Darwin's insight
We experience the natural world as complexity. In geology we see many and complex formations with few obvious connections. In the 17th and 18th centuries geologists adopted a more analytical approach. They observed individual processes such as sedimentation, erosion and vulcanology and realized that these could combine to shape the world. In 1835 Charles Lyell collected these observations and suggested that Earth could be understood by studying existing geological processes. The analytical approach has dominated geology ever since. Although we can't explain evolution of mineral Earth in detail, we can study and explain individual formations and how they changed over time. In the last 200 years geological processes have become more fully understood and new processes, such as plate tectonics, have come to light.
Similarly in biology we see many complex organisms with no obvious connection among them. Darwin, like Lyell, adopted the analytical approach. He observed individual process and realized these could combine to bring about the biological world as we know it. Darwin wasn't the first to see biology analytically, but he was the first to document the processes and convince the scientific world of the value of the approach. For example. he realized that to understand speciation one should examine similar species and study processes that drive common ancestors in different directions. He conceived of variation and natural selection as driving forces. He observed corals and realized how geology and biology could combine to create immensely large structures. He realized that variation was an important aspect of biology and that animal breeding could shed light on evolution.
The critical point is that science looks at the world not holistically, but analytically. It divides nature into individual steps and studies these. The automobile is an appropriate analogy. We can't repair autos by treating them holistically. We must know the individual parts well enough to diagnose problems.