This handbook provides both an overview of state-of-the-art scholarship in philosophy of science, as well as a guide to new directions in the discipline. Section I contains broad overviews of the main lines of research and the state of established knowledge in six principal areas of the discipline, including computational, physical, biological, psychological and social sciences, as well as general philosophy of science. Section II covers what are considered to be the traditional topics in the philosophy of science, such as causation, probability, models, ethics and values, and explanation. Section III identifies new areas of investigation that show promise of becoming important areas of research, including the philosophy of astronomy and astrophysics, data, complexity theory, neuroscience, simulations, post-Kuhnian philosophy, post-empiricist epistemology, and emergence. Most chapters are accessible to scientifically educated non-philosophers as well as to professional philosophers, and the contributors - all leading researchers in their field -- bring diverse perspectives from the North American, European, and Australasian research communities. This volume is an essential resource for scholars and students.