[retroflexzy]

A nice segue into a key point about Linguistics, and some Japanese facts.

The study of Linguistics, explicitly, does not deal with orthography, or the written system of languages. There are of course exceptions with good reasons, but orthography systems are rarely, if ever, good representations of the systems of auditory communication that are formally considered languages. An orthography system can be heavily influenced by geopolitics (Chinese), have severe ambiguities (Arabic, the various Latin alphabet systems), or have been created retroactively (many languages of indigenous peoples). While it is convenient to map a spoken language to its related orthography when discussing topics such as syllables, inflection, and morphology, it is rarely appropriate when studying linguistics formally.

As for Japanese, while it is true that its alphabet system has a relatively straightforward mapping to its phonology, the mapping itself is, unfortunately, not unambiguous. Japanese has a tonal system[1] that is not explicit in its orthography. There are examples of phonemically distinct words that are identical when written in hiragana/katakana.

Finally, there exists a moraic system[2] which sits between the phonemic and syllabic abstractions. Japanese, especially, have many phenomenons that cannot be adequately modelled unless working in this in-between system.

[1]: http://en.wikipedia.org/wiki/Japanese_pitch_accent

[2]: http://en.wikipedia.org/wiki/Mora_%28linguistics%29