I'm reading Voyage of the 'Beagle' as a travel or adventure book, not as a science journal. But one aspect of Darwin's scientific background is striking to me. Darwin is in the first generation that could take the concept of "deep time" for granted, that did not have to argue about whether the age of the earth was in the thousands of years, or the millions. The latter position had won the field, and then some. I think even the debates between the Neptunists and Vulcanists were over by the point Darwin was working.
So Darwin and his colleagues were out in a world with this new, powerful way of seeing things. Literally seeing - a rock or riverbed looked different to someone trying to deduce its million-year history. Combine this with the Linnaean system, and the flood of specimens and descriptions brought back by travellers from all over the world. Explanations were suddenly available for all sorts of phenomena that had been mysteries for centuries. People were looking at animal and plant physiology, geology, oceans and currents, fossils, almost everything, with new, wide-open eyes. It must have been an incredibly exciting time to be a natural scientist.
I thought Stephen Baxter's short book on James Hutton (Age of Chaos) was an excellent amateur introduction to deep time. Amazing to think of great intellects like Johnson or Hume, Johnson pious but indifferent to whether the world started 6 or 10 or 100,000 years ago, Hume dismissing the traditional chronology as nonsense, but neither with any idea, any imaginative conception, of the truth, of an earth that is 4.5 billion years old.