(First a correction: By the parentheses absorbing commas I really meant that they /include/ them. The verb "absorb" was a poor word choice given that I used it a bit differently elsewhere in that same email.)

All of which may be ignored by people with mathematical or programming
training! One of the advantages of the demise of copy-editors in
scholarly publishing is that there's no longer anybody to interfere
with one's logical punctuation.
Yeah! Some of them seem to believe in the wrong traditions, such as inverting commas and periods that belong after closing quotation marks. but then, whenever I try to convince people of the advantages of {directional commas} or constituency indicators, I encounter lack of appreciation ،if not funny looks,。

But there is a different type of copyediting that is useful. Document-internal consistency (wrt spelling, citation formatting – too many aspects to enumerate here) is something that authors that are not semantically minded might not be good at, if they pay attention to it in the first place. If the content is valuable, it's annoying to learn it from a poorly copyedited/typeset book.

But as in many cases where neither option seems quite right, there's a
third option that's better than either. Had you marked the parenthesis
with commas instead of parens, as would be usual in non-technical
writing, there would be no problem.
Parentheses have a different feel (I was gonna write "semantics", but it's also a pragmatics issue), but in this case the difference is small indeed.

A different reason is that I often find too many commas confusing; using different symbols makes for easier parsing. (Overloading of symbols leads to ambiguity; this needn't be literal ambiguity but can be garden-path ambiguity. Perhaps that's why I prefer to have a variety of symbols.)

I wondered how familiar I was, and couldn't come up with an example!
Do you have a real-life example? (In non-technical English rather than
Englished mathematics.)
I think everyone has had the experience of enumerating items in some – often meaningful – order and ending up with a list like "a, b, (c,) d, and e". Let's see ... say we're enumerating the languages of a geographical region in alphabetical order. Oh, wait, every country and organization has different definitions of what's an {"official", "co-official", "working", "recognized", "regional", "minority", etc} language, and do we include recent immigrant languages with a home traditionally considered to be elsewhere? A simpler example is if someone asks me who's attending some party I'm organizing. Perhaps I would like to list
    John, Bill, Mary, (me,) Rob, and Amy ,
just because that's what's naturally coming out of my mouth. I could italicize "me" or rephrase or add an explanation. But the point is that the punctuation symbols that are normally available for a certain purpose and that I want to instinctively use in their usual meaning in a particular place might be blocked only due to a de-facto orthographic constraint.

Stephan

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