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How do we know all these things? How do you know that when you cut a branch off a tree it doesn't hurt the tree -- only it can't express its pain because it can't move? (Or maybe it loves having its branches pruned.) How do you know that the muscle cells in your heart don't feel pain or excitement when you run up a flight of stairs? How do you know that a kleenex doesn't feel anything when you blow your nose into it?

[What does it all mean? Thomas Nagel]

What does the word "only" mean in the context?

I think it means "but". Is it correct?

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  • There's quite a significant "non-explicit assumption" being made in your cited context, to justify including contrastive / refutational only = but = except here. The implicit "assertion" being contradicted / qualified here is [perhaps] it "hurts" the tree when you cut off its branch, with the further implication that the tree "feels pain". BUT we cannot know if that's true, because the tree can't "move away" from the pruning saw to convey "fear" of "pain". May 28, 2020 at 14:00

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only serves as a conjunction in this sentence, linking together two clauses. If you look it up in the Cambridge Dictionary, there is only one meaning of only as a conjunction, defined thus:

used to show what is the single or main reason why something mentioned in the first part of the sentence cannot be performed or is not completely true

In your sentence, it is explaining why you cannot know whether the tree feels pain, though it's couched as a rhetorical question- one that you are not expected to answer- "How do you know".

but can also be used to explain why something cannot be performed, for example:

I went to the bakery to buy some baguettes, but they didn't have any left.

but can be used in a much wider range of situations, though. Here is the definition:

used to introduce an added statement, usually something that is different from what you have said before

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Yes, it's about the same as "but". It's easier to see if it's removed from the rhetorical question and negation "how do you know that it doesn't".
With a slight adjustment so that it's grammatical by itself, we have:

It hurts the tree, only/but it can't express its pain because it can't move.

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