I was going to write up a treatment of Rav Kook's position on Torah and Science but Rav Chanan Morrison beat me to it. He did such a great job, all I need to do is cut, paste and enjoy:
Contradictions between Science and Torah appear particularly irreconcilable with respect to the Torah's descriptions of the creation of the world and the beginnings of mankind. Are these accounts meant to be taken literally? Should we believe that the universe came into existence 5,760 years ago? Must we reject the theory of evolution out of hand?
In a letter written in 1905, Rav Kook responded to questions concerning evolution and the geological age of the world. He put forth four basic arguments:
1. Even to the ancients, it was well known that there were many periods that preceded our counting of nearly six thousand years for the current era. According to the Midrash, "God built worlds and destroyed them", before creating the universe as we know it. Even more amazing, the Zohar states that there were other species of human beings, in addition to 'Adam' who is mentioned in the Torah.
2. We must be careful not to regard current theories as proven facts, even if they are widely accepted. Scientists constantly raise new ideas, and all of the scientific explanations of our time may very well come to be laughed at as imaginative drivel.
3. The fundamental belief of the Torah is that God created and maintains everything. The means and methods by which He acts, regardless of their complexity, are all tools of God, Whose wisdom is infinite. Sometimes we specifically mention these intermediate processes, and sometimes we simply say, 'God formed' or 'God created'.
For example, we find that the Torah writes, 'King Solomon built'. The Torah does not bother to mention that Solomon spoke with his advisors, who in turn gave instructions to the architects, who gave the plans to the craftsmen, who managed and organized the actual building by the workers. It is enough to say, 'Solomon built'. The rest is understood, and is not important. So too, if God created life via the laws of evolution, these are details irrelevant to the Torah's main message: the ethical teaching of a world formed and governed by an involved Creator.
4. The Torah concealed much with regard to the process of creation, speaking in parables and ciphers. Creation - referred to as "Ma'aseh Breishit" by the Kabbalists - clearly belongs to the esoteric part of Torah [see Chagiga 11b]. If it were all to be understood literally, what secrets would there be? If everything was openly revealed, what would be left to be explained in the future?
God limits revelations, even from the most brilliant and sublime prophets, according to the ability of that generation to absorb the information. For every idea and concept, there is significance to the hour of its disclosure. For example, if knowledge of the rotation of the Earth on its axis and around the sun had been revealed to primitive man, his courage and initiative may have been severely retarded - by fear of falling. Why attempt to build tall buildings on top of an immense ball whizzing through space at high speeds? Only after a certain intellectual maturity, and scientific understanding about gravity and other compensating forces, were human beings ready for this knowledge.
The same is true regarding spiritual and moral ideas. The Jewish people struggled greatly to explain the concept of Divine providence to the pagan world. Of what interest should the actions of an insignificant human be to the Creator of the universe? The idea of the transcendental importance of our actions is a central principle in Judaism, and was spread throughout the world by her daughter religions. But if mankind had already been aware of the true dimensions of the cosmos, and the relatively tiny world that we inhabit - could this fundamental concept of Torah have had any chance in spreading? Only now, with our greater confidence in our power and control over the forces of nature, is awareness of the grandiose scale of the universe not an impediment to our basic ethical values.
To summarize:
- Ancient Jewish sources also refer to worlds prior to the current era of six thousand years;
- One should not assume that the latest scientific theories are eternal truths;
- The purpose of the Torah is a practical one - to have a positive moral influence on humanity, and not as a primer for physicists and biologists. It could very well be that evolution, etc., are the tools by which God created the world.
- Some ideas are intentionally kept hidden, as the world may not be ready for them, both psychologically and morally.
[adapted from Igrot vol. I, pp. 105-7]