Sentence:  The [Isaac] Newton that emerges from the [unpublished] manuscripts is far from the popular image of a rational practitioner of cold and pure <WSD>reason</WSD>. The architect of modern science was himself not very modern. He was obsessed with alchemy. 
Meaning of the word marked with <WSD> tags:  Rational thinking (or the capacity for it); the cognitive faculties, collectively, of conception, judgment, deduction and intuition.