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I'm trying to do an audio transcription (for fun—I'm a complete amateur at this) and struggling with how to punctuate this part.

Could anyone please help?

We've designed this around the functions of nature, so, at certain times, and it's very relevant we choose the right time—
    more timing, not just technique—
        strategy again coming in, another time element—
not when the rainfall is less than the evaporation—
    if the evaporation is very high at that time of year, you leave the shade—
        shade is better than mulch—
but when the rainfall is higher than the evaporation,
we can speed up this cycle.

I've put in em dashes (and indented the inner clauses) where they might belong, except that I'd be nesting them 2 or 3 levels deep, which I don't believe is allowed.

In general, what would you do if you had 3, 4, or even 5 or more nested layers of clauses?

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    You can use a mixture of dashes and parentheses. If I were a complete amateur, I'd start with a more cogent original. – Edwin Ashworth Sep 7 '14 at 11:18
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My primary suggestion is to break the transcript up into small paragraphs that accurately reflect moments when a speaker's train of thought breaks off, and the speaker launches into a syntactically unrelated sentence.

In the example you provide, it seems to me that such a break occurs after the first occurrence of the word evaporation: Even though the next words ("If the evaporation...") seem quite closely connected to the thought that the speaker has just expressed, I think that they represent the start of a new thought that is sufficiently different from what went before that they deserve a separate sentence, which I would punctuate as follows:

If the evaporation is very high at that time of year, you leave the shade—shade is better than mulch—but when the rainfall is higher than the evaporation, we can speed up this cycle.

That sounds like a fairly coherent sentence—and I think that it is one. Admittedly, in cutting off what precedes this sentence, in order to give it a fresh start, we leave the previous thought hanging. But that's okay because (I believe) that is precisely what the speaker did. I don't see any way to connect the opening words "We've designed this around the functions of nature, so, at certain times" to the concluding words "we can speed up this cycle" without doing grave violence to the coherence of (for example) the phrase "but when the rainfall is higher than the evaporation."

The problem is that we want to impose order (in the form of coherent nesting punctuation) on an extemporaneous statement that simply isn't coherent in that way. To be true to what the speaker actually said, and yet not render the coherent parts of the speaker's address incomprehensible, I think that you have to record the break point(s) in coherence as faithfully and as cleanly as possible.

I recommend doing this with ellipsis points and a paragraph break, for several reasons. First, ellipsis points are unlikely to be needed for any other purpose in the transcript, so readers can gradually come to recognize their consistent function in the transcript. Second, dedicating ellipsis points to this task allows me to reserve both em dashes and parentheses for use in nesting situations where I may need to use two levels of such punctuation, without suggesting breaks in coherence. Third, using the ellipsis points in conjunction with a paragraph break produces the visual effect of an idea trailing off, which is exactly appropriate in situations where the speaker has become tangled up in an increasingly complicated snarl of syntax. And fourth, as I noted before, the paragraph break is clean and decisive, which encourages the reader to take the ensuing sentence on its own terms, rather than trying to work out how it happens to have emerged from its predecessor.

Here, then, is how I would punctuate and present the sample audio transcript:

We've designed this around the functions of nature, so, at certain times (and it's very relevant we choose the right time: more timing, not just technique; strategy again coming in, another time element), not when the rainfall is less than the evaporation...

If the evaporation is very high at that time of year, you leave the shade—shade is better than mulch—but when the rainfall is higher than the evaporation, we can speed up this cycle.

Obviously, clues from the speaker's intonation and pace (especially pauses) on the recording can help you make sense of things that seem opaque in the raw transcript. But the crucial task is to frame the blocks of coherent thought in such a way that they are not rendered less intelligible by adjecent blocks of incomplete or incoherent thought.

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Your example nicely illustrates the difficulties of representing unrehearsed spoken language in written form. A simple answer might be: "there's no right or wrong way".

The approach you should take will depend on the purpose of the transcript. If you're transcribing to create a readable representation of what the speaker said, then you'll probably find that using a mixture of dashes, parentheses and ellipses should do the job:

We've designed this around the functions of nature, so, at certain times, and it's very relevant we choose the right time—more timing, not just technique… strategy again coming in, another time element—not when the rainfall is less than the evaporation—if the evaporation is very high at that time of year, you leave the shade (shade is better than mulch), but when the rainfall is higher than the evaporation, we can speed up this cycle.

If you're more interested in getting across the speaker's content and meaning, it might well be acceptable for you to edit (carefully!) the speech so that it reads more cleanly and concisely:

We've designed this around the functions of nature, so it's very relevant we choose the right time: if the evaporation is very high at that time of year, you leave the shade (shade is better than mulch) but when the rainfall is higher than the evaporation, we can speed up this cycle.

Of course, if you want to analyse the details of the exact words the speaker used, and the way in which s/he spoke, you would need to use one of the conventions developed by linguistics and social sciences researchers:

Speaker; […] We've designed this ((gestures)) around the functions of nature… so::: at certain times… and it's very relevant we choose the right time (1.0) more timing… not just technique… ((chuckles)) strategy again coming in… another time element (1.5) not when the rainfall is less than the evaporation… if the evaporation is very high at that time of year you leave the shade… shade is better than mulch… but when the rainfall is higher than the evaporation… we can speed up this cycle ((makes circling motion with hands))

Alessandro Duranti gives a brief run down of one transcription system, along with some references for deeper reading.

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