article: How to Train Yourself to Be a More Rational Thinker, by Mark Hutson. I immediately started drafting this blog post, but I discovered that Hutson’s piece has so much excellent advice that summarizing it here would become an act of copying. Rather than do this, I just recommend you follow the link and read it for yourself, gentle reader. There is just one bit that I will quote verbatim, to whet your appetite. It comes from one of the more provocative and interesting thinkers I have encountered, Daniel Dennett, and it is quoted here from the Hutson article:

Psychologist Anatol Rapoport diverted people from straw-man arguments for their own good. Daniel Dennett summarized Rapoport’s advice in his own book, Intuition Pumps and Other Tools for Thinking:

  1. You should attempt to re-express your target’s position so clearly, vividly, and fairly that your target says, “Thanks, I wish I’d thought of putting it that way.”
  2. You should list any points of agreement (especially if they are not matters of general or widespread agreement).
  3. You should mention anything you have learned from your target.
  4. Only then are you permitted to say so much as a word of rebuttal or criticism.

Not only will you conscript a more willing accomplice in your search for truth, but the exercise in itself will help you extract valuable material from the other side’s beliefs.

Big news on the Wolfram language

Wolfram Alpha has been freely accessible on the Web for some time now. It allows anyone to do some of the work that Mathematica can do, in a browser. Now, it looks like the new Wolfram language, a very ambitious project to open up programming to many more people, is also going to be freely available on the Wolfram “cloud”. Details in this post by Wolfram himself. When I get some time freed up, I want to play with this!

A dissection of the humanities-sciences distinction

Philosopher Massimo Pigliucci published a great essay on Aeon, entitled “Who knows what”. In this essay, Pigliucci argues that neither the humanities nor the sciences should “have the last word on culture”, to quote a part of the URL of the essay. (It is not often that I find that the URL of a web page has a better title than the page itself, but this one certainly does.) EO Wilson’s book Consilience comes in for a thorough critique, without disparagement. Lots of topics that fascinate me make an appearance and Pigliucci discusses them well: culture and its evolution, the problem of induction, Gödel’s incompleteness theorems—these are some prime examples. I recommend this essay to you wholeheartedly, curious reader. Here are the two concluding paragraphs, which resonated with me perhaps more than all the others:

Seen this way, the differences between philosophy, biology, physics, the social sciences and so on might not be the result of the arbitrary caprice of academic administrators and faculty; they might instead reflect a natural way in which human beings understand the world and their role in it. There might be better ways to organise our knowledge in some absolute sense, but perhaps what we have come up with is something that works well for us, as biological-cultural beings with a certain history.

This isn’t a suggestion to give up, much less a mystical injunction to go ‘beyond science’. There is nothing beyond science. But there is important stuff before it: there are human emotions, expressed by literature, music and the visual arts; there is culture; there is history. The best understanding of the whole shebang that humanity can hope for will involve a continuous dialogue between all our various disciplines. This is a more humble take on human knowledge than the quest for consilience, but it is one that, ironically, is more in synch with what the natural sciences tell us about being human.

Good news about a new antibiotic

I don’t write about science and medicine enough here, which is a pity, but I do want to emphasize the promise this new discovery carries. For a long time, scientists have been warning us that microbes are evolving resistance to existing antibiotics. Unnecessary use of antibiotics, in humans and animals, speeds up the advantage of microbes in the ongoing arms race of antibiotic resistance. This latest discovery is very good news, because it shows a new way to develop antibiotics, in addition to showing a specific new antibiotic that apparently is effective against the fearsome MRSA.

Scientists hold back progress by not being open enough

Daniel Lemire, a computer science professor at the University of Quebec, has written a scathing post about scientists who care so much about their status that they do not share their data and code, even when they are obligated to, as in the case of those conducting clinical trials. Lemire’s diagnosis of the problem seems on the mark to me; his post is underlined by such fury that he has left in it some editing infelicities, doubtless created in the heat of composing it. Even researchers working in industry are better at sharing than big-shot academics, Lemire points out. Wouldn’t you be just as furious as he is on realizing this? His post is highly recommended reading.

It seems that economists need to devise a better incentive system for governing research done in universities, as well as a method for convincing the powers that be to implement these new incentives. The public shaming Lemire calls for would be a good start.

Here is a pithy quote from Lemire’s post:

The problem is that academic researchers are overly obsessed with their own personal social status. It is a stronger pull than the desire to advance science, the public good or even commercial interests.

Do patents inhibit research?

A newly published paper by Fiona Murray, Philippe Aghion, Mathias Dewatripont, Julian Kolev, and Scott Stern asks whether patents inhibit researchers from exploring new directions for their research. The American Economic Association published a research highlight post today explaining the methods and conclusions of the paper.

Here is a quick summary: data and research tools in the sciences are increasingly covered by patents, making it costly or impossible for researchers who did not develop a set of data or a set of tools for analyzing data in their field to use these data or tools. In cancer research, many studies are conducted using genetically engineered mice. DuPont had patents on two methods for the genetic engineering mice, patents which it agreed to open up to researcher at a much lower cost than before, in two Memoranda of Understanding with the NIH in 1998 and 1999. A third method was not included in these agreements and remained as costly as it had been for researchers to access. This set up a natural experiment.

The result: mice covered by the DuPont-NIH agreements were involved in more research exploring new directions than mice that were not so covered. The authors of the paper found good ways to use citation and keyword data to capture this effect. Quoting from the research highlight post, we get to the crux of their findings:

The authors find clear evidence that the patents protecting Cre-lox and Onco limited the scope of scientific inquiry by genetics researchers, but the best policy for reducing this type of harm isn’t clear.