Proposed change to Biological Sciences

As I was doing my PhD, I started to question most of what I learned from molecular biology textbooks. I noticed similar trends in other PhDs. It is not that the textbooks are incorrect, but intuitively, I think most people who are educated in biological sciences "sense" that something very fundamental is missing in our knowledge of biological systems. Systems-based approaches tried to address some of the defects of looking at individual molecules in isolation. However, even then, the fractal-like complexity of biological systems make it extremely difficult for us to understand how it is "working". And perhaps that itself is the flaw in our thought process. How do our thoughts and emotions "work"? How to relationships between people "work"? The word "work" is probably not the right choice for these questions. An adaptive, highly responsive, and intelligent system does not work in one defined way - rather, it changes based on the thing that it is interacting with. 

It is arguable that "intelligence" (let's keep that word loosely defined), like evolution and adaptability, is a quality of most, if not all, biological systems. Intelligence of an entity can only be observed if we can communicate with it. We humans have difficulty communicating properly with other humans; it is fair to assume that we are very poor in communicating with other biological systems. In this case, it is possible that there are highly intelligent (again, loose definition of intelligence) systems all around us and within our bodies. By "highly intelligent", I mean that they are comparable to human tool-making intelligence, but in a different context. 

If we look as nature's biochemistry of cells and the human body through the perspective that they are all intelligent systems (like aliens), then it is not a matter of understanding how they work, but rather how we can communicate with them. These systems are more than capable to solving problems - from health to environmental problems. Humans need to communicate with them. Biological sciences should be an effort to communicate, not to understand these systems in the same way that we understand mechanical human-constructed devices. When I smell a flower, what is it communicating and what is the conversation that I should start in order to become friends with that plant?