One quirk that learners of Japanese get to see pretty early in their studies involves the verb 入る. How should we read this word? The default reading is supposed to be はいる - but then we have derived words such as 入り口 (entrance), which is read いりぐち. What happened to the initial は?
The reason for this apparent irregularity is that はいる and いる were originally two different words. First there was いる, "to enter", which was then used as an element in the verb はいる, which also means "to enter" but originally put more emphasis on the motion or change from the outside to the inside.
Unlike the current confusing practice, though, in the past the two verbs used to be written differently - and the older spelling of はいる makes it easy to distinguish from いる whenever you see it in the text you're reading.
Here's an example from Natsume Soseki's story, Empire Day, which is featured in Reajer book 12 (read the free samples on Amazon and iBooks):
This sentence says that the teacher entered from the hallway (into the classroom, as the complete passage shows). But look at 這入って. Yes, that's the te-form of はいる. Why is it written like this?
It is generally thought that はいる comes from the combination of はう (這う) "to crawl" and いる (入る) "to enter" - giving the sense of "crawling into" a place (which may have had a humble connotation at one time). This was originally はいいる, and later shortened to はいる.
So basically, whenever you see 這入る in a text, it's はいる. Unfortunately, in the later standardized language, someone decided to "simplify" the situation by writing both はいる and いる in exactly the same way - 入る. It does make sense in that these two verbs share a single meaning that is neatly represented by the kanji 入. But it also means we have to develop an intuition for deciding which reading should be used where. This is one problem we usually don't have when we read the good old books of Japanese literature.
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