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Nature's Information Efficiency

[Nature Information]

Nature manages information, the currency of life, with exquisite efficiency.

Today we have a (one of many) fantastic article from my favorite science magazine/blog: nautil.us. The (e)magazine is exquisitely well-written, edited, and displayed. I highly recommend adding it to your bookmarks, or just stay tuned as I continue to re-post their amazing content.

(Un)Surprisingly, today’s post is about information, and its use in biology. How would you recognize life on another planet? Well we’d look for the kinds of life we already know to exist. But what if life on other planets doesn’t look like it does on earth? I don’t just mean physically, but also chemically:

“Look for order. Every organism is a brief upwelling of structure from chaos, a self-assembled wonder that must jealously defend its order until the day it dies.” - James Lovelock

What a great quote! Conveniently also a fantastic O.S.S.!

Order, complexity, computation, information. These are the kinds of words that engineers use to describe abstract systems, and yet here we are talking about life in this way. It may seem strange, but in fact this kind of language is sweeping through biology! Increasingly scientists are talking about the flow of “information”; not just from one generation to the next, but from one piece of the body to another! This article not only looks at how awesome that is, but the striking efficiency with which biology performs these “computations”! It gives three examples, but we’ll look at two:

DNA

[DNA]

Not only does DNA store information at a density per unit volume exceeding any other known medium, it can achieve one quarter of the maximum information density allowed by the laws of physics (set by the entropy of a black hole). It’s so dense that all the world’s digital data could be stored in a dot of DNA the weight of eight paper clips.

Whoa… I knew DNA was a super dense storage medium, popularized recently in Science when a group of researchers stored the entire library of congress on a DNA chip [link]. But I never knew that it can store all of the petabytes of the worlds data in such a small area!

So nature created a system that is incredibly efficient at storing data, you might expect an incredibly efficient way of reading/writing that data as well and thats exactly what we have! Organisms have to not only read the information stored in their DNA, but then use it to rapidly specialize cellular growth - fancy way to say some cells become the head, while others the arm, etc. Alan Turing, the father of modern computation (one of my heros and a devastatingly interesting person - look out for a future blog post on him) spent time pondering if these processes could be “modeled” (computed) by a machine, and (semi/mostly) correctly predicted that spatial patterning of tissues during development could be controlled through the concentration of chemical signalers, called morphogens. He was recently proved (mostly) correct!

The article discusses one very interesting example: in a fruit fly the concentration of a certain morphogen (bicoid) leads to different specialization pathways. However, in measuring its concentration gradient (how much is there and how fast it changes), they estimated that it would take over two hours for the cells to measure the concentration with enough precision for accurate differentiation. But the fruit fly’s development period is way less then that! To get around that, they proposed that cells could be sharing information with each other using a second signaling chemical. Lets pause for a second and marinate on that for a second. Cells communicating with each other, sharing information to achieve a task faster then if each of them was acting independently?! Thats awesome! This processes would allow them to compute a “spatial average” of the concentration, rather than relying entirely on individual readings. This communication processes was later found to operate at 90% of the theoretical maximum!

Quick side note here: It is things like this that lend credence to the idea that all of nature can be modeled as following an optimization principle: Nature will try to do things as efficiently as possible - always. And if it doesn’t seem that way to you, there are hidden variables in the problem that you haven’t accounted for yet.

The Brain

[Brain]

The article then goes on to look at the brain, and touches on neural communication, signaling, and coherence. Here I feel the article fell a little short, possibly because I’m much more familiar with this area then the previous.

To summarize, we think of neurons communicating with each other using their “spikes”. However, the brain has 100 billion neurons so we’re still figuring out whether its appropriate to think of one individual neuron communicating with another, or whether its more appropriate to think of a group neurons communicating with another, or even entire brain regions communicating with each other. In other words, should we pay attention to what tiny individual neurons are saying? Or is that missing the orchestra to pay attention to the flute? This is a huge field and we’re still figuring out.

The article mentions how increasingly the role of “slow oscillations” we can actually see in an EEG (the electrical shower caps we slap on peoples heads in the hospital) are used to “synchronize” different brain regions, and how we used to think of it as electrical noise. One famous scientist I had the pleasure of seeing speak on campus, Tony Bell, argues its not even appropriate to label anything in the brain as “waste”! If it seems like “waste” to us, its probably important on some other “level” we haven’t examined yet!

My favorite part of this piece of the article is when it touches on the future:

Artificial intelligence, when it arrives, may not be built from silicon, but repurposed biology.

But it gives us a word of waring:

Before we get there, though, we will need a vastly different approach to science in order to understand the higher-order, emergent capabilities of nature’s self-organizing structures.

Then comes the real knockout punch, my favorite sentence in the entire article:

Form is transient in Nature, cast to meet shifting needs in a given niche. Determining the rules by which biology struck upon these ingenious solutions in the first place will spark the true revolution.

Note: This post (and most of the ones to follow) is a combination of paraphrasing, copy/pasting, and my own thoughts/questions.

Image Credit: All images were shamelessly taken from the original Nautilus article

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