Abstract
The biomedical literature makes extensive use of the concept of a genetic program. So far, however, the nature of genetic programs has received no satisfactory elucidation from the standpoint of computer science. This unsettling omission has led to doubts about the very existence of genetic programs, on the grounds that gene regulatory networks lack a predetermined schedule of execution, which may seem to contradict the very idea of a program. I show, however, that we can make perfect sense of genetic programs, if only we abandon the preconception that all computers have a von Neumann architecture. Instead, genetic programs instantiate the computational architecture of Post–Newell Production Systems. That is, genetic programs are unordered sets of conditional instructions, instructions that fire independently when their conditions are matched. For illustration I present a paradigm Production System that regulates the functioning of the well-known lac operon of E. coli. On close reflection it turns out that not only genes, but also proteins encode instructions. I propose, therefore, to rename genetic programs to biomolecular programs. Biomolecular and/or genetic programs, and the cellular computers than run them, are to be understood not as von Neumann computers, but as Post–Newell production systems.
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Notes
Let us note that cis-regulatory elements are not the only genes that encode instructions in biomolecular programs. CREs are located next to the structural genes that they regulate. Conditional instructions, however, may also be encoded by genes located in trans, i. e., relatively far from what they regulate. A classic example is transvection (Lewis 1954). Transvection occurs in diploid organisms in which a gene A is regulated by another gene B, with B located on the chromosome homologous to A’s.
Abramson et al. 2003.
Gilbert and Maxam 1973.
Reznikoff et al. 1974.
At the level of chemical hardware, the implementation is slightly more complex than our functional software description above. LacI is a tetramer that can bind allolactose at each of its four constituent parts. If one or two allolactose molecules bind on the same side of the tetramer (on the same dimer), what results is functionally what we have labeled LacI + 1allolactose. If two allolactose molecules bind on opposite sides of the tetramer, then we obtain LacI + 2allolactose.
It is also true that if we want to implement a production-system virtual machine on top of an ordinary von Neumann computer, then it is an excellent idea to make the virtual machine multi-threaded. But this is an implementation detail.
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Acknowledgements
This research was supported through a Nazarbayev University Faculty Development Grant (110119FD4539). My research asssistant Dariya Kassybayeva has performed valuable work. I am grateful to Ulrich Stegmann for useful conversation. An early version was presented in 2019 at the ISHPSSB biennial meeting in Oslo, as well as the University of Aberdeen.
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Capraru, M. Making sense of ‘genetic programs’: biomolecular Post–Newell production systems. Biol Philos 39, 6 (2024). https://doi.org/10.1007/s10539-024-09943-3
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DOI: https://doi.org/10.1007/s10539-024-09943-3