Bacon's main interest for philosophers lay in his philosophy of science. This was to come in two parts. First, a radical criticism of the Scholastic and Renaissance approach to science would be needed to wipe away the confusions of the past. Second, a methodology would be needed to put science back on a sound footing. He called his project to reform the sciences the Great Instauration, which meant “restoration” or “renewal.” In fact, he completed only the first of three parts, called the New Organon, which refers to Aristotle's logical works, known collectively as the Organon.

The first part of Bacon's philosophical project focused on sweeping away what he considered to be past errors in philosophy. Bacon's attitude toward what had gone before can be summed up in a set of similes. Bacon took issue with the metaphysicians and the empirics, such as alchemists and scientists. He termed the metaphysicians “spiders.” Like spiders, the metaphysicians spun beautiful and ingenious webs, produced purely from within themselves. The empirics were like ants, scrambling about and collecting quantities of material, and piling them up, without making anything new of them. Instead of being spiders and ants, people should be more like bees — working together not only to collect but to transform what they've gathered. Scientists should interpret the data that arises from experience, should carry out experiments to collect new data, and so slowly build up humankind's knowledge of the world.

These similes point out the culprits that Bacon viewed as stymieing the advance of human knowledge. More specifically, his targets were two philosophers who by Bacon's time had cast enormous shadows for nearly two millennia: Plato and Aristotle. Bacon was critical of two schools of thought that had emerged from Platonism and Aristotelianism, respectively. He was opposed to the rationalist tendency, inherent in Plato, that knowledge could be attained by examining the content and meaning of words.

This tendency was found not only in Plato himself — who was always concerned with finding precise meanings of terms like justice, goodness, and love, but also in rationalists under Plato's influence, like Anselm. Anselm (as discussed in Chapter 7) thought that by simply defining a supreme being as a “being than that which none greater can be thought” you can know that such a being exists. Bacon descried this as a spidery tendency to spin something from one's own mind.

He also made attacks on Aristotle, the other giant of the classical period. Aristotle was a naturalist, a biologist who studied more than 500 species in order to note their tendencies for change and growth. To Bacon this was a useless enterprise, since Aristotle was intent upon amassing data but could not arrive at any scientific hypotheses. Bacon thought that there must be a new way of collating and organizing data that would help generate inductive hypotheses. Further, Bacon thought that Aristotle was “only strong for disputations and contentions, but barren of the production of works for the benefit of the life of man,” according to his biographer, William Rawley.