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The phrase "differ fundamentally" is correct and usable in written English.
You can use this phrase when you want to emphasize that two things or ideas are not the same in a fundamental or essential way. For example, "The two theories differ fundamentally in the way they explain the origin of the universe."
Exact(60)
Mr. MacIntyre claims that different schools of philosophy must differ fundamentally about what counts as a rational way to settle intellectual differences.
For cigarette combustion, smouldering and puffing differ fundamentally and are known to produce smoke of quite different compositions [ 1].
These cases differ fundamentally from Singh's.
Catalytic mechanisms differ fundamentally from catalytic events.
Collaboration networks also differ fundamentally in their form of governance.
The metabolomes of plants differ fundamentally from those of animals.
But on the best way to achieve this they differ fundamentally, and, probably, irreconcilably.
Waseem said of Mazher: "We differ fundamentally in our interpretations of what the media is for.
In addition, the two sides distrust each other deeply, and their negotiating styles differ fundamentally.
It was shown that pneumatic or pressurized tube structures differ fundamentally from conventional metal structures.
The pleurodiran and cryptodiran turtles differ fundamentally in lower jaw architecture and musculature.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com