Thursday, May 23, 2013

Planets and cells

Spend enough time looking at cells under a microscope and they’ll start to look like little planets, teeming with a hidden life of their own.

Pretty much the same thing, right? Looking at Earth, the picture is familiar. The shape of the continents, the cities marked by the light- all of these things and more are immediately understandable because of our experience. We know that the light represents people living in clusters, defined by political, economic and geographic constraints.

The cells, on the other hand, are more enigmatic. They are immortalized early B cells from the GM12878 line, one of the most well studied and deeply sequenced cell lines to date. Yet, in comparison, the mRNA spots are mysterious little lights whose meaning we are only beginning to decipher.

The scale of a system is a curious thing. When we think about our planet and how it got to that state of light that is so familiar, the answer seems simple enough. Indeed, historians have documented in extensive detail the various ways in which interactions between civilizations, empires, countries, and corporations ultimately led to the present state.

But what if we didn’t know any of this? What if we were gargantuan beings and saw the earth through special microscopes like we see cells? What sort of narratives might we invent to explain the pattern of light? Would we capture any of the nuances that are so obvious to us now?

For me, it's a fun thought experiment to think about what I might conclude from my "earth cell". I'd likely define the light as an autonomous entity- completely oblivious to the human activity that drives it simply because I could not measure it. I might hypothesize some repelling factor for the dark blue areas since light never appears there without ever understanding the difference between land and sea. Though I wouldn't have the slightest notion of what a port is, I might conclude that the light is enriched along the borders between the light blue and dark blue areas. I could make these observations, and though correct, they completely undercut the depth of understanding that we take for granted.

So then, going back to the cells, it's mind-blowing to imagine what is "really" going on. Systems are crazy things. Sometimes, it seems like they are far more than the sum of their parts, leading to incredible complexity from a few simple rules. Other times, it seems like they are much less, filtering a wide range of inputs into a few reliable outputs. And somehow, they repeatedly emerge in nature no matter what scale you look at. For now, I find those little spots deeply intriguing, and I think the only certain truth is that too much time in a dark microscope room can make yourself a little loopy...

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