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- 4.2 - The Biological Ontostat.

by Denys L╔PINARD

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1 - The Two Mediums.

Biological mediums are complex, but in order to find again the observations of the preceding pages concerning economical mechanisms, I will try to highlight in the living matter the two different types of mediums :

A structured medium, constraining, which I describe as contracted, where each molecule, each active site occupies a quite precise place, necessary condition for the good unfolding of a sequence of successive actions. As example, I present the electron transport chain in the photosynthetic membrane :

ATP synthesis in Thylacoid membrane.

This example is rather characteristic of what can be a contracted medium in living matter, I could have presented many other as the chain of the cytochroms, a ribosome etc. this list can include also transmembrane transport as well as that along cytoskeletal filaments, in or outside vesicles.

A dilated medium where the molecules move freely, are mixed in great number, meet randomly. One can quote the cellular cytoplasm, the blood medium, the external medium.

During biological or physiological activity, the molecules travel through or come in contact with those different mediums. In this analyse, we must take into account that the valuation of the medium can be different according as we consider small or large molecules : small molecules, ions, can appear free when larger ones are fixed on membranes, for instance.

2 - The Regulation in Biology.

In order to establish the fundamental points, I take back the works that AndrÚ Lwoff has reported in his book, The Biological Order; these are the first presentations of the regulation of the enzymatic synthesis.

Summary of the regulation of the enzymatic synthesis :
On the bacterial molecule of DNA, the genes of the ▀-galactosidase and the ▀-galactoside permease are preceded by an operator gene and a repressor gene. The product of the repressor normally goes and binds to the operator, preventing so the synthesis of corresponding enzymes and, I quote AndrÚ Lwoff : When lactose is present in the medium, a few molecules diffuse through the membrane even in the absence of permease. One product of the lactose metabolism, when it binds on repressor, produces on it an allosteric modification. So the repressor loses its affinity for the operator gene. Thus it is unlocked, and the synthesis of ▀-galactosidase and of ▀-galactoside permease can begin.

Taking back these lines, we can schematize the control of protein biosynthesis in two main phases in each of these mediums :
Statistical information in dilated medium :
When lactose is present in the medium, a few molecules diffuse through the membrane even in the absence of permease. This dilution by free diffusion, or by a mechanism of hazardous sample, is a permanent test the cell exercises on its medium in order to measure the level of sugar. From the large number of lactose molecules, only one will finally bind on repressor. Conversely, if a molecule is detected by this way, it is for the cell the statistical certainty that many are crowding outside. It can, without any risk of error, produce enzymes for consuming them.
Action in contracted medium :
And then begins the deterministic and constraining phase. The process unfolds in an ineluctable way with DNA transcription and enzyme production, ▀-galactosidase and ▀-galactoside permease, which will cause the lactose to penetrate in the cell and will consume it. Sequences follow each other, every one being determined by the previous, until the consumption of sugar ; the level lowers, the repressor is freed and the phenomenon stop ; if sugar is added, the amount goes up and the enzyme production begins again.

Thus, we pass alternatively from a phase of free motion for molecules to a constraining one. Between the two is the act of decision, achieved here by the repressor/operator couple. It is at this very moment that are fixed what we could call the initial conditions.

This regulating mechanism is possible owing to the permanence of the presence, to the stability of the amounts characteristic of the dilated states : the cell, when it is aware by this way of a sufficient quantity of lactose, bets on the fact that this state will vary only slowly, that gives it a little time - a few minutes - for building the chain of treatment of this molecule. It does not receive information from future but knows it with certainty, as if it was already there because it is aware that it will be very much like the present (at least for what concerns the level of lactose) ; thus it can rely on this stability which stops the time for preparing its action.

3 - Setting up the diagram of Biological Ontostat.

Diagram 3 - The biological ontostat.

On the diagram 3, I took back the stages -with same numeration although reduced- of the virtuous 8 presented on the previous page, with this difference that I placed the two waves with a partial phase displacement, 2π/10, and not in total opposition of phase. We will have the full explanation about this on the following pages with at the same time a lighting on the mechanisms of Evolution.

For the moment, let's consider the red curve, directed by the red arrow which indicates the direction of action. The points of intersection (2 and 6) of the two curves are shifted, releasing the ascending part of the curve.
The point 2 is that of decision of starting of making. It is pushed back downwards, towards a compressed environment; that squares with our observations of biological regulations where decision is at the very heart of molecular mechanisms, in DNA and in the structure of allosteric proteins and so..
The point 6 is that where the just synthesized molecule, say here the galactosidase, leaves the deterministic process of making and transport for freely meeting and combining with the lactose molecule. This point is gone up in order to take into account the fact that synthesized molecules are actively carried, along micro filaments of the cytoskeleton or in vesicles, very near the site where they will meet the product with which they will interact (8). The active transport is totally programmed by cell mechanisms; it does absolutely not depend on the product to metabolize.

Then the information feedback is done by 18. It needs a certain freedom of diffusion for the molecules which will regulate biochemical mechanisms quite near their action (2).

The pages 4.4 (The formation of an ontostat) and 4.5 (The going back on origins of causes) will bring us more explanation on how the biological ontostat could evolve during past times and how was formed the economical ontostat. We will be near the general explanation.

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February 2006