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Every one of my lecturers have always called it this, as do I, despite the fact that I know its properly called 'tilde'. Does anyone have any clue where this convention comes from and why it might have became (somewhat) standard?

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    $\begingroup$ A mathematician may call ~ twiddle if his teacher did. Personally, I call it tilde because my earliest teacher did. $\endgroup$ Commented Nov 28, 2018 at 22:43
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    $\begingroup$ Tilde is from Spanish tildar (Latin titulus), a diacritic sign above some Spanish letters, twiddle is similar sounding and means wiggle, so it is a pretty apt name for it. $\endgroup$
    – Conifold
    Commented Nov 29, 2018 at 0:30

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I'm not convinced they are exactly the same, as a tilde is an accent mark over a letter, while a twiddle is a relationship operator sitting between letters (or numbers, or whatever).

But you might as well ask why an exclamation point is referred to as "bang" and as "splat" by various software (and math) people. And don't get me started on the ridiculous renaming of "poundsign" to "hashtag" . (Insert rant about misusing pound sign vs. number sign vs. musical sharp sign -- yes, they are not the same symbol)

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    $\begingroup$ I think that the question is exactly that why is it that the word "twiddle" is used for the diacritical mark "tilde" over a letter as in saying "ay twiddle" for $\tilde a$. It is possible that this usage is restricted to mathematics (as in the question). The fact that they are not the same is the underlying reason for the question. $\endgroup$ Commented Dec 4, 2018 at 6:07
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The OED gives a citation for the noun "twiddle" possibly meaning the tilde sign dating to 1894:

‘e’ for ‘æ’ is just as much a contraction as ‘r’ with a twiddle for ‘rum’.

This might or might not be a description of an "r" with a tilde, analogous to "u" with a tilde meaning "um" which I have seen in 16th century printed books.

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