The Molecular Organism

The living cell is a goal-oriented organism and may be taken as a perfect example of a computing system. It is as complex as any man-made computer, and moreover it is as flexible, robust, autonomous, situation-aware and interactive as we wish our computers were. And yet, the living cell is not algorithmically controlled in any practical sense: it is not digital, it is not deterministic, and there is no algorithmic division of labor between the working cell and a separate programming entity.

The living cell is a self-organized system. It has at its disposal powerful molecular tools for synthesizing, copying, constructing, cutting, shaping, moving, filtering and sorting. The cell's protoplasm is the ultimate in self-organization, being able to shape itself into almost arbitrary form and to construct the most intricate living molecular edifices (such as the complex dance of molecular motion and synthesis of cell division).

The living cell has a rich behavioral repertoire and is capable of moving, sensing, orienting, eating, foraging, defense, flight, aggression, reproduction, communication, and environmental adaptation. Some of this repertoire our multi-celled organism may have inherited directly from our single-celled ancestors.

The living cell is a vast tangle of interacting molecules. There is not only a linear cascade from DNA to RNA, proteins and enzymatically synthesized molecules, but there is a complex web of reciprocal interactions forming a rich network of intracellular and intercellular communication. The genes of eurkaryotic cells are embedded in complex molecular machinery for their maintenance, reproduction and read-out. A gene's decision to be transcribed is controlled by cis-regulatory modules that in turn are controlled by transcription factors --- proteins produced by other genes --- and signaling molecules. Each gene may have many such cis-regulatory modules, which may be activated in the different contexts in which the gene can play a role. Also the direct or indirect gene products interact as a rich network, and together this molecular computer ultimately constitutes, constructs and regulates the molecular target systems dong the cell's work proper.

Molecular biology is waking up just now to face the challenge of back-engineering the molecular organization of cells and organisms, of developing the conceptual tools to understand cells as molecular organisms. Micro-arrays now make it possible to see genes switching on and off (as for instance when cells of baker's yeast revert from aerobic to anaerobic metabolism) but from there to understanding the causal relationships that are responsible for such action is a long way to go. Experimental perturbation analysis (manipulating individual genes or signals to see the effect) is a direct though very arduous method of network analysis. Direct computer simulation of molecular rate equations will be bugged eternally by insufficient information, e.g., on binding and rate constants.

This conceptual challenge is complicated, but also tremendously simplified, by the necessity to understand the cell under evolutionary and ontogenetic variation. It was a big surprise of recent decades to see molecules, genes and whole ontogenetic toolkits preserved over vast arrays of organisms and tremendous evolutionary time-spans. As a result it is now realized that molecular organization is not an un-principled spaghetti-code, raising hopes that it may be governed by general principles which the molecular machinery of the cell is sharing with other goal-oriented systems, principles that evolution has discovered hundreds of millions of years ago, just as software technology had to in order to make progress.