Saturday, January 23, 2016

How fresh are your bananas? An exploration of functionality in biological computing

A recent conversation got me thinking about how to explain quantification of "function" in biological circuits.  This is a critical issue and one of the key inhibitors to engineering complex biological systems, but it's not easy to explain because it involves a lot of technical electrical engineering / computer science concepts like signal-to-noise ratio, input/output transfer curves, non-linear amplification and threshold matching.  I think, however, that there may be nice biological metaphor that can make this concept easier to understand.

You see, a biological computing device is like a banana.

Let's say that I want something to eat, so I go into my kitchen and find a banana.  Is my banana "functional" as food? Well, it's very important for food to be fresh and healthy, so I'd better make sure my banana is fresh. But just how fresh is "fresh enough"?  Let us consider some different ways that my banana might look:
A spectrum of banana freshness (credits: yellowspottedbrownrotted)
The banana on the left is beautiful: no question that it's fresh, and indeed so perfect that I am sure that my three-year-old daughter would eat it without the slightest protest.

The second banana is getting on in age and starting to develop spots.  It might be a bit mushy inside, and my daughter will definitely not eat it, but I'd be happy enough to chow down.

The third banana probably won't taste good to eat on its own, but it's just perfect for making banana bread or other recipes that transform a banana from centerpiece to simply tasty flavoring.

And as for the fourth... I don't think I'd even want to feed that melted mess to livestock.

As you can probably see, the notion of a "fresh banana" is not a fixed concept, but a spectrum, and "fresh enough" depends entirely on what exactly we want to do with that banana.

Biological computing devices are the same way: a device has to be very high-performance in multiple dimensions (uniform yellow) to be safe and useful for complex circuits or applications like precision medical therapy, while simpler and less safety-critical circuits can tolerate some problems (spotted yellow), some applications just need a nudge or two in the right direction (brown), and some devices probably aren't good for anything at all (rotten).

Right now, the vast majority of our available biological devices are metaphorical brown bananas, with just a few spotted bananas available.  Understanding that fact is the first step, and getting on with building some fresher bananas is the second.
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