Dual focus driving intentionality down and defining the biological contrasted with the physical

The operation of rules is seen also in the link between DNA, RNA, and protein structure. The sequence of nucleotides in the DNA is not constrained by a physical law, and many sequences other than those found in DNA are physically possible. The physics permits, but does not constrain. The constraint derives from the rules linking nucleotide sequences in the DNA to the RNA structure and thence to protein structure. The rules are integral to the inten-tionality of the genetic code with respect to protein structure and function. This constraint also ensures that information about biological structures is passed from one generation to the next. The genetic code has intentionality with respect to structure and function of the organism in the environment. If the construction of genes were determined by physics they could not serve the function of passing on this information; there would not be the flexibility for the sequence of molecules in the DNA to correspond to structure and function of proteins. The primacy of the code over the physical determinants is also demonstrated in that some areas of the DNA molecule do not code for any amino acids, and in some instances nucleotides can be interchanged without altering the information about protein synthesis. By contrast other nucleotide replacements alter protein structure with radical implications for function.

The concept of rules is also central to our idea of the way that evolution occurs. As Polanyi 9 argued, the fact that DNA structure is not specified by physical laws, creates the 'slack' which opens up the opportunity for mutations that are essential to evolution. However of itself such slack would simply be chaos if the rules for the assembly of molecules into biologically active structures were not operating. The rules ensure that structure and function are preserved.

Thus rules are essential to biological processes in at least three ways: they define the causal links between the environment and the organism, they ensure replication of structure and function over generations, and they create the conditions of balance between the physical indeterminacy of biological systems and order that is required in evolution.

However, three further aspects of the operation of rules are implied in this account, and need to be spelled out. Firstly rules are conventionalized within biological systems. They have to be followed throughout the system for the information to be preserved, and for this to happen the elements in the system have to use the same convention. The term 'agreement' adequately captures the essential point that how a rule is specified is open to substantial variation, but that rule has to be adopted throughout the system, for it to work. This is linked to the point made earlier in respect of Wittgenstein's view of what is involved in a person's following a rule: the rule is made in a shared practice. In respect of a person that means it is made in their shared social interactions, and for a biological system it means that elements of the system work in consort with other elements. In both cases the idea that the rule is made captures that there is a convention that things will be this way rather than that; that it could be otherwise, at least within the constraints of natural laws. That the making of the rule occurs in a shared practice indicates that the convention is shared among the participating elements.

Secondly the operation of rules creates the possibility of mistake and deception. If a rule specifies how the physical events in a system correspond to a state of affairs A in its environment, then any other state of affairs that creates the same physical events, will lead that system to respond as if the state of affairs A exists. This echoes definitions proposed earlier of correctness and error in terms of functional activity. For example if the nerves leading from the baroreceptors are stimulated electrically over the range of frequencies that convey information about blood pressure changes the system will respond as if those changes had occurred. This principle is exploited in the production of some vaccines. The immune system normally responds to infectious agents, however molecules that resemble sufficiently the key features of those agents that trigger the immune response can also trigger that response.

Finally, quite simply, a system can fail to operate according to the rules, leading to malfunction. Function and dysfunction, success and failure, health and disease, are in constant juxtaposition in rule-bound systems. By contrast there is no sense in which physical events determined solely by physico-chemical laws, malfunction, fail, or become diseased. In making this observation it is crucial that we see that the concept of malfunction is closely bound up with that of adaptation, and both are integral to the way rules operate in biological systems. A departure from the rules for the encoding of states of affairs leads to malfunction in the environment of those states of affairs, whether blood pressure, oxygen, or changes in light intensity. However it may lead to function in respect of a different state of affairs. If the outcome is adaptability to that state of affairs, then for the organism in that environment the departure from the rules for state of affairs A becomes following the rules for adaptation in state of affairs B. This process describes the role of mutations in evolution. For example a mutation of a gene involved in the synthesis of haemoglobin leads to the condition, sickle cell disease. However the sickle cell trait confers resistance to malaria and so is advantageous under some environmental conditions.

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