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This is something that has always bugged me. I am never sure where to place the question mark, or whether to place it at all when the end of the sentence does not finish with a question, or a number of questions from the begining

For example:

The question nagging me is to what extent can we encapsulate all what we observe in nature into a set of simple computational rules, within which we can leverage our existing knowledge.

Should the final full-stop (period) be replaced by a question mark? Or perhaps even the comma?

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    In this case, replace "can we" with "we can" and you're golden. Generally speaking, you can always rephrase an embedded question into its less questiony form.
    – Jon Purdy
    Commented Nov 12, 2010 at 7:26

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A question within a sentence should be preceded by a comma, and end with a question mark.

I am wondering, how long has that fish statue been there?

There are three important issues that this committee must address. What was the chairman doing in that YouTube video? is not among them.

If a question is particularly long or complex, then for clarity it could begin with a capital letter.

In the daydreams of my youth I would look at the clouds and wonder, Will I find happiness and fulfillment soon after getting a business administration degree, or must I amortize my well-being return on investment over the next seven to ten calendar years?

The sentence in the original question ends with a subordinate clause that does not, by itself, ask a question (“within which we can leverage our existing knowledge”). This is modifying a noun phrase that is part of the question (“set of simple computational rules”). Therefore, this subordinate clause is part of the original question, and should end with a question mark.

Putting all of this together, I would punctuate the sentence like this:

The question nagging me is, To what extent can we encapsulate all what we observe in nature into a set of simple computational rules, within which we can leverage our existing knowledge?

(Some of this advice is based on The Chicago Manual of Style 15th Edition §6.55 and §6.71.)

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    Is that second quoted example ("There are three ...") actually correct? Doesn't a question mark end a sentence? If so, shouldn't the "is" be capitalised? Maybe it'd be easier on my brain if it was in quote marks, which would probably work in work that example, but not all examples..
    – naught101
    Commented Jul 14, 2013 at 21:37
  • @naught101 - That example appears as I intended, and I believe it is correct, though uncommon. There are similar examples in the cited sections of the CMOS, and I have also noticed it a few times in the wild. I do think it likely that most people would surround a question like that with quotation marks, since a mid-sentence question mark is rarely taught or used. But I also think that the bare form is often better, and I personally prefer the example sentence as it appears (for whatever that's worth). Quotation marks would make it—to me—incorrectly emphasize the form of the specific question.
    – Jeffrey L Whitledge
    Commented Jul 15, 2013 at 0:54
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You could have a question mark at the end of your sentence... if it were an interrogative one.
But I find it rather descriptive, and not so much a request for information.

However, with other punctuations, you could make it more like a dialog, in which a question would more naturally be presented:

The question nagging me is: "to what extent can we encapsulate all what we observe in nature into a set of simple computational rules, within which we can leverage our existing knowledge?"

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    I would say that the quotation marks are not really necessary. The key here is the colon, I think it is enough to justify the question mark.
    – RegDwigнt
    Commented Nov 12, 2010 at 11:27
  • @RegDwight: I agree. I added them for emphasis.
    – VonC
    Commented Nov 12, 2010 at 11:59

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