Musings on DNA, code and otherwise

From college days, I recall microbiology as one of the more fascinating fields I never opted to pursue, but still developed a latent interest in. The evolved, highly complex and cross-connected execution context of biology, at the deepest levels where it meets (or indeed is) the realities of chemistry and physics speaks to my geek genes. There are so many levels of exciting, beautiful and interesting stories, events and developments woven together and buried in genome! Not to mention it is open source!

You want to grok something? UTSL! If you don't yet understand it, it's because you are not knowledgeable enough. Go learn! Experiment. Think hard. Figure it out. And then share what you learned, so others can reach longer, make it do more, be more efficient, go faster, taste better, or what have you. I think choosing mad computer science over mad genetics was more of a cultural thing gut draw towards openness; away from the lock-ins of lawyers of looming heavy corporations protecting the intellectual off-spring stemming from the money invested into powering their geeks' forays into the unknown, and toward the almost open eco system of what today amounts to the web and places like github, where people promiscuously and chaotically spin off of each others' work making stuff better together, for fun and profit.

But back to genetic code, as inspired by a read of an article on MS, schizophrenia and bipolar disorder as related to endogenous retroviruses (meaning stuff we all carry as common heritage, though not activated in most of us). One of the things we were taught in my classes was about the huge amount of introns (DNA between genes that is seemingly not active, as it isn't observed to ever get transcripted into proteins -- which is essentially how microbiological code execution happens) observed in all living organisms (about 98% of human DNA is non-coding DNA). Of course the depth level of the insights we absorbed were rather meagre, and although omnipresent easy-access Wikipedia was not yet around, it felt fairly obvious that the rest, at the very least, would end up having all sorts of other functions or effects under conditions and circumstances that would relate to it somehow. If you have ever researched (or exploited) a buffer overflow in some program, you probably know that wherever the program pointer accidentally ends up, whatever junk or data happens to be in that memory region is suddenly, for all intents and purposes (or despite them :-), is now code! Maybe it will do something interesting. Or nefarious. Probably nefarious, really.

Biology, chemistry and physics, of course, just add a gazillion more dimensions to "functions and effects of things", while also imposing a bus-load of peculiar constraints, and introducing still more environmental conditions from the rather chaotic virtual machine of physics, chemistry and biology (being three different zoom levels at which things happen to shoot your code in the foot) combined.

If you thought debugging code is hard, it's actually a delightful walk in the park, for the most part -- free of all sorts of concerns like the ethics of feeding useful test arrays into your debugger, that your test subjects can't keep dying all the time until you figure it out, and so on, and that we're probably not debugging software that co-evolved on a planetary scale, over a couple of billion years, but was probably caused by, at the very most, a couple of decades worth of ingenuity from probably less than thousands (or at most millions) of humans, all more or less acting with actual intents, often worthy of words like "design" and "intent". We're kind of lucky, that way! And oftentimes, the whole code base is even your very own damn fault! And you could even know full well what every line of your code is supposed to do, even though you might not yet have discovered all the things it should probably also do to work under the conditions it'll be subject to when unforgiving users run it. (Even yourself!)

I wonder how far into the future we have to go to see iLife speaking to the creative class doing justice to its name, providing us with the tools to be creative with the workings of micro- (or, for that matter, even macro-)organisms, in the same manner it's letting today's happy amateurs go wild with arts like graphics, music and video. Lots of people have rather rigid ideas about what amounts to art, science, work, life style, communication and so many other arbitrary things you can do for whichever reasons propel you, based, among other things, on rules, rulers or methods used in each field, motivations behind them, et cetera. Try breaking a few; you end up in far more interesting places. And make and bring friends, along the way!


Reading Chrome, Firefox and Opera extensions in Emacs

If you're a fan of emacs' archive-mode that lets you load zip files and the like as it lets you load regular directories, and know that Firefox xpi, Chrome crx and Opera oex extensions are really just thinly wrapped zip files under the hood, you might expect Emacs to grok them, just the same. I did, and was a little surprised when it didn't plain work. (So maybe I'm running an old Emacs build?)

Anyway, I looked into the matter and did a little poking about to see what setup would do the trick. In the case of Firefox and Opera, it's really easy, as the xpi and oex "formats" only amount to changing the filename extension and making sure you have the right files in there -- so all you have to do is make sure that ("\\.xpi\\'" . archive-mode) exists in your auto-mode-alist, and ("\\.xpi\\'" . no-conversion) in your auto-coding-alist (there is a little snippet for your .emacs at the end of this post), and the corresponding oex variant.

In the Chrome case (which prepends a Chrome header with a format version, an RSA public key and signature from the extension author), besides the corresponding crx change for same variables, I also had to patch the lisp/arc-mode.el file lightly:

If you try loading a crx and find it already works, someone upstream already applied the same or a better patch than mine to your installation, but otherwise, read on. To find where it is on your system, type C-h archive-mode <return> and follow the archive-mode is a compiled Lisp function in `arc-mode.el'. link, apply the patch and M-x byte-compile-file the result again.

The .emacs snippet that makes it all kick in automagically:

Note that for the Chrome extension case, you won't be able to edit and save any of the contents in place, as you can with plain zip (xpi, oex) files; the magic to remove/re-add public keys and signatures will be somebody else's late Saturday hack to complete. :) Enjoy!