Mechanical Philosophy and The Nature of Order
Noam Chomsky writes often that the mechanical philosophy of the 17th century, i.e. "the universe as clock", i.e. "contact mechanics", obviously influenced by clocks and automata and strides in industrial technology, inspired late renaissance science, but was destroyed around the end of the 17th century by Newton. He could not find a mechanical explanation for the forces of gravity, and we have not bettered him to this day. Beyond describing the mathematical laws -- which gravity, for some reason, obeys -- Newton says he would "frame no hypothesis". He didn't want to invent anything or idly speculate. This means that mechanical explanations, perhaps among the most natural for humans, are insufficient to explain the underpinnings of the world. Any first year physics student learns this today. Our modern models are like Newton's laws of gravity: mathematical and abstract when we cannot even begin to model the underlying mechanism.
Christopher Alexander has gone to great effort to uncover a geometry, a morphology, a developmental pattern of life (as a technical term he introduces) -- this is explained, to his current level of research, within the book The Nature of Order. This book does not use a mechanical worldview, nor a mechanical criteria for intelligibility and explanation. It is 'natural', but it's not the naturalness of the human mechanical view, which is innate and easy to understand, but ultimately wrong. Alexander presents a harder-at-first-to-grasp natural criteria for the quality of life, but one which, with training, it is possible to get agreement on in brand new cases ... which means that it is objective to humans, and so taps something innate within us. I say "innate" and not "genetically determined" because it's unclear what the role of genetics is in Alexander's perception of this quality of life. Chomsky would say that these qualities are just as likely to come from a "third factor", i.e. laws of nature, and possibly unknown laws. That is, the coherence that Alexander describes might be something that natural law, rather than genetics, determines for the organism.
But of course, we don't know where human 'life-recognition' abilities lie. They may be partly or mostly epigenetic; they may not be. This is a scientific question, once Alexander's qualities of life are well-enough understood to pose specific, partial experiments to determine where in the human organism these perceptions might originate. It is a very difficult project, well beyond current frontiers of research. But it will be import to consider these qualities in human biological and cognitive simulations in the future, and I have a feeling that, if one considers these to be born of 'third factors', they could change the structure of human simulations, of the hypothesized computational abstraction of the human machine, so that Alexander's unfolding mechanism, and structure-preserving operations, may be central.