I wanted to leave the question title as is so as not to take away from my amusement
What is raining? Is it the sky? The clouds? The weather? The rain? What is "it"? Any historical insights on the statement?
Definitions for it in my Webster's 3rd New International Dictionary include:
2a used as an expletive subject of an impersonal verb that expresses a simple condition or an action without implied reference to an agent about the weather ... or time.
It is raining or It is two o'clock are examples of 2a.
2b used as an expletive subject in other statements or questions having an undefined subject
If it hadn't been for your help, I couldn't have finished in time is an example of 2b.
3a used as an anticipatory subject of a verb whose logical subject is another word or phrase or clause
It is I who have the answer to the question is an example of 3a.
In some languages, a subject is always present in the sentence, even when conceptually there is no subject. English is one of them, as well as French ("il pleut" for "it's raining").
In other languages, like Portuguese for example, you don't use any word for the subject when it doesn't exist. We say "chove" (just the verb) for "it's raining".
Well, the short answer is that it does not matter. The widely accepted explanation is that the “it” in “it is raining” does not refer to anything.
If you are curious, the verb “rain” is sometimes used with a subject such as the sky and clouds. The Oxford English Dictionary (the link requires subscription) gives many examples of this usage from Old English to the twentieth century. One of them is:
1972 Nature 24 Mar. 139/1 The primary purpose of the experiments with seeding clouds was to increase the amount of rain from the clouds, or to cause them to rain if they would not otherwise have done so.
(Emphasis added on “cause them to rain.”)
Note that I am not implying that the “it” in “it is raining” actually refers to the clouds or the sky.
It isn't referring to anything specific. It's just a grammatical construct of English, which requires that sentences have a subject. Other languages like Latin or Japanese (known as pro-drop languages) don't require an explicit subject and omit the it. You can, for example, express the same meaning simply with "pluit" (Latin).
"It" doesn't refer to anything here. It's just a stand-in for the subject. "It" is the noun of the sentence, but it is not behaving as a traditional referent.
Standard English syntax requires a subject and a verb in each sentence, but some ideas become bogged down by this. To say for example, "The sky is raining," in English is obvious. However, English has evolved into very simple nouns and verbs (and all the rest). We don't deal in declensions anymore, and as our verb conjugation is comparatively very simple, it does sometimes lead to a few awkward structures.
In Spanish, we'd just say, "Está lloviendo." Verb + Gerund. The verb construction is third person singular and in that context just implies a state of being.
Or, in Latin, it would be "pluit", which can mean, "It rains" (habitual), "It is raining" (current action), or "It does rain" (emphatic). Alas, Latin is both awesome and at the same time terribly, terribly limiting.
Just musing ...
Suppose your child says "My friend Sally's dog died," and you reply, "Yes, it is sad." Who or what is being "sad"? Sally may be sad, but your comment isn't really about Sally. The dog isn't sad -- he's dead. (Or if dogs have immortal souls, maybe he's sad and maybe he isn't, but in either case that's not what you're trying to say.) Really you're saying that the fact that pets die is a thing that causes general sadness for humanity.
Or if a physics teacher asks, "Do you understand why photons cannot penetrate an opaque barrier?", a student might reply, "It is clear." What is "it"? Certainly the opaque barrier is not "clear". :-) Myabe the concept being discussed is clear. Maybe in this case you could say that "it" is "my understanding of the concept being discussed".
One could go on with other examples. My point is that in such sentences, "it" is a very amorphous word, I don't think you could pin down a single thing for it to refer to in any such sentence. Rather, the reader is supposed to intuit it from the context.
Thank you for your interest in this question.
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