Sometimes I just can't help myself.... Science has not just "[begun] to voyage into the real world more and more"; it began to do so at the very moment, figuratively speaking, when O-sensei withdrew from it.
O-sensei gave up the agronomic (in his terms, "scientific") life in the first half of 1938. He experienced his satori, described eloquently on p. 8 of TOSR, on May 15 of that year. His mind had been deeply shaken by several months of serious illness--pneumonia--during which he feared for his life. Because 1938 is the very moment in time when antibiotics were first being consciously and purposefully developed and used by scientists to combat previously fatal diseases and infections, O-sensei's pneumonia may or may not have been treated with antibiotics. He might have recovered as slowly as he did due to their absence, and his recovery *at all* may have been due to being basically a healthy man in his 20s. Pneumonia still kills people, even when it's not an antibiotic-resistant strain. It can weaken a person for months afterward, even today.
In this weakened physical condition, and possible state of depression, F-san forsook his position at the governmental department. I believe he left the field of science and its methods, viewpoint, and all else just when the trajectory of science began to diverge, however slowly, from its 19th-century carapace.
The non-linear possibilities of quantum physics were being developed in the late '20s and the '30s, first in Germany and then in the intellectual Diaspora after Jewish scientists fled the country in the face of anti-Jewish policy and laws. The Paradox of SchrÃƒÂ¶dinger's Cat ( https://en.wikipedia.org/wiki/SchrÃƒÂ¶dinger's_cat ) was presented in Austria in 1935 and discussed internationally among physicists and mathematicians. This "thought experiment" had *no* single solution.
A scientific experiment with *no* single solution was controversial when it first appeared, and many people, to this day, still refuse to try and wrap their brains around the possibility. It was--and is--very unsettling to them. It wasn't black-and-white; it was...something else.
Yet many situations in daily life and, of course, in growing plants present paradoxes, and we wave them off with remarks like, "Well, yes, but without X, the system will be unbalanced." The paradox is dismissed with a mere sentence, leaving only newcomers to shake their heads in puzzlement.
(Here I have in mind leaving plant-destroying insects around so that predator insects will be enticed to stay. This takes a little getting used to for gardeners/growers new to non-chemical methods, and is a difficult paradox for them.)
F-san himself, in the Second Principle of Natural Farming, says "no compost," yet he himself applied prepared compost to his kitchen garden (note on p. 28 ). Another paradox.
Science today has become much more self-aware than it was in the '30s, when O-sensei resigned his agricultural position. The authors of major reports include, in those reports, as much disclosure as possible about the observer effect as they can and immerse themselves in conditions as close to those of their subjects as possible, realizing that there is no such thing as a completely separate observer of a living system and wanting to experience the process of what our ancestors made/underwent themselves. (Here I have in mind the author of "When the Sea Saved Humanity" https://www.helpfulgardener.com/forum/viewtopic.php?p=152922 and Prof. Elizabeth Wayland Barber's work in prehistoric textiles; https://press.princeton.edu/titles/4816.html .)
So O-sensei withdrew from the outside world at a critical juncture. We have benefited from his insights, but perhaps those insights and principles would have reached more people much sooner had he not been so isolated. The thirty years he glosses over with a page turn might not have been so painful if he had still received some respect and acknowledgement from the outside world. There have always been a few who will listen to those in advance of their time; it's a shame that his "time" seems to have been so delayed due to his withdrawal from the outer, "scientific," world.