When at last Darwin had come to present his ideas he followed faithfully the method advocated by Herschel and adopted by Lyell. Set out in modern terms, it comprises the three steps: first, making observations, asking questions and seeking explanations; secondly, constructing an explanatory model; thirdly, examining the adequacy of the model by applying it to new data and, whenever possible, to data derived from experiment. In advanced sciences today this procedure is followed systematically; in Darwin's day it was not only exceptional but mistrusted by the philosophers.
In Darwin's work the historical sequence had been: first, the array of observations he had made during the voyage, leading to questions about species and their distribution in time (the fossil record) and in space (on islands and continents). The second step, model-making, had been accomplished during the three extraordinarily fertile years of 1837-9. The third step was to be his application of the model to a vast array of observations, some old, some new, some made by himself, including the results of his imaginative experiments, but most of them derived from books and journals and from replies to questions put to his huge circle of specialist correspondents. A most important part of the third step was his systematic examination of the many difficulties that he was aware of. It has been unfortunate that in his own descriptions of his scientific procedures Darwin uses words and phrases that have misled readers and have resulted in the misconceived criticism that his methods were largely speculative and deductive. Thus, he tells us in his Autobiography that he adopted 'the true Baconian method', which is usually interpreted to mean amassing facts unguided by theory and then deducing a theory from them. Moreover, where we would say he built an explanatory model, Darwin refers to himself as 'speculating'. The fact is that Darwin was one of the first scientists to adopt what has become the current method. This is made explicit in Darwin's Introduction to his great work.
In this Introduction Darwin starts by referring to the observations he had made when on board HMS Beagle, which he says, 'seemed to me to throw some light on the origin of species—that mystery of mysteries, as it has been called by one of our greatest philosophers'. A little later he continues:
it is quite conceivable that a naturalist reflecting on the mutual affinities of organic beings, on their embryological relations, their geographical distribution, geological succession, and other such facts, might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and co-adaptation which most justly excites our admiration.Then, after pointing to the inadequacies of some current ideas, he describes how he had found illumination from a study of the breeding of domestic animals, and he proceeds to formulate his novel theory:
As many more individuals of each species are bom than can survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary, however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected. From the strong principle of inheritance, any selected variety will tend to propagate its new and modified form.