Last I blogged I mentioned that building an ontology on top of scientific models currently strikes me as a bad idea. Here's why.
A rough outline of what ontology is is the study or question of that which exists. It includes exploring the meaning of "Being", "Essence", and questions such as "How can anything exist at all?", "How do you know if something exists?", the existence of God, or universal laws, or questions which reflect upon the meaning and nature of time and matter. I wrote this in order of seeming increasing relevance to scientific questions to give the impression as to why it is one might seek the answers to the questions of ontology in scientific investigations. Surely, scientific investigations use concepts of matter, time, natural law, and attempts to elucidate the mechanism and relation between all that is posited as is to give a cohesive picture of existence. There is an attendant epistemology, and supposedly, there isn't a reference to ethics outside of the confines of this epistemology (things like "Don't fake data", etc.)
What is posited as is, in science, is posited as is not on the basis of asking what is, but on the basis
of asking a general research question. This research question is formulated on the information already present from previous generations scientific careers. The information generated previously was generated not to find what is (usually), but to also answer questions that seemed relevant on the basis of what was passed onto that scientific generation. In short, science progresses towards seemingly relevant research questions generated upon data that was generated on previous research questions. This process can be directed towards other things than asking what is, especially given that one's career depends upon their publications, and the citations to these publications. This process of information generation seems to be predominantly directed towards economic benefit for those who are able to invest, military applications, and the health of those who are able to afford care. So, the process of science, current science, whilst I won't deny the position of scientific realism, isn't trying to answer questions one would prima facie think belongs to a scientific realist's set of questions -- instead, a good demarcating point for scientific knowledge is the knowledge which assists in humanities power over nature, and due to our economic situation, this power of humanity over nature becomes the power of the rich over that which isn't rich.
I will note that this isn't a necessary evil. It just makes science non-ontological, at least in the sense where one attempts to answer ontological questions primarily. Since science doesn't usually answer ontological questions, it follows from this that referencing science in answering ontological questions can be faultier than one might first assume.
Another good reason to not mix these two disciplines is that if one were to mix ontological questions with the scientific enterprise, the scientific enterprise would likely come to a halt -- if one runs a quick probability calculus on the history of ontological questions, one could easily conclude that it is highly probable that ontological questions are insoluble. Based upon this, we wouldn't even want to build an ontology on science for the fear that science wouldn't operate, at least if it is the case that we want science to operate as most people who build ontology on science do. Instead, science assumes an ontology (A formal, universal ontology based in the concept of "energy", and thereby an ill-defined sort of physicalism, upon which general principles of other disciplines that are supposedly "smaller" are loosely attached to), and then gets to work attempting to describe the universe with that ontology, as well as with a ever-morphing epistemology. I can't stress enough that these are good things for the scientific enterprise, so long as the scientific enterprise continues to value producing knowledge which generates support from governments and industry.
Approaching science from the questions of ontology, one realizes that science isn't the "objective" viewpoint that ontology looks for, as is often thought. It's an approach to ontological questions that tends to beg the ontological questions with a rough rational-empirical epistemology of some kind (and even this varies with the discipline, the scientist, and with history). If one is not a scientist but wishes to build a scientific ontology, then one will often employ a half-hearted Popper reference. Science seems to operate underneath a value-set, in the same way that Popper's Scientific Logic operates underneath a value-set, and proclaims this value-set as a methodology to mask the fact that it is, indeed, a value-set. Now, I have no problem with mixing my epistemology with my values -- but I'll mention that my value-set doesn't include falsifiability, numerical accuracy, and prediction-of-outcomes as prime. There likely somewhere down the line, but my prime values include compassion and equality far before what experimental parameters supposedly require, and it would do so whether or not the current psychological theory proclaimed that this should be so.
This leads into my final point on why I, on a personal level, have stopped attempting to build an ontology on top of science: politics. While this process is more self-correcting in my view, the scientific enterprise would mirror some religious power structures in an uncomfortable way the moment that science starts proclaiming ontological truth to individuals not trained in the abstract difficulties of scientific knowledge. It seems to me that a better approach is to relegate science as an epistemic approach to solving abstract puzzles related to power-over-nature, an end that is valuable unto itself, but not valuable as ontological constructs -- at least, not as ontological constructs to anyone outside of the scientific community. If one is able to retort to a scientific argument, then I don't have a political problem with a scientific approach to ontological questions. However (and note that this is with good reason -- the problem isn't with the scientific enterprise, only with mixing science and ontology) the majority of the population can't reject scientific claims because they lack the background. Any structure that can proclaim uncriticized truth (to those who aren't in the community) is just asking to become a political structure. This would likely destroy the scientific enterprise.
Seeing as I don't want science to become a political entity, and seeing that both ontology and science seem to mutually destruct one another, it seems wise to me to perhaps allow each to inform the other, but to keep them separate in some sense... I'm not sure exactly how to succeed in doing that, however. Science jumps out as a source of answers to some pretty basic ontological questions, and it answers these in a pretty successful manner. I just don't think importing this ontology to ontology, or other areas of life, academic and otherwise, seems to be pertinent at all -- science doesn't have a general epistemic approach (unless one wishes to interpret it teleologically), and it really only deals with pre-defined description problems that themselves are highly oriented towards control over nature. Honestly, this has about zilch to do with what's important in life, excepting the fact that scientific exploration is interesting unto itself for some people and therefore important to some lives.