Simon and Schaffer argue that debate between Hobbes and Boyle has been misunderstood, and Hobbes's arguments again the experimental way of life, as well as Boyle's defense of it, were an important contribution to political thought in Restoration culture. Rather than simply being a "bad scientist" out of his element, as he was later characterized, Hobbes refuted Boyle's experiments on a point-by-point basis and with arguments that were not -- in their time or context -- illogical and which had implications in fields no longer considered contiguous.
Boyle evidently thought Hobbes 'deserved the compliment of rational opposition' and engaged him in debate over a long series of years. Hobbes argued against the spring of air and advanced his notion of the simple circularity of motion in particles. He suggested that Boyle's apparatus was never able to eliminate the pure aetherial air and so never able to disprove his alternative hypothesis. Futher, Boyle's experiments, set in the newly established Royal Society, were private, open to the charge of being partial and aimed at Royal patronage. Moreover, experimental "proof" could never be proof on the level of philosophical and unanswerable proof. To avoid social discord, the Leviathan Hobbes envisioned was a plenist entity: materially full, holding central (philosophical) authority and power in all things.
Shapin and Schaffer argue that Boyle's experimental truth was another way to achieve social harmony. Nothing that could be defined as philosophical was to be admitted in experimental inquiry; and nothing that could not be proved materially would be pronounced upon philosophically. Boyle published prolix accounts of his experiments, gathered gentlemen of unimpeachable reputation to attest to his work, and constantly refined the air-pump, his central apparatus. In this way private disagreement was permitted on matters that could not be tested, and public disagreement was placed on "open" experimental grounds. However, the authors argue that Boyle's defense of the spring of air could not truly be proved by the air-pump mechanism he had in hand, and that Boyle had therefore pre-decided that an agreement with "the spring of air" theory was necessary for admittance into the experimental community. (224) Continuing, they set out their own belief: "Any institutionalized method for producing knowledge has its foundations in social conventions: conventions concerning how the knowledge is to be produced, about what may be questioned and what may not, about what is normally expected and what counts as an anomaly, about what is to be regarded as evidence and proof." (225) This belief links them to Knorr Cetina and to Barnes, Bloor and Henry. For non-competent Latinists, Shapin and Schaffer have translated and publish Hobbes's Physical Dialogue, an offering which I found very helpful in understanding the argument of the work.