According to some philosophers and scientists science does not explain anything at all, it gives a description of reality. Much like a recipe for an apple-pie. The recipe does not tell you anything about the sensation of eating the apple-pie or the taste of it. It only gives one description out of many of how you could make it.
There are still a lot of things that we cannot describe in a scientific way. Of many of these things we are totally unaware. Of some of it we are aware, but we find it hard to find words for it.
That is were poetry, metaphor, myths and stories come in. They have value to us in many different ways and can give us at times more comfort then science.
Being connected to nature is an important aspect of most budo. To me, living in the forests, this means in a very practical sense being aware of all the things that are happening in these forests, in other words being aware of the structure and the connectedness of everything.
I am surprised that your uni friend separates teaching Aikido from his understanding of how nature works? Combining these are for me the challenge.
I know what you're saying but in a sense the hard sciences explain lots of things, e.g. how planes stay up in the air, what's going on in the ecosystems of the forests where you live, or the mountains where I live, and ecosystems (and planes) are very much about structure and connectedness for sure. However, whether these explanations encompass values and meaning as well as matters of fact is one of the big areas of philosophical contention. I'm not sure what I think about that stuff as I try to avoid doing that sort of philosophy these days, it makes my head hurt
I'm loathe to speak for my friend about this stuff as he does that sort of philosophy on a daily basis but I suspect he'd say that his approach to aikido is entirely congruent with his understanding of how nature works, since he's a metaphysical naturalist, but then he'd probably get into a long discussion about what exactly we think we mean by nature.
In this I go along with him - I don't hold with supernatural stuff, be that deities, ghosts, souls, etc. so to that extent we agree with Matthew's OP. Where I differ is that I don't see why ki/chi shouldn't be useful shorthand. I guess what I think of as ki/chi is pretty much synonymous with IS/IP, the choice of terms is a matter of tradition (I prefer "shomen-uchi" to "overhead strike to head" for the same reason). Visualising my breath going down to my hara and coming up from there is useful, and interesting, and effective, even though I know it stops at my lungs and the effects are probably to do with relaxation, increased oxygen uptake, meditative effects from concentrated focus, etc. not the permeation of a mysterious universal force through ever expanding and diminishing concentric circles or something.