Sounds, meanings, kanji (元・本, gen/hon/moto).

Last night in 日本語の授業 we were going through the section 「相槌とフィラー」 from the とびら textbook, about the various conversational sounds and phrases that demonstrate that the listener is engaged and paying attention, or that express surprise, disbelief, etc. The phrase 自然 ("natural") kept coming up, as in 自然に話せるため。。。。 So I've been thinking about "shizen", and in particular about the kanji 然, "zen". Together, the kanji equate to something like "self-like", so that makes sense as "natural" and is reminiscent of many combinations with 元 and 本 (GEN, HON, moto, and other phonetically related kanji) that seem to imply "getting at the root" of something, or basic/original truth. 例えば。。。。

元気 genki, "original spirit" (health, vitality, etc.)
元素 genso, a chemical element (in which both kanji have meanings of origin)
元治 genji, origin
元手 gende, motode, capital, the basic funding one starts with

元日・元旦 genjitsu (gennichi)/gentan, New Year's Day
元年 gennen, first year of a reign
元来（に）・元は genrai (ni), moto ha, primarily, originally
元祖 genso, founder or originator ("root parent"? 租 also carries the kun'yomi おや, like 親さん)
本意・本音, hon'i/honne, one's true motive or intent
本気 honki, seriousness or truth
本家 main family, birthplace, originator
本土 hondo, one's home country
本部 honbu, headquarters
本義 hongi, true meaning
本字 honji, original (unsimplified) kanji
本当・ 本當・ 本真 honto(u)/honto(u)/honma, truth or reality
本館 honkan, main building
本質 honshitsu, essential nature
本心 honshin, one's true feelings
本体 hontai, substance or real form
基・素・ moto, origin, source, basis, foundation, cause
元々・本々 motomoto/motomoto, originally, by its nature

Etc., etc. I'm sure some of these are used much more frequently than others, but they're all worth considering. This is a part of Japanese that I really enjoy: the often imperfect fit between phonetics (kun'yomi & on'yomi) and semantics. It seems that when kanji traveled to Japan and began to "take root", the Chinese "HON" and "GEN" sounds, associated with roots and origins, mingled with indigenous Japanese "moto", resulting in a kind of instability in both sounds and kanji (eg, gende/motode; 本々・元々). I guess the only way to navigate it all is to immerse and listen to people's usage.

(Perhaps coincidentally, that's also my favorite part of the legal system: laws as written almost never exactly fit the situation in question, so the legal system exists to resolve the discrepancies as far as possible and decide on a plan.)