How can the organs of an organism cooperate so well?

I had an interesting thought about living things. We tend to think of living things as a single entity composed of "parts", each with its own specialization.
A plant has roots, leaves, flowers etc', a human being has a liver, eyes, blood vessels etc'.
And it seems mysterious that all these specialized organs come about in perfect cooperation with one another.

But there is a different way to think about it.
We don't question why predators have the teeth and body that they do. We know that they developed the way they did because there was an abundance of prey around, and this was the best way, most suitable way to capture and digest it.

But we can think about the parts of a single entity in the same way.

The cells that compose the roots of a plant may have developed gradually in a specific micro-environment. What do I mean? Imagine for a moment that you have a plant-like organism, without roots, but that extracts its nutrients from above the surface of the water. However, some of the cells of that organism are attached at the bottom. Those cells are constantly surrounded by the chemicals secreted from the cells above, as well as the moisture and darkness in their current location. Over millions of years being in a similar environment and replicating, those cells will adjust to using the specific chemicals and degree of light and moisture in that part of the organism, eventually changing from the standard cells above it and specializing into a "root cell". A similar thing happens at the top of the plant, where some cells develop over time into leaves, or flowers. The final result is a conglomeration of cells, each with its own specialization, and we don't understand how something so complex came to be, and how the different parts developed such intricate cooperation.

But, if we think of how each of those parts individually adjusted to its own micro-environment, it is not surprising that it is so well suited to communicate with the rest of the plant, or to take advantage of the moisture in the ground.

Our limbs and eyes developed over time, based on their own micro-environment.
Think of a worm-like creature, swimming in water. Its head is at the end of the body that is first to move toward or away from things (the "steering wheel"). That is the single most sensitive part of the organism that will benefit most from sense perception (sight, smell) because it is the first to die if it runs into the wrong thing. So it is no surprise that eyes and mouth develop at that particular part of our worm. Just like root cells develop where it's dark and damp.

So my idea is that each one of those components develops the way it does to survive in its own micro-environment, given the by-products secreted into that environment by the rest of the organism. That's how complex systems get created with the ability to synchronize and communicate so perfectly.
It's not that the plant said to its cells: "you there, go to the soil and become a root, and you there, go up toward the sun and make a leaf", but rather, this mass of cells started specializing according to the micro-environment of each part. But the products of each of the other part became part of the constant micro-environment that that part needs to adjust to. Just like a predator evolves to be able to hunt. :-)

I hope this will be interesting for someone and worth reading. There is probably writing about this somewhere.. Maybe eventually I'll get to it. For now I just like thinking about this on my own and sharing these ideas.