nor any spirit in nature, nor God. This is very important to keep in mind. The notion of genetic information was not thought to be intentionalist but purely mechanical.
Before developmental geneticists in the 1980s and subsequently could investigate more and more of the actual mechanisms of developmental processes, and elucidate the precise roles that different genes and gene products play, two of the most productive molecular biologists of the earlier time, François Jacob and Jacques Monod, in a historic paper of 1961, used the term ‘program’ to explain how the imagined development was possible. The paper was about their discovery of gene regulation in bacteria, the Lactose operon. In the concluding section they observe:
‘The discovery of regulator and operator genes, and of repressive regulation of the activity of structural genes, reveals that the genome contains not only a series of blue-prints, but a co-ordinated program of protein-synthesis and the means of controlling its execution’ [15, p 354].
Protein synthesis was the essential process for the development and life of the organism. As we will see later, the crucial part of this quote is the statement that ‘the genome contains’ the program. DNA contains a program for development, and therefore the cells can execute this program if they are properly equipped. The genome, according to Jacob and Monod [15, p 221], even contained the means of controlling its execution [4, 5]. The DNA molecule was thought of as a central organizer of all essential steps in the life of the organisms. The Lactose operon provided an example of how this could work: genes are regulated by regulator molecules that are again synthesized from other genes. The genome is a self-regulatory system controlling the development and behavior of the cell.
In the same year, 1961, another biologist who was more preoccupied with evolution and inheritance than biochemistry, Ernst Mayr [16], published a somewhat similar idea also using the program metaphor. But for him, the metaphor served other needs. His problem was teleology, i.e. the question of how it can be thought possible within a strictly Darwinian framework that allowed for no reference to vital forces, that organisms are such miraculously well-functioning constructions and show goal directed behavior. The assumptions of Modern Synthesis Darwinism combined the molecular evidence of DNA-copying and the ‘central dogma’ of molecular genetics (information flow goes from nuclear DNA to protein, not back from proteins into DNA) with the Darwinian mechanism of random variation and the survival of the fittest. This excluded the possibility of inheriting phenotypically acquired functions from the previous generation. Everything had to be in the genes. The solution that Mayr saw was given by the idea of a ‘genetic program’. If the previous generation passes a program to the next, containing all the information that the system needs to reconstruct itself and to behave, then we do not need any more assumptions to explain an apparent goal-directedness in development and behavior. Programs evolve by chance and selection. Teleology, the obscure old doctrine of nature following certain aims, could be replaced by a cybernetic model of goal-directed, negative feedback systems, or ‘teleonomy’ [4, pp 196, 221; 16]. The processes seem to be goal-directed, but this is only their appearance to us. Actually, development is programmed by DNA information, and it is the program that is passed onto the next generation, perhaps including mutations that may give advantages or disadvantages to the organism and to its chances for reproduction.
This was an argument against vitalism. Vitalism was a basically metaphysical doctrine arguing on the level of ontology. It claimed that living processes contain a nonphysical force or principle that make them what they are, which can never be explained by the physical sciences. Therefore, in Mayr's text, the assumption of the genetic program was also a metaphysical argument, working on the level of ontology. It explained how is it possible that living beings come into existence, and their way of existing in the world. In terms of theory building, the idea of the genetic program replaced intentionality in nature and the vitalist non-physical forces. It was therefore negative metaphysics that Mayr was arguing for. With the physically plausible assumption of a genetic program it was no longer necessary to believe in nonphysical forces and intentions to explain the apparent functional organization and goal-directed behavior of organisms. Jacob and Monod [15] were comparatively more constructive in their approach. They saw how such a genetic program could be conceptualized: as a sequence of regulatory steps whereby genes are regulated by the products of other genes.
But was this discursive move to the programs containing genome just a step towards dropping unnecessary metaphysical ballast and therefore in itself ontologically or metaphysically ‘innocent’ or neutral? I do not think so. In order to see this, we need to advance another 45 years in the history of biology and look at the ideas of contemporary systems biology. Kunihiko Kaneko, a Japanese biologist and influential theorist of complex molecular systems, summarizes the current approach to explaining the emergence of relatively stable and regular developmental pathways of organisms in a very simple way as follows:
‘Thus the situation is one of mutual influence, not unidirectional causation. Hence, although the genes can be thought of as in some sense controlling such processes, in fact it is not true that an understanding of the genes alone is sufficient for their complete description. For example, even if we were somehow able to obtain the DNA of a dinosaur, unless we also knew the initial conditions of the cellular composition that allow their proper expression of genes, we would not be able to create a Jurassic Park. The conclusion we reach from these considerations is that… we should be studying models of interactive dynamics. Then, we should inquire whether, within such dynamics, the asymmetric relation between two molecules is generated so that one plays a more controlling role and therefore can be regarded as the bearer of genetic information’ [17, p 20].
If we compare this idea that Kaneko is outlining, referring to vast experimental evidence and to mathematical models, with the image inherent in the ‘genetic program’, several important differences become obvious. The relation between different molecules and processes in the cell are seen as mutual influence, instead of a unidirectional causality contained in sequences of linear if-then events. Parts interact in many ways, loops of causal influence going forward and backward, branching in many directions and making the system as a whole relatively open or relatively closed. The division of roles within such a system is not a precondition, but must itself be explained as a result of the interactive dynamics of the system. Therefore, the apparent specialization of DNA as the bearer of genetic information, and the many very important roles singular genes can play in the development of the organism, are products of the interrelation of the parts of the system and their dynamics. This is the second striking difference to the genetic program approach. There, it was thought that a causal program is a precursor of development in the shape of the sequential composition of the DNA polymer. Thirdly, a regularity of developmental events that could be described as something like a program is to be located on the level of those interactive dynamics, not on the level of one component of the system. In terms of the distinction between genotype and phenotype, the assumption of systems biology is that the program (if anybody still wants to talk of programs) is a phenotypic regularity. What behaves regularly in foreseeable and reproducible sequences of events is the whole organism within an environment, not one isolated molecule.2
Molecular genetics, particularly in the context of developmental biology and genomics, has contributed to this enlargement of the picture. A wide variety of mechanisms that enable the cell to use DNA sequences in different ways have been discovered. The active RNA molecules (still suggestively called ‘messenger’ RNA) are compiled in much more complicated ways, and most of the RNA molecules (MicroRNAs) are no templates for proteins
