When dealing with a complex question of this sort, which involves humans as the meter of the quality under investigation, you can take the mental faculty in performing the judgment, and begin to test the mental faculty with the method of impression. Usually we just look at two things and ask our selves which thing is more natural, and then continue to adjust the presentations in order to understand more about the impression of 'natural' and 'natural process'.
At the same time, we can ask what is going on in nature to create these processes and structures. If we discover anything interesting, useful, or enlightening, we can incorporate this into our emerging body of doctrine, but we can also do one more thing.
We can see if any of these enlightening doctrines helps people to act in natural ways to produce these natural things, and satisfy our faculty to judge these things.
The first thing Alexander did was more like natural history than natural science. This is the work on patterns and pattern languages. You need to use the life-perceiving faculty to make judgements on things in the real world that provide this natural quality. You need to organize them as best as your can, share them, discuss them. That's what patterns are. This gives you some stuff to talk about. You can't do natural science, that is, you can't get very far asking "what's going on in nature" if you don't have a topic. So, we can't really talk about factors in biological systems without identifying some biological systems to discuss and further investigate and further define. That's natural history. You can then start doing natural science, which will start to produce theories that will lead you to throw out your old categories, because categories and qualities and features are impositions of the human mind on the natural world, and you make assumptions implicitly which form a kind of theory. And you need to re-examine the world in light of changing theories. That's how naturalism works. We did chemistry for 200 years before physics had a sufficiently sophisticated body of theory that would allow chemistry and physics to integrate.
The same is true for Alexander's work. Patterns and pattern languages were not the right theory with which to look at the world. But it was an important first step.
What he learned next came from studying the natural world, and the world of people doing natural work, using this meter. It produced the next level of somewhat explanatory descriptive theories, approaches to examining shape and process that had a number of effects on the three groups of questions under investigation. So, let's look at those descriptive theories, and see how they moved towards natural science from the natural history approach of patterns and pattern language, and where we go from there -- including how in general the sciences resolve the tension between natural history and natural science.
Keeping in mind the primary investigative goal -- life and feeling -- the resulting explanatory-descriptive theories were:
Let me explain what these mean, and then how they moved towards natural science from natural history.
Christopher Alexander's research, probably best exemplified by The Nature of Order, presumed that since we're already on the other side of the scientific revolution, we need to move closer to the right approach by tackling the complex scientific project of understanding more about this natural way of building. The questions are far beyond contemporary scientific frontiers, but we can discover important principles just by investigating. We might make interesting observations on the processes in the non-human world that lead to structures we perceive to be natural. We might discover something about how our perception works, and about how humans build when they work in what we perceive to be a natural way.
This reality -- which leads us call our efforts "investigating the mystery" and to divide our efforts into application, pedagogy, and science -- effects the research methodology of good natural science. It's fundamental in natural science to respect the mystery and avoid the "I understand! I know everything now!" mental trap, and to hold any theoretical construction or assertion tentatively. To assume that we have "figured it out" would be dogma and scientism. The quest for enlightenment is not a quest for absolute truth or for omniscience -- that would be a misunderstanding of the nature of natural science. This was the point of, for example, Wolfgang Köhler's 1938 book The Place of Value in a World of Facts -- we cannot say that people are "only chemicals" simply because we have learned a great deal about the chemistry, or that cities are made of "just buildings" simply because we don't understand the complexity of human life in cities. Jane Jacobs made a interesting point in The Rise and Fall of the Great American City: cars, traffic, and highways came to dominate the interests of planners because they felt it was easy to study cars, and they had no idea how to study living systems of people. The technocratic planners, along with the interests of the wealthy and powerful, took these respectable-looking "facts" and proceeded to destroy everything. They defended their destruction as "practical", "adult", and "realistic", a psychological state that C. Wright Mills called "crackpot realism" in The Power Elite (1958).
Studying the natural science of what we do, does not mean that we'll only do that which we understand about ourselves. If that was the case, we couldn't even talk, since the neuroscience of talking is poorly understood. So when we study how a human builds a natural, harmonious thing, and we believe that our results can offer us some insight that might be helpful in this craft, that does not mean that all the mystery has been lifted. In fact, it's the mystery that we're studying, and we don't know where it "stops", if such a thing were possible. So, we need to continue the applied mystery of the craft, improve the approach to teaching it, and continue the natural science, in the hope that we can continue to uncover enlightening and useful results.
We need to become good at building such things, which is a challenging artistic and engineering performance. But we also need to understand what is actually going on, within us and outside of us, when we do it. This difficult question lies within the natural sciences, and we approach it because we need to assure ourselves and others that we're doing the right thing. Others may even try to automate aspects of the design and build process, and we need to demonstrate whether or not a particular approach is valid.
We want to build the right things. And we want to build things which are as harmonious as possible, supporting both human activity, and life in the rest of natural world.
Despite centuries of study within the natural sciences, we don't yet have a good understanding of any human ability. But there's at least one thing we have discovered: we are almost completely unaware of our own abilities. When we do become aware of some specific ability -- such as our ability to perceive natural structure -- it's a bit of a mental trick to stop studying the ability, for a moment, and explicitly use it. It's just as difficult to remember to ask others to stop introspecting and start using. Take 'advantage' of the ability starts to feel like a shortcut. But it's a critically necessary one.