Tuesday, November 15, 2005

Headspace

I've recently become quite fascinated with the mechanics of biological systems - how cells work, genetics, the 3D physicality of nanometer sized organic molecules. There are two amazing videos by a company called Hybrid Medical Animation (their demo reel and Stages of Mitosis) that capture the essence of it beautifully.


I've become especially fascinated with neurobiology. A number of years ago I developed a number of adaptive real-time signal processing algorithms for echo cancellation that used a "stochastic iteration" error estimation and adaptive feedback algorithm similar to the learning algorithms used in Neural Networks, and that's when I first started getting interested in how the brain works. Recent advances in brain imaging and neurobiology have really been amazing, and have shown that the brain is much more than the matrix of adaptive electrical elements I used to conceptualize it as - it's a complex organic, evolving, chemical driven 3D environment where dendrites and axons are much more than simple wires, where neurons are not the only cells actively involved in learning, where everything has a role to play. The picture below really helps to drive home how truly organic the brain is:

Neocortex: Output neurons (gold), neocortex neurons (white) (link)

I've been wondering for a while how cells 'know' where they are in the body and the role they need to play and cell structure they need to adopt. Found a good overview (a bit technical, but worth the effort):"Molecular Neurobiology of Development".

It appears that there are gradients of mRNA and proteins that get set up on the ova that identify top/bottom, left/right, front/back:
"The concentration gradient orchestrates a coherent set of cellular behaviors that will eventually result in the proportionate growth of an organ, including the finest details. For example, different scalar concentrations may specify the type of cells and their relative position within the field; the slope of the gradient may be correlated to the degree of growth of the intervening cells, and the direction of the gradient with respect to the compartment may determine polarity."


I guess if you inject stem cells into a damaged heart, the gradients are still there to tell them what kind of cells to become...

Then there are timed genetic programs that control the fate of the cells, including homeobox genes that "encode transcription factors, proteins which turn on other genes. A single homeobox gene can cause a cascade of other genes to be turned on, producing an entire body segment or limb."

And at certain critical points in the development, new markers get established which set up localized chemical gradients to guide the accurate formation of detailed microstructure - e.g. the "match maker" protein SYG-1 acts as a "guidepost" during development, directing two neurons to join.

I can't help but wonder what we will be able to do once we understand how to uniquely determine a cell's "address" by decoding the gradients at it's location and how to alter the genetic blueprint to create novel structures of our own design.

Looking at that image of the neurons in the neocortex, and thinking about dendrites and axons growing along chemical gradients, it strikes me how intrinsically organic we are - axons and dendrites, growing like roots reaching for water, winding through the mind in a mass of complex, interwoven, highly physical fractal connections that define meaning.

Wow.

Brian



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