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I don't like your analogy. We understand the physics of falling pretty well. We do not understand the chemistry of this reaction.
Maybe "the glass fell because of humans". Did they push it off a table? Drop it? Place it inn the counter wrong?
Edit: let me put it this way - the water could turn orange without a melting permafrost right? So while the change in this instance may be triggered by melting permafrost it is not a necessary condition. The cause is something more necessary.
What makes your think that we do not understand the chemistry here?
Where do we start the "x is caused by y"? The way it actually happened? Then melting permafrost is indeed the first step. If you want to go by how we ended up perceiving it, then you need to start, for example, at how the brown color came to be. Then where that came from. Then what caused it to be made. Etc.
There's definitely a long chain of events that led to these rivers turning orange.
It would be unsatisfying to say "the universe coming into existence caused it". You need to pick a level to stop at. You're satisfied with "melting permafrost causes water to turn orange" but I think it's very reasonable to step a level down. The title is accurate in that regard. The people complaining seem to want the article to be more political.
BTW this discussion reminds me of when Feynman was asked about magnetism.
https://youtu.be/MO0r930Sn_8?si=k45lFqc0729QQHjX