The Scientific Method was formalized by Francis Bacon during the seventeenth century following the success of the process of inductive reasoning by Nicholaus Coperncius and Galileo Galilei. Use of the Scientific Method lead to the founding of the first scientific organization in the world, the Royal Society dating back to 1645. The use of inductive reasoning by Isaac Newton for the discovery of the laws of motion and gravity secured the role of the Scientific Method as the only reliable means for discovering a natural law.
Darwin was clearly knowledgeable about the problems with deductive in place of inductive reasoning, the Scientific Method, Darwin was forced to abandon the known foundations of science.
I am quite conscious that my speculations run quite beyond the bounds of true science. Charles Darwin, 1857
What you hint at generally is very, very true: that my work is grievously hypothetical, and large parts are by no means worthy of being called induction. Charles Darwin, 1859
Darwin was concerned about the effect of abandoning the scientific method. To console Darwin, just 2 weeks before the publication of The Origin of Species in 1859, Erasmus Darwin, his brother wrote :
In fact, the a priori reasoning is so entirely satisfactory to me that if the facts [evidence] won’t fit, why so much the worse for the facts, in my feeling.