Once upon a time (back in the 70's and 80's) I used to be into the "hard sciences" and almost majored in astrophysics. Spent a lot of time reading books in that area and since I had dropped out of high school this was pretty much how I gained an education. When I look back it amazes me that I was so interested in astronmy, physics and chemistry yet majored (when I came to my senses, got my GED and enrolled in college) in anthropology in an effort to avoid math (big mistake - avoiding math - which came back to haunt me). One of the more interesting books in the area of astronomy is "The Planetary System" by Morrison and Owen. In particular, the first two chapters are fascinating. They start by walking you through what can be learned by just looking at the night sky without the aid of a telescope (via things like retrograde motion, path of the sun and planets across the night sky, etc). From there they introduce telescopes, Kepler, and Newton. At this point you can deduce several other things such as distance, radius, mass and density. With this knowledge you can determine a few things such as the compostion of the planets, types of atmosphere the planets have, types of moons and, if the moons have an atmosphere what type. With this information a few guesses can be made about how the solar system was formed. All in all it's pretty amazing what can be done, scientifically speaking with just a little bit of information.
Unfortunately, evolutionary biology is not so lucky. The building blocks are smaller and it takes more of them to build a good picture. Take the work of R. L. Berg, for example, during the early 1940's. Berg attemtped to correlate mutation rates in Drosophila melanogaster with the environment. She concluded that mutation rates are easily modified during the course of evolution. A few years later Mampell discovered a dominant gene on the second chrosome in D. persimilis which increased mutability in heterozygous flies by about 34%. Mutability in flies homozygous for the gene was increased by 70% (clearly not a case of heterosis, examples taken from "Genetics and the Origins of Species" by Dobzhansky).
Approaching the question from a different route , Brown and Gurdon demonstrated the role of maternal ribosmes in embryogenesis in one paper published in 1964 (Absence of Ribosomal RNA Synthesis in the Anucleolate mutant of Xenopus laevis) and one paper published in 1966 (Size Distribution and Stability of DNA-like RNA Synthesized During the Development of Anucleolate Embryos of Xenopus laevis). It is not till later in the developmental process that the paternal genes start functioning.
During the mid seventies Australopithecus afarensis was discovered and in the late nineties A. garhi was discovered. In the meantime, things like Basilosaurus were being discovered. And most recently an Oviraptosaur with an egg still in the mother allowed us to compare egg layin in dinosaurs, crocodiles and birds.
What holds this laundry list of items together? First, a devotion to experimental research. Each of the scientist mentioned above developed a hypothesis and then spent a lot of time coming up with experiments designed to test that hypothesis. Contrary to what, say, the ID crowd would have you believe a great deal of time is spent on designing experiments that carry the necessary weight of evidential proof. You may not find a lot of writing about the "Philosophy of Biology" (or anthropology or paleontology) instead you will find a lot of stuff about research design (a big topic when I was in grad school). Second, a rigorous analysis of the data (and, it goes with out saying, a rigorous method of determining exactly what constitutes relevant data.
The discovery of A. afarensis is a good example of this. One has but to read Johanson and Edey's "Lucy: The Beginnings of Humankind" to understand how methodical the process was. Better yet go read the incredibly thorough descriptions by Johanson et al in the AJPA (Volume 57).
These are but a small sample, a few small pieces of a larger picture. A pciture that in recent years is becoming clearer and clearer. Why stop now? Why should we turn our backs on the processes and methods that have allowed us to do so much?