Principle Of Life

Solution 1:

The essential part of the question is in the interrogative.

Whence (adverb) : From what source

The author is saying that though he believed he had accomplished all that he could at his current position, he was still routinely plagued by a question regarding the source of life.

Considering he's discussing natural philosophy I would assume he's referring the source of life from abiotic material. In this case I would consider "principle" to not mean belief, but rather the foundation of something. The question, in my mind, is something like:

What is the foundational source of life?

Solution 2:

The phrase you are asking about is really Whence ... did the principle of life proceed?. In other words

What is the source of the principle of life?