Some personal remarks on molecular interaction maps

SOME PERSONAL REMARKS ON MOLECULAR INTERACTION MAPS

In molecular and cellular biology compact and elegant theories of the sort familiar in physics are rare. Rather, explanations of phenomena are typically couched in natural language narratives that describe the interactions of large numbers of distinct molecular entities. Protein A, say biologists, switches on protein B, which then activates protein C, and so on... So let's look at some of the advantages and the limits of such a representation model.

Advantages

extreme synthesis : in theory each interaction symbol may represent at least one article in a scientific journal ! One A4 sheet may contain years of research articles, i.e. kilograms of paper !
rapid deduction of the final effect of a perturbation in the pathway, expecially useful to predict alterations in monofactorial mendelian diseases. Such a deduction is somehow more difficult when :

divergence is present in the pathway
we are not sure that all the components of the pathway are present (i.e. : expressed) in a given cell type

rapid availability of information on a particular reactant and on a particular interaction only by clicking on the symbols characterizing them (e.g. : STKE connection maps and Boehringer-Mannheim Biochemical Pathways maps) or by looking at a separated annotations list (e.g. : Kohn's map). These 2 sorts of information are displayed, respectively, by clicking on the shapes or on the symbols above the relation arrows in a pathway graph.
there are 2 types of maps: canonical connections maps represent consensus knowledge obtained from multiple organisms and processes, and specific connections maps document known components and relations that exist in a particular organism, tissue, or cell type.
computer-designed pathways are dynamic and can be actively constructed.

Limits

no knowledge on starting conditions
no knowledge on quantitative relations among metabolites involved in dynamic transformations
no knowledge on temporal relations in dynamic transformations : temporal relations are very important when divergences and convergences are present in the pathway
necessity of standardized symbols : I am not aware of any institution having coded symbols for molecular interactions pathways till today. Here I collect those I have seen.

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