Tolle Lege!.

All popular science books should take a clue from this book. There is no 'one scientific method' there are just many different possible ways we determine our justified true beliefs.
This author is never afraid at talking above the listener. He's perfectly comfortable at using the appropriate terms that our needed, and he takes a stand on many of the issues within the Philosophy of Science. As the author says, science before Galileo thought in terms of causes and purpose (teleology), and afterwards started thinking in terms of patterns and laws (rules).

I would say the book is essentially divided into two parts. The first part lays the foundation for the nature of science and introduces the listener to the nature of being, the study of ontology, and the foundations that are created which we use in order to explain. He'll actually get into some deep discussions on possible building blocks for the universe (monads, dyads, substance, forms,....). The importance of emergent properties because of the different regimes that are created by our "domains of appropriate applicability". Anti-realist v realist, the entailing of different theories by other theories, Bayesian statistics and why it's so necessary to understand what it is, and most of the other standard topics from the philosophy of science.

There's multiple ways to understand the world. Sometimes we have to get at the particular before we can understand the whole or the universal, and other times we must understand the whole before we can get at the particular. The judgement we use by subsuming the particular under a universal rule gives us the bridge from reason to understanding.

I saw the second half of the book as a refutation for all of the classical arguments for the existence of God. He doesn't frame them that way but uses the argument as a departure point in order to educate the listener on how to think about the world and ourselves such that we are a part of nature not apart from nature and how everything that can be explained (understood) can be thought of in 'poetic natural' terms. (Look, he's an incredibly gifted writer, but I think he could have done a better job on his 'fine tuning' counter-argument. But his refutation on the prime mover argument, that 'nothing is not a state of being' was superb).

Science is always underdetermined. The scientific facts that we have can be explained by multiple theories. Just read any issue of Scientific American and you'll see an article on a new scientific phenomena such as Dark Energy and you'll see a statement such as that there are three different explanations for the phenomena under consideration (e.g. gravity changes over distance, a dark energy field exist similarly as the Higgs field does, or the vacuum energy of space creates it). "Grue', green before a date and blue after a date, is my favorite color for a reason. It quickly shows that science will be underdetermined. I mention this because I think that the graveyard is full of scientist who makes such a claim as he does in the book that the "bending of a spoon by mental telepathy is not possible because our current theory would never allow it". It is wrong to make that statement. There can always be a different ontology that will entail the current one but allow us to realize different perspectives.

I really like the book a lot. He merges the nature of science with understanding science as nature. I saw the bibliography on this book before it came out. I read over 2/3s of the books mentioned in it and knew before I read this book it would be fairly redundant and it was. I slowed down reading popular science books because most of the ideas in popular science books I read I have read elsewhere. Even in this book it mostly consisted of things I've read elsewhere. But, he does something that I wish all pop science books would do, he understands the issues in the Philosophy of Science and he knows how to relate that to the science that is being told.