Tuesday, January 30, 2007

Some Thoughts on Information - III

This is taking a lot longer than I thought it would, and I'm still not to where I really want to be. So, tolerance, tolerance, please. Also, once into the nitty gritty here if I make a big boo-boo, please let me know.

I think we all agree that one of the most important events in life, maybe even the definition of sentience, is the reception, use, and ultimately dissemination of information (just gilding the lily on the dictionary definition of sentience.) So, the next thing to think about is how information gets to the human brain. Consider that, at the very root of this process, as, indeed the root of all biological processes, is a bimolecular chemical reaction. Hopefully, if I make it through this stage, that fact will lead to some interesting conclusions, if not many more questions, about information and its uses.

What follows is extremely simple at the basic level. The details (like the details of our discussion so far that seem to branch out further and further as the Mandelbrot set) become unbelievably complicated, e.g. the physics of photoisomerization. Please ignore the details if you wish. I will try to bring it to a very simple scheme at the end. Throughout, I have used Wikipedia. It is the current library of Alexandria.

First, consider a human who is in a tank of water that is at a temperature that is completely neutral (skin temperature). This person is able to breath with an apparatus and there is no light or sound. In other words, consider a person in an “Isolation Tank.” For short periods, this can lead to an enhanced state of self awareness, creativity, etc. However, after prolonged periods, the subject can experience anxiety, depression and, I suspect, just go crazy. (That sensory deprivation has been used routinely in the detention of “unlawful combatants” at Guantanamo and elsewhere is one more crime by the Bush administration, because it is certainly tantamount to torture.)

The point here is that the human brain has to have sensory input to function in a normal manner. In other words, it needs information. Without constant information input, the human brain and mind would go off on some wild tangent from reality. So, it makes a lot of sense to examine in detail how information gets to the brain and, by extension, how it is handled once there.

I would like to go through the process by which a visual sensory input (photons) makes it to the brain. Again, please try to see this in its simplest terms, since the devil is not in the details (except one, which I will come to).

It is of extreme interest that visual sensory input is quantized into photons. Please recall that Einstein won the Nobel Prize for this discovery, and the photoelectric effect, that he published in 1905 (along with the theory of special relativity!). While light behaves both as a wave and a particle (a photon), it is the latter that is of most interest here. In spite of this “quantization” it is my view that quantum mechanics plays no real part in the mechanism that we are about to discuss. We could talk about this at length later. Indeed, Einstein himself never really accepted quantum mechanics since it could not be brought into his general theory of relativity (i.e. couldn't explain gravity.)

I will try to show that at each stage of the process the information is digitized at the most basic level. This has profound implications for how we process the information and, ultimately must have some reflection on how we think. It also has a real world prediction about free will (don't choke, please).


Figure 1 - Structure the eye and retina


Figure 2 - Structure of the retina

First, consider the retina. It consists of multiple layers (see figures 1 and 2) with the rods and cones, the photon sensors, at the bottom of the layers (this is arrangement counter intuitive since you would think the photon receptors would be the first thing that a photon encountered). The rod cells of a human eye are capable of reacting to a single photon! That is, they are as sensitive as the Hubble Telescope since this is the ultimate limit of electromagnetic information.

In the cell membrane of a rod cell (cones are similar but are used for color perception) is a molecule called opsin (Figure 3).


Figure 3 - 3D structure of opsin

Buried in the center of opsin is a molecule called retinal (tiny red figure in Figure 3 and Figure 4 A). This is actually Vitamin A and, of course, the favorite of Bugs Bunny (carrots). It is also, sadly, very low in the diet of some third world children leading to blindness. We give it as a supplement to infants. Too much, though, is toxic. It is related to Retin A for acne, and, most interestingly, to the treatment of acute promyelocytic leukemia with all-trans -retinoic acid. How this causes differentiation of the leukemia cells to mature, non malignant cells probably involves G proteins, but I digress.


Figure 4A - Cis-retinal and 4B - Trans-retinal

When a photon of light hits retinal, it can be absorbed, causing the photoisomerization from the cis configuration to the trans configuration (Figure 4A -> 4B).

How exactly this is accomplished appears to be quite complicated. It can be understood in various ways. Since I am an aficionado of molecular orbital theory (vs valence bond theory) I prefer to think of it as the photon exciting an electron in the bonding orbitals of the retinal molecule to a higher orbital. Once in the higher orbital, the molecule is more stable in the trans configuration. However, if you are really interested, fly to here. This isomerization takes place pretty fast, somewhere on the order of 200-500 femtaseconds.

In the trans configuration, the retinal molecule doesn't “fit” into the opsin protein, and this causes a G protein signaling pathway to be activated. I am not sure of the exact mechanism of the pathway activation.

A nice animation of this process can be found here.

G proteins are ubiquitous in metabolism as “second messengers.”

The G protein in the rod cells is Transducin. Transducin contain both G-alpha and G-gamma-delta subunits. Activation of Transducin by the conformational change of retinal causes GDP (guanine diphosphate) to be exchanged with GTP (guanine triphosphate) from the cytosol at the G-alpha subunit. In turn, the now activated G-alpha subunit dissociates from the G-gamma-delta and increases the activity of cyclic GMP phosphodiesterase. This enzyme closes ion channels to passage of Na+ and K+ causing hyperpolarization of the cell membrane.



To be continued.....................

1 comment:

Cicero said...

Hah! To be continued....
What the heck? OK, I'll wait.
Meanwhile, to embark on one of those tangents: "the definition of sentience, is the reception, use, and ultimately dissemination of information." Now, if you watch a bunch (hundreds) of ants going back an forth, they all stop each other in the line momentarily to recept, use and disseminate information (maybe about where the hell the food is, or how to get there, or how to get home, or something). But I'm thinking maybe not "sentient."
I am having fun trying to read all the physics/chemistry/biology stuff about the eye!