Software Emulates Organism's Entire Lifespan

An anonymous reader "Scientists have developed a software simulation, running on 128 computers, of an entire organism, a step toward carrying out full experiments without traditional instruments (abstract). 'For their computer simulation, the researchers had the advantage of extensive scientific literature on the bacterium. They were able to use data taken from more than 900 scientific papers to validate the accuracy of their software model. Still, they said that the model of the simplest biological system was pushing the limits of their computers. "Right now, running a simulation for a single cell to divide only one time takes around 10 hours and generates half a gigabyte of data," Dr. Covert wrote. "I find this fact completely fascinating, because I don’t know that anyone has ever asked how much data a living thing truly holds. We often think of the DNA as the storage medium, but clearly there is more to it than that." In designing their model, the scientists chose an approach that parallels the design of modern software systems, known as object-oriented programming. Software designers organize their programs in modules, which communicate with one another by passing data and instructions back and forth. Similarly, the simulated bacterium is a series of modules that mimic the different functions of the cell.'"

OO vs real life

[robi5]

I wonder how naturally an object oriented design worked out, given that molecular pathways are extremely complex and there are causal links between almost any pairs of phenomena. While OO is OK for CAD and man-made things, nature was much less restrained about high cohesion, low coupling, encapsulation and other heuristics. So the details would be interesting about inheritance, state representation, graph complexity, time-varying behavior etc.