In: Are We Spiritual Machines? Ed. Jay Richards
Michael Denton’s chapter is critical of the prevailing brain as a machine paradigm. He claims that the underlying design of organic systems is not at all analogous to the design of machines. All the parts of an organism influence each other, in a way which is not true of machines.
Denton says that this principle is well illustrated by the structure of protein, the basic building block of life. The arrangement of the atoms in protein is unlike anything found in machines. In contrast to machines built up out of modular parts that can be replaced by like parts, proteins are characterised by the chaotic nature of their arrangement. This was the impression gained by the first researchers to detect the molecular structure of protein. A later paper says:-
‘Perhaps the most remarkable features of the molecule (protein) are its complexity and its lack of symmetry. The arrangement seems to be almost totally lacking in the kind of regularities which one instinctively anticipates, and it is more complicated than had been predicted by any theory of protein structure.’ _____ M. Perutz – European Journal of Biochemistry
The structure of protein began to be disclosed in the late 1950s. In the early stages, it was assumed that each amino acid made an individual contribution to the three-dimensional structure of the protein. This assumption was based on the concept of proteins as machines, molecular machines, that were expected to be built up of independent parts that all made a contribution to the whole, but was quite distinct from the contribution of other parts. This idea of a molecular machine is still advanced in text books, but Denton regards it as false.
Research progressively showed that in protein, the contribution of each amino acid was influenced by interactions with many of the other amino acids in the protein. It was discovered that the spatial conformation of each part of the amino acid chain of a protein was the product of a complex web of van der Waal force between electrical dipoles and electro-chemical interactions. These involved almost every section of the amino acid chain. Almost every one of thousands of atoms in the protein macromolecule contributes to the shape of the molecule via interactions with most of the other atoms. The impression is sometimes given that protein components such as the alpha helix can be treated as separate modules, much like components of a machine. In fact, the stability and form of these elements is dependent on van der Waal and microchemical interactions, in turn dependent on larger scale interactions within the protein. The properties of each component within the protein are not fixed, but are dependent on the local conditions within the protein. While a module in a machine, such as a wheel on a car, is still a wheel when it is removed from the car, the same is not true of the component of a protein. The components of proteins are only components when they are interacting with other components. The form and function of each part is determined by the whole and vice versa, in a manner that is alien to human technology.
What is true of proteins is true of other important macromolecules. RNA molecules, like proteins, fold into three-dimensional forms in which all parts are shaped by reciprocal interactions. The constituent parts of these only hold their shape when they are part of the whole molecule. Removed from it they take on another shape, or disassemble into a random chain.
The proteins form into multiprotein complexes, such as the ribosomes that manufacture the proteins, and the cytoskeleton that comprises microtubules, microfilaments and intermediate fibres. The same principle applies as with the component proteins, that the parts have a reciprocal formative influence on one another, and change and no longer exist in their previous form if removed from the whole. The same principle applies to the cell as a whole, the parts only existing as part of the whole, and disintegrating if they are outside the cell for any length of time. This view of proteins, RNA, cell components and the cells themselves suggests that attempts to understand organism in terms of fixed organic components or parts of something like a machine are likely to fail.
At a more general level, this view of organic matter emphasises the superficiality of mainstream consciousness studies in regarding the neuron as a simple switch, and refusing to look at the possible functions of microtubules, other proteins and the quantum forces that bind them.