Is there some branch of biology that deals with the entire organism?
I was thinking of Systems/Integrative/Predictive Biology reading your question. Studying the wikipedia entry it looks like a research approach with many problems trying to understand organisms from a biochemical perspective, identifying control circuits and macro-quantities like temperature and its relation to such biochemical control circuits. Basically you have to give up reductionism and use holistic/systemic perspectives and methods. While physics was successful with such research approaches (climate simulation, many particle systems,...), biology is lacking very accurate and proven mathematical theories to implement and test reasonable models of an organism, not surprising when biological systems have so many degrees of freedom compared to something like a ideal gas in physics. The wikipedia link doesn't show a lot of proven knowledge that this field/research approach has already created.