Tuesday, February 13, 2007

Some Thoughts on Information - IV

Before we go any further, I wanted to point you to a collection of animations that are, in my humble opinion, superb in delineating the cellular processes that we are talking about. I will be using screen shots from these animations, and refer you to the particular animation in the future.

The animations can be found at: Max Animations

Review: We observed that the human brain is strongly dependent on information received through its senses. In spite of being in thrall to the imagination, I am sure you will agree that abstract creativity is not the primary purpose of the brain.

We have begun to follow information as collected by the eye on its path to the brain. To date, we have investigated the reception of a photon in the retina by rhodopsin in the rod cell, and have begun to examine the cascading pathway that will generate a nerve impulse. The next step is to view this as sequential chemical reactions. I promise that this is the lowest level (no quantum entanglement).

Axiom: In a series of chemical reactions, the overall reaction can only proceed at the rate of the slowest reaction in the series, i.e. the rate determining step. (I know this is obvious, but I really do think it is at the crux of many observations about information processing in the human.)

Observation: When I first started thinking about this I realized that any organism can be viewed in a number of “spaces.” The one that concerns us here is the kinetic space. The organism is a gigantic intersection of innumerable chemical reactions where almost all are catalyzed by enzymes. In other words, DNA, which determines the structure of enzymes, maps a metabolic profile onto kinetic space.

[A corollary of this observation is that the ultimate function of enzymes is to bring the kinetics of chemical reactions in the organism onto the same plane, i.e. within the appropriate time framework. All chemical reactions in the organism would eventually proceed in the absence of enzymes. Enzymes simply lower the activation energy of reactions so that they are time compatible. Otherwise, metabolism would only proceed at a snail’s pace, if at all.

What we are saying is that one part of evolution is changing the configuration of enzymes (proteins) by alteration of the DNA bases so that the rates of particular reactions (e.g. energy metabolism) are more efficient. In this sense, evolution is unidirectional and one cannot foretell what the upper limit will be. We can discuss the current limits though, see below.]

[Observation: Diseases such as cancer and the process of aging can be viewed in terms of kinetics. I have for some time felt that cancer is a kinetic disease. That is, that the basic biochemical defect (stemming from genetic defect) will be alteration of the kinetics of cell growth. This alteration not only produces abnormal cells, the cells themselves, of course, proliferate at a rapid rate (Burkitt’s lymphoma can double in 24 hours). Conversely, if cells in the blastocyst, which double in 12-24 hours, were allowed to grow without restriction, the blastocyst would soon be the size of a small universe. Evolution must have put into place a slowing of growth. Eventually, this would lead to the slowing of growth of the organism and, eventually, to programmed cell death (apoptosis).]

As we have stated before, all biological reactions are bi-molecular, and reversible.

A + B <=> C

Ah ha, you might say, isn’t an enzyme catalyzed reaction trimolecular?

A + B + enz <=> D

Well, I am almost certain that if the reaction time coordinate is divided into smaller and smaller intervals, you will always find that a substrate first binds to the enzyme then this complex reacts with the second reactant. The reason for this is simply statistics. A trimolecular reaction is vanishingly rare.

A + enz -> A-enz
A-enz + B -> D + enz

That is, the enzyme’s main purpose is to bring one reactant closer to the activation energy making it statistically much more likely that the reaction will proceed.

Here is an animation of an enzyme (I don't agree that both substrates bind at once).

This seems a good place to throw in my only equation so far, the Arrhenius equation:


where k is the rate coefficient, A is a constant, Ea is the activation energy, R is the universal gas constant, and T is the temperature (in degrees Kelvin).

A schematic of how a bimolecular reaction proceeds is:

Now examine the Arrhenius equation. Please note that the higher the temperature, the larger the rate constant. This is one more clue that statistics are involved. Temperature simply increases the number of collisions that molecules have and their kinetic energy.

Consider the scenario: Many, many molecules are present in the interior of the cell. These molecules are constantly colliding with one another and with the enzymes (molecules) present. Many of the collisions do not result in a reaction of A + B -> C. It is only if the sum of both kinetic energies of the involved molecules equals the activation energy will the reaction proceed.

We have now gone to the very heart of the situation in an organism.
All metabolic processes, including the assimilation and transfer of information (such as the visual stimulus of a photon in the eye) ultimately depend on the bimolecular reaction of molecules which reaction is more or less statistically probable depending on the activation energy. Enzymes are no more than adjuncts to this by making the reactions compatible in a kinetic space.

[I cannot resist jumping ahead a little and asking you to please remember that this is purely statistical and mechanical phenomenon. If we were a Fermi genius and could track each and every molecule and its kinetic energy, metabolism would be entirely determinable.]

In the next installment, I hope to cover how the information transferred from a photon to rhodopisin makes it to the brain.

To be continued ………………

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