Posted by: ericmjl | June 10, 2009

Making Your Own Rules: Three Heads Are Better Than One

Yesterday, I spent an entire afternoon trying to figure out how binary counting works in a two-bit biological counting system using Single Invertase Memory Modules (SIMMs). SIMMs were developed by Friedland et. al. at the Collins lab at Boston University, and it represents a superior way of storing biological counting events compared to current systems out there.

Current biological systems, such as the telomere/telomerase system or the Peking University 2007 iGEM Team’s conjugation counter, rely on sequential deletions of DNA to perform counting, which thus sets an upper limit on the amount of numbers you can count – basically, rather than counting up, you are counting down.

The RTC by the Collins Lab basically is a count-down mechanism too, but the SIMM relies on invertases to flip chunks of DNA around, which thus allows for a gene on that piece of DNA which was originally “on” to be turned “off” and vice versa. This “on-off” mechanism presents an awesome opportunity for binary counting, and so I went about thinking how it could be done.

Now, to hark back to the title of this post, as I was biking to my friend’s place in Acadia Park, I chanced upon some kids playing a game, and they were making up their own rules as they went along. The rules they were making up were in line with rules from other games that they had played before, but had ignored other rules that didn’t make sense to their “world” (i.e. the scenario where the game was being played in). It suddenly struck me that such a skill is so valuable that we actually should encourage kids to play like this. And let me elaborate on why.

When figuring out the binary counting mechanism, I also had to make up my own rules and ignore other commonsensical stuff. For example, in figuring out binary counting, I had to make up an order of events that occurred following a pulse of input. I also had to state my assumptions clearly, while stating clearly other rules that had to be obeyed in order for the “world” (i.e. binary counting scenario) to make sense. I had to ignore intrinsic leakiness in biological systems to keep the presumed world simpler. The same skills those children were using to make up rules were being used by myself in making up rules for biological binary counting.

Moreover, three heads are certainly better than one. I kept getting stuck halfway through the system because I wasn’t able to adequately figure out how binary counting could ever work, and without input from Calvin and Janny (Calvin especially, as he loves these puzzles just as I do), I would never have figured out the complete set of rules that would make the binary counting system work. Yes, indeed, the power of collaboration.

Okay, back again to prepping the Journal Club meeting.

Update: I found a more elegant binary counting solution than before. That came after talking with many, many people about it. Thanks to Charles, Hank, Calvin, and Heather!


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