People have been classifying species for hundreds of years. Aristotle was one of the first to attempt a logical system of classification. Using characteristics such as structural complexity, behaviour and development, he classified about 500 organisms into 11 categories. He placed organisms into a hierarchy of categories, each more inclusive than the one before, a concept that has remained with us to the present day. In fact, much of the evolutionary theory finds its origin in Greek philosophy.

Carol Linnaeus (1707-1778), the father of the modern classification system, placed each organism into a series of hierarchically-arranged categories based on its resemblance to other life forms.

He also introduced binomial nomenclature, whereby the scientific name of an organism is based on the genus and species. Linnaeus believed in the immutability of species, and classified thousands of life forms into different species even though there were relatively minor variations between them. It was not until nearly 100 years later that Charles Darwin added a new significance to the categories created by Linnaeus and other taxonomists that reflected the evolutionary relatedness of organisms.

What Darwin saw was so different to the concept of immutability that he felt he had no option but to reject this concept. The finches he observed on his journey were obviously related and must have shared a common ancestor. This conflict led him to reject Creation altogether (kind of like throwing out the baby with the bath water) and develop the concept of evolution by natural selection.

A very important point to note, however, is that the science of genetics had not yet come into existence at the time of Darwin. This means that Darwin's conclusions were based on what he saw physically on the animal—the phenotype. If Darwin had known what we know today about the genetic basis of an organism (the genotype), his conclusion might have been quite different. The good news is that the genome is endowed with a marvelous capacity to produce variation, and all of these are governed by very complex mechanisms. Variation, therefore, need not be caused by chance mutation, but is possible because of the built-in variety available within the organism itself, as has been learned through the science of genetics. 

Read more about the genotype and phenotype in Natural Selection as a Creative Force