In biology, organisms are classified thusly: Kingdom, Phyla, Order, Class, Family, Genus and Species. The organisms in the final category can mate and produce fertile offspring.This has been the standard method of classifying organisms (cell clusters) for quite some time. There is nothing arbitrary about it. Either two organisms can mate and produce fertile offspring or not. The scientific method can be applied quite readily to this system of classification. Firstly, gather the following organisms: cow, chicken, frog, kangaroo, squid, bear, bull, panda, fern, elephant, deer and human.Secondly, spend the next 14 years trying to mate each organism with the other. Once you have gone through all the permutations, you will discover that the cow mates with the bull in a very repeated and provable way (veal anyone?). Once it has been proven that a cow can indeed mate with a bull and produce fertile offspring, we then scientifically classify the two organisms as the same species.
Furthermore, evolutionary theory has branched out into many different disciplines of study, molecular biology being just one of many. Your backhanded attack at Charles Darwin, Thalmus et al. is akin to attacking Newton for not beginning the race to the moon directly after publishing Principia Mathematica. It does not make sense to me to do so. Perhaps I am not quite understanding exactly what it is you're trying to articulate here. I don't think anyone discounts the importance of cellular understanding (Monsanto sure doesn't).