I came across a N1 vocab list and came across 魂 with the reading as こん, and I had known that as たましい. I know is one is 'on' and one is 'kun', but if it's just by itself I was under the impression that it's read たましい.
Does anyone know definitively?
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2 Answers
It can be either, and if there are no furigana, there is no way to be 100% certain. However, certain tendencies can be identified.
If 魂 is used on its own with no special context, it will usually be たましい. But there are many situations where 魂 is used as "jargon" with a specific meaning. In these cases, using the pronunciation こん helps to distinguish the author's special use of 魂 from the general concept of たましい.
For example, if you Google around a bit you will see people discussing the duality of 霊 (れい) and 魂 (こん) [cf the word 霊魂, "soul"]. Or you can find 魂 (こん) vs 魄 (はく), a similar duality with Taoist overtones (this is the one cypher mentions in comments).
It is hard to know when a character uses 'on' or 'kun'. It is usually not distinguished by meaning. But usually in a word, the characters tend to use the same variation of reading. I even know a word that both reading are accepted 国境 can be read as both こっきょう(on) or くにざかい(kun), with no difference in meaning. (Can't find the article that discussed the problem of "国境" now)
One way to guess which variation should be used is: words originated in Japan usually use "kun", and words originated in China usually use "on". But that works only to those who are familiar with Chinese.
So you may have to remember the reading in individual words.
こんis used particularly in reference with Yang energy.