Alan Kay applied to synthetic biology... And other late night notes.

I always find it very hard to blog. Even when I have the time to write something, not necessarily sitting in front of a laptop, mind you (I'm rather known for writing stuff that needs some word processor access and sending it in straight from my handset). It's only that I always feel that whatever I'm writing or trying to write at the moment just doesn't feel exciting or important enough. Which is why I keep multiple blogs around the net, each serving as a rant template for the other. Something would begin as a rant template on place A only to be edited into another form for place B, to place C, so on and so forth before the same yet radically altered post ends up as a follow up at the place of origin.

I know I should be writing about some other things as well, like how the diybio nyc might be amazingly close to getting a real lab space, or how I'm prepping to stop by for this year's iGEM jamboree. Oh or the pictures from this year's major diybio nyc event, where we set up a stall on the green market and extracted dnas from the natural produces with common household material (with the city people of course). Each of those things would probably make for some lengthy and interesting reading, and the list goes on (my life's actually kind of exciting right now). Yet whenever I find the time to write something down, nada. Nothing. My mind just shuts down and nothing I can commit to paper or the keyboard seems good enough.


Tonight though, aided by my weird bout with insomnia, I'll just write something down I've been meaning to say for a long time. I'm not even spellcheck this thing (god save my soul).

I've been looking into the history of computing and computer languages recently. I've always had some level of interest in computers, not just the spiffy brand-new muscle machines but in what most people would refer to as 'retrocomputing' (I once ended up practicing some AIDA because of that. Ugh), which is a story for another time. It's not that I think old ways of computing were better than others. It's just that it's much easier to trace the evolution of the concept of computing when you see beyond the immediate commercial products.

Synthetic biology is effectively a pursuit of engineering biological organisms. Biological organisms are based upon very singular information storage and processing system that has quite a bit of parallels to computerized systems. I've been wondering whether it would be possible to predict the future development of synthetic biology by looking at how computer programming languages evolved (because they deal with information processing systems applied to physical counting medium). Maybe it might even be able to predict some of the pitfalls that are inherent in developing any kind of complex programmable information processing system that will apply to the synthetic biology in the future. Maybe it would be possible to bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally within mere years.

While I was rummaging through the texts in both real life and the web (with many of the promising links on the web leading to dead-ends and 404s) I ran into a programming paradigm and environment I was only superficially familiar with before. Smalltalk and Squeak, respectively, both the brainchild of the computing pioneer Alan Kay.

Here's an excerpt from Alan Kay's biography I found on the net (I can't find the website right now. I swear I'll edit it in later, when my brain's actually working!)

“Alan Kay postulated that the ideal computer would function like a living organism; each “cell” would behave in accord with others to accomplish an end goal but would also be able to function autonomously. Cells could also regroup themselves in order to attack another problem or handle another function.”

This is the basic philosophy behind smalltalk/squeak and object oriented computer programming paradigm. It is no coincidence that Alan Kay’s vision of the ideal computer language and computing environment would take to a biological allegory, since he came from molecular biology background.

While I’m reading through the history of different computing paradigms for the purpose of figuring out how it might be applied to understanding and usage of synthetic biology, there’s something else I found awesome and perhaps a little heartwarming. Alan Kay throughout his life as a computing pioneer held onto the belief that the ideal computing platform isn’t a platform capable of crunching the numbers the fastest, but a platform that can be integrated into the educational function of the user through ease of manipulation and control. Ideal computing platform should be hackable because it makes logical sense to do so.

Can we say the same of synthetic biology? Perhaps not. The direct comparison of a complex biological system to computerized circuits and cathode ray tube projections can only take us so far. Yet I can’t shake the nagging feeling that synthetic biology might be looking at some very unique opportunities for change precisely because it is different from regular electronic systems, with documents of the early days of computer and programming already here for our perusal.

A good, elegant system that allows programmable extension must be at the same time easy, or at least logical to learn. And there are systems that both run and learn better compared to other systems. This might become something of an issue of how synthetic biology parts/devices/systems are put together in the future as the capacity of the synthetic biologists to handle complex systems increase.

I think it might be able to pursue this idea further. As it stands this is nothing more than an interesting parallel in concept without substantial scientific reasoning.

Which is why I should get myself to learn smalltalk/squeak sometime in the future. Maybe I should knock on the hackerspaces in the city, see if anyone's willing to mentor me.

Now, it's about time for me to get some sleep.