An interesting article authored by Antoine Danchin from the Pasteur Institut was recently published and is sure to bring forth much discussion.
Bacteria as computers making computers
Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.
The quantum teleportation experiments have demonstrated that information can be viewed as a fundamental irreducible property of physics (informationalism). Information in the sense that energy supervenes on information. Energy is understood to be the ultimate foundation of all matter in this universe. From Einstein’s equation, E=mc^2, all matter was ultimately created out of energy, and is theoretically reducible to energy. From there it can also be derived that time comes to complete stop at the speed of light. In addition, the first law of thermodynamics states that energy cannot be created or destroyed. The quantum teleportation experiments showed the entire information content (properties) of one photon can be teleported instantaneously onto another photon whereby the second photon assumes the complete identity of the first photon, while the first photon loses its complete identity. So from there, energy can be viewed to supervene on information, and information can be viewed as a fundamental category of Nature.
Systems biology is moving in that same direction, as viewing cells as computers with machinery and software makes it possible to view information as a fundamental category of nature and all future developments of systems biology can include this concept when looking at cells.
There are many interesting passages in this article. A few of these are going to be highlighted for discussion.
From the article:
Historically, systems biology follows on from molecular biology, a science based on many concepts more closely linked to arithmetic and computation than to classical physics or chemistry. [b]Molecular biology relies heavily on concepts such as ‘control’, ‘coding’ or ‘information’, which are at the heart of arithmetic and computation.[/b] To accept the cell as a computer conjecture first requires an exploration of the concept of information, in relation to the concept of genetic program.
Cellular processes are exquisitely controlled and carried out by remarkable biomolecular machines. The software needed to coordinate these processes is located in a very optimal genetic code that is optimized for evolution and maintains its own functional integrity.