A Great Motto for Science

Snapped this during a recent trip in Ireland following our IRB-SIG. Almost an oxymoron, but not…..

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Note Taking and Squirrelly Software

In the past year or so I have been growing discontent with my method of note taking. I started using Evernote during my postdoc years though admittedly with some reservation: putting all my notes in some new company’s propriety database that can only be accessed via dedicated software seemed problematic. Still, it helped me (and apparently many others) get better organized. And so my list of notes grew longer through the years, as did Evernote’s feature list. Recently though Evernote seems to have shifted its focus to business solutions: integrated group chat, collaborative note editing, etc. As a result, the software seems to have bloated, becoming more slow and more buggy. Moreover, many features you get for free from your OS, like offline note taking or searching in PDFs, are only available for premium costumers. So I started wondering: if I am interested simply in note taking, is Evernote the way to go? The last straw was when I was writing a post for this blog and Evernote managed to sync it out of existence, with no hope of recovery. Writing is painful enough without having my notes deleted, thank you very much.

So what went wrong with Evernote for me? besides the basic reservations about propriety database etc. it seems to have gone from a sharp tool for a specific task (note taking) to a dull one that does not excel at anything. Sounds familiar? Yes, it can be seen as another example of the squirrelly approach to Budo, interdisciplinary research or, in this case, software development. Not surprisingly, I was not the only one feeling discomfort. My grief with Evernote has been crystallized in Alex Payne’s excellent post where he calls Evernote and similar software an “Everything Bucket”. One of his rules for achieving computing bliss is to “not use software that does many things poorly” i.e. “Squirrelly Software”.

What did I end up doing to solve my quandary about note taking? I followed Adam’s Pash recommendation for SimpleNote combined with nvALT. I get fast and reliable note synching, in a format that is also searchable directly on my local disc, with matching apps on all OS and mobile platforms.You can easily hook nvALT to your favorite text editor (Emacs with markdown extension? VI?) or directly start notes in the synced directory with your editor of choice. So far I am a happy camper. Good luck with your note taking, and beware of squirrelly software!

The squirrelly approach to Budo, interdisciplinary science, and software development

In his book Moving Towards Stillness [1], Dave Lowry discusses the squirrelly approach to Budo*, citing ancient writings by Hsun Tsu**:

The squirrel can do five things: He can climb a tree, swim, dig a hole, jump, and run. All these are within its capacity, yet he does none well.

The analogy is to people who try to train in many different Martial Arts but end up not excelling at any, with a superficial understanding of all.

I find that in interdisciplinary fields like Computational Biology we, and more worryingly our students, may end up like the squirrel. Admittedly, I find quite a few papers in the Bioinformatics field to be like that: Yet another method which is not particularly interesting computationally, accompanied with shallow understanding of the underlying biology. Such papers end up not really advancing our methods, tools, or our biological understanding. Many are well intended I’m sure, but the end result is not great. So what are we to do in our own scientific practice and when raising the next generation of scientist?

Dave’s advice is to concentrate on a single discipline in which you gain significant expertise and deep understanding. In Martial Arts, that can take a good ten years or so. However, Martial Arts tend to have many shared principles (more on those in later posts) and so by identifying and internalizing those one can later more easily learn from other Martial Arts, bringing more insights and depth to his/her original practice. Practicing hard and earnestly also teaches you *how* to learn, an ability that serves you well when you later expand to other disciplines.

The analogy in Science is to have a good foundation in some area, then add to it. If not, we run the risk of creating Bioinformaticians (including ourselves) that will have a hard time pushing the boundary of current knowledge.

Now, with all that said, to be perfectly honest squirrels do seem to excel at something (a point Hsun Tsu may have not realized or chose to ignore): They are very good at being squirrels. In fact, squirrels are one of the few mammalian families endemic to Eurasia, Africa, North America and South America, starting some 36 millions ago in North America [2]. So, while they may have not excelled at Hsun Tsu’s five tasks, they certainly have been around far longer than us, having their place in the grand scheme of things. And they probably don’t care much if some philosophers think highly of them or not.

P.S: Wait, didn’t I promise a connection to software development as well?
Well, this post has grown long already, so this will have to wait for the next time.

*Bu – Martial, Do – way; a Japanese term referring to the Martial Arts.
**An influential Chinese Neo-Confucian philosopher from the third century BC

[1] Moving Toward Stillness: Lessons in Daily Life from the Martial Ways of Japan, Dave Lowry, Tuttle Publishing, 1999
[2] The effects of Cenozoic global change on squirrel phylogeny., J.M. Mercer & V.L. Roth, Science, 2003

What is this blog about?

About a year ago I was riding the train back home from work and bumped into my colleague and friend, Arjun Raj. Arjun writes a popular blog about everything science related that I highly recommend [1]. He described how liberating it was to write a blog and how he realized it actually reached people. I found this quite interesting and opposite to my experience: I struggle with writing (lets face it, this is not even my native language) and for as long as I can remember I did not like to say things in public unless I was absolutely sure I got it right. On the other hand, I found from conversations I had with students and colleagues that they found some of the observations I made quite useful. And so, I decided to step out of my comfort zone and start putting out there my musings about the world. Like so many things in Science, It just took me another year.

So why “Martial Arts Life Science and everything in between”?
Research, specifically in Life and Computer Science, is what I do and love doing. Martial Arts is another key component in my life experience. Besides the obvious physical/defense aspects, I see it as a way to learn about ourselves and the world, I like the philosophical aspects of it, and I like to find how I can bring insights from my Martial Arts practice to my everyday life to make me a better researcher, mentor, father, and a person. So here we go.

[1] http://rajlaboratory.blogspot.com/