Chapter 1
For the logic of living system as a complex system
・ Preface
One of the most important purposes for biophysics is to extract some universal structure out of living phenomena and make clear the logic standing over the structure.
※ For example, thermodynamics and the theory of evolution are known as some of its successful examples.
We need to know processes in a living body deeperly to further understand living phenomena.
This tide itself was a main motivation for the birth of molecular biology.
But, at present ( about 2001 ), the viewpoint of molecular biology for life is insufficient to catch the logic of life.
In some sense, its viewpoint for life is very mechanical, it's suitable 'to compose an elaborate molecular machine' with the theory of evolution.
Roughly saying, stances of molecular biology are as follows.
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( 1 ) making clear roles of respective components in micro level (≒ drawing genes bearing specific roles)
( 2 ) next, drawing grammar rules to determine combination relations among respective components ( for example, searching for rules to activate and suppress some gene through other genes )
( 3 ) respective components are combined on rules to know how functions appear ( observing how respective genes in genomes are combined for the expressions of functions )
( 4 ) checking how efficient elements, patterns in function are chosen through evolution out of enormous cases in combination
For example, the cell-biology at present ( about 2001 ) is taking a way to think that the concentration of signal-molecule is varied through the appearance of gene, the gene also is generated beyond the threshold of the concentration.
Namely, it's still the main stream to find out a gene with specific role ( namely, '1 to 1 - correspondence' type method ).
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But, after the completion of the Human Genome Project, the course has been steered in the direction to look for functions of living being which are originated in combinations of such genetic expressions.
In other words, the progress of sequential generation is interpreted as a combination of logical operations such as 「If ( the concentration of signal-molecule is bigger than some threshold ), then ( some gene is at on or off )」.
As the concentration of signal-molecule is varied according to on/off of the gene, processes of generation are expressed with combinations of tremendous logical formulae.
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We take ways different from complexities in the combination theory.
Namely, as there are problems which can not be caught only by dividing into if-then type logical processes, we take a standpoint to first understand 'the whole' for understanding 'parts' .
Here, we review in-sufficiencies of molecular biology to understand life more detailedly.
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( a ) Considering a problem on if-then type logical rules, as only molecular reactions are generated in each cell, consequently, errors on logical operation can appear.
Meanwhile, living phenomena including cellular phenomena, molecular machines make progress under very large fluctuation.
※ For example, the number of signal-molecules N ＝ 1000 for one generation, taking the fluctuation √N into account, errors on the appearance of gene occur at the rate of 1/√N beyond some threshold.
Then, the variation on the expression of gene through the concentration of signal-molecule is equal to dividing the state of some cell into two fields for respective states of chemical composition.
In a word, considering many patterns of genetic expression is equal to dividing some state into many fields.
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But, taking a fact that some genetic expression itself is fed back to the state of gene into consideration, the number of border-lines for dividing rapidly becomes enormous.
And, if each division has a fluctuation of about 3 % , those divisions turn to be chaotic.
So that, the probability of the progress of generation according to 'program' gets to be about 0 .
※ Namely, dividing or classifying itself becomes a general catastrophe or a wild space in general topology.
So, the fed-back-ground tends to be a chaos or a random noise.
The above question is one of the universal problems in natural phenomena.
An other viewpoint for the stability of system is required to solve this problem.
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Actually, a group of cells may be stabilized through interactions among cells.
For example, in the case of equivalence (cellular-) group, if parts of equivalent cells are influenced by a fluctuation, the interaction among cells prevents surrounding cells from branching in the direction toward such influenced cells.
And, the community-effect is known, a synergetic effect makes embryonic cells determine the direction of differentiation in this effect.
Accordingly, mechanisms of stabilization through interactions must be investigated.
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( b ) Roles of molecules ( genes ) depend on various conditions such as time, position on the process of generation.
And, if a molecule as a cause ( origin ) is removed or specific genes are knocked out under some situation, other molecules or genes act in place of those removed carriers.
So, it's not desirable to determine roles of respective elements at the first step.
It's needed as a viewpoint that roles of respective elements are dynamically determined and varied through interactions over the whole system.
And, we have to consider of the cause of living system including the network of genes, the metabolic network and the transmission system of signals.
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( c ) Furthermore, the living system seems to have an universality which can't be reduced to mere combinations of individual genes with individual molecules.
※ For example, stability, irreversibility on the developmental process.
As in the thermodynamics, the stability in macro scale and the irreversibility are two different aspects of the same thing.
Actually, a specific directivity to lead from an ES ( Embryonic Stem ) cell to a determined cell through a stem cell can be found out in a cellular system.
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Possibilities of differentiation successively go to be reduced in an usual developmental process.
Of course, ultimately, we must be able to explain the irreversibility of life and/or death of an individual.
Clearly, the combinational method is not enough to this subject.
We think that it's effective to study dynamic complementary (≒ mutually compensating) relations between a whole and its part for making clear the universal properties of living system.
Outlines for that are shown in the following.
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Chapter 1 For the logic of living system as a complex system
・ Constructive Methods
By the way, which holds on life, A 「Complexity in the theory of combination」 or B 「Dynamic relation between part and whole」？
Probably, a living being has both features.
Therefore, to understand the essence of life, we should question which is more effective for that, A or B .
However, as living beings at present are historical, they are very intricate.
Accordingly, even if we study them in a frontal way, we can't decide whether they are originated from accidents on ways of evolution or necessary characters of living system.
So that, we have to face to 'synthetically created living systems' as a possible way.
Then, in the viewpoint of 「the theory of combination」, as existing lives have been extracted from very ingenious combinations, we must imitate existing living beings as faithfully as possible to create a living system.
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