Based on the inseparability and correlativity of the biological systems, we discuss the nonlinear whole biology and four basic hypotheses. It may unify reductionism and holism, structuralism and functionalism. Further, the loop quantum theory, which constitutes a very small discontinuous space, as new method is applied to biology. From this we propose the model of protein folding and lungs. In the model we apply some known results, and obtain four approximate conclusions: their structures are quantized, their space regions are finite, various singularities correspond to folding and crossed points, and different types of catastrophe exist. Moreover, it is discussed that the fractal is combined with a Gambini’s quantity. Finally, the medical meaning of the theory is discussed briefly.

biology, nonlinearity, complexity, loop quantum theory, protein folding, lungs