Over the last week, I heard a lot of comments on the Nature paper by Jessica Bolker that discusses the issues with model organisms in Biology (Nature 491, 31–33). The author asks “How did a handful of species become central models?” She also goes on to successfully argue that “Choosing a research model should be more than a matter of convenience or convention. Scientists need to ask more questions — about the goals of a specific experiment, how suitable a given model is to reaching those goals, and what environmental or other external factors might be relevant to how well the model works.” Whether are not they agree with the merits of a living model system, all my friends, ranging from biochemists, mathematicians, systems biologists, immunologists and geneticists agree that in place of traditional model systems, we need to include a wide variety of models, that are evolutionary beacons and have complex environmental interactions. That’s when I began asking “Why not model instead of making a model?”
The bombardment of genomic data, molecular methods and sophisticated programming tools all made me wonder where the world of systems modeling stood today. I am aware of the landmark Cell paper, which assembles the whole Mycoplasma genitalia by computational modeling. That was a unicellular bacterium, with only 525 genes. What about a human cell, an organ or an organ system? Why would we want to model if we cannot use it to understand us? My search took me to http://systems-biology.org. From Pathway builder to Virtual cell, there was a gamut of cool tools that can simulate anything you want in a living system. I further learnt about the “Virtual liver project”, a complete site to model the human liver, from single cells to the whole organ funded by the German Government. One of its goals is to enable “Informed decision making based on network interactions rather than reductionist data”- something that more researchers and drug developers are increasingly aware of.
Sophisticated modeling can bring about the integration and translation of large volumes of networks and associated molecular data- a change that is already upon us. I am waiting with bated breath for the final models of the European Commission funded Human brain project, which will use supercomputers to recreate the human brain.