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According to rule No. 4 in this link, the suffix "-ist" does not affect the stress of a word. Hence the stress assignment rule σ → [+stress] / ___ ((˘) σ) ]word should apply to both words. What makes them different from each other?

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    "Economy" should be counted in as well. – user7065687 Jun 18 '16 at 11:28
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Taking economy into account as well, I think the problem doesn't come from the economist, but from economics:

economy has stress on the second syllable.
economist has stress on the second syllable too - hence, adding the suffix -ist doesn't change stress, like the site suggests.
economics has stress on the third (second-to-last) syllable and is thus different. I assume this comes from the suffix -ics; this suffix is not listed on the site, but -ic is and my guess would be that -ics behaves just the same, changing stress from the the second syllable to syllable before the suffix (i.e. -no-).

Therefore, the difference in stress between economy, economist and economics arises regularly due to the suffix -ics in economics, while -ist in econonomist preservers stress and is thereby equally stressed as economy.

This reasoning obviously presupposes economy as the underlying form from which we judge changes in stress. If we took e.g. economics as underlying, then things would indeed look different. But it seems just more reasonable to me to assume the semantically more "basic" economy as underlying and the other forms as derived.
Actually, to be precise, we should anyway start from the root (as econom-y has already undergone derivation and we can not just add a suffix, but most remove -y and then replace it by -ist or ics), and in the root econom- (if this is pronouncable at all - I assume you would find it nowhere free, I think this morpheme has the morphological status of a confix - a lexical morpheme which does not occur free but does not serve as an affix but clearly as a root, also e.g. fanat- in fanat-ic, so one can probably only judge the "standard" pronounciation intuitively and not from an underived form as such an underived form doesn't occur freely for such confix morphemes), stress should be on the second syllable as well - so neither econom-y nor econom-ist differ in stress from the root, like we would expect, while econom-ics does, like we would expect as well.
Under this assumption the stress behaviour fits well with the site's claims.

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    Actually when you point out -ics the first word I thought of was politics. But then I searched for a few words with the suffix -ics, they are indeed stressed on the syllable before the suffix. Your reasoning seems otherwise persuasive, but is politics an exception to the suffix -ics? – user7065687 Jun 18 '16 at 11:59
  • Good point - I don't have a good explanation for the moment why politics behaves differently. Maybe the total number of syllables play a role? (politics has only two syllables before the suffix while economics has three.) I would need to take a look at more examples. Damn, I really thought my explanation worked ;) – lemontree Jun 18 '16 at 12:01
  • It almost works for me :P This list should suffice. – user7065687 Jun 18 '16 at 12:06
  • Thanks, I was just about to start searching through a corpus for words with -ics, but this list seems perfect. (Except for really only looking for the ending -ics disregarding its morphological status and therfore also listing e.g. chics or comics, but most of the words on the list fit what we need.) By quickly skimming that list I found absolutly no word mathing this pattern that would NOT be stressed on the second-to-last syllable, so it seems to me that pollitics is really an exception. Maybe stress has changed since this word is so often used? – lemontree Jun 18 '16 at 12:14
  • Here is a post discussing exactly our problem. It seems like politics is not the only exception, but one out of just a few. If I understand the given expanation correclty, those words differ from the usual pattern due to very specific conditions, so I would think the behaviour described on the site and in my explanation can be regarded as a general rule, from which some words might differ under very special conditions. Not that satisfactory, I admit, but I hope that those are really just special cases. – lemontree Jun 18 '16 at 12:24
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Peter Roach's fourth edition of English Phonetics and Phonology: A Practical course (2009) has a more detailed list of rules and explanations than your link, if you're interested (Chapter 11: Complex Word Stress).

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