Discuss three clues that Sherlock Holmes uses to solve the case.

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When Helen Stoner first visits Sherlock Holmes, she describes sounds that she has been hearing in the night:

during the last few nights I have always, about three in the morning, heard a low, clear whistle. . . .

and

As I opened my door I seemed to hear a low whistle, such as my sister described, and a few moments later a clanging sound, as if a mass of metal had fallen.

Holmes mentally files away this information and will retrieve it when he is staying at Stoke Manor during his active investigation.

In the same initial interview, Helen Stoner tells Holmes that, because of some renovations to Stoke Manor,

I have had to move into the chamber in which my sister died, and to sleep in the very bed in which she slept.

These are two clues that Holmes uses to determine that the death of Miss Stoner's sister was a murder. Holmes also deduces that these strange occurrences figure prominently in the imminent threat to Miss Stoner's life. The sounds are significant, as is the location of her new bedchamber, and Holmes recognizes that right away. He has only to determine the particulars.

When he arrives at Stoke Manor and begins inspecting Helen Stoner's quarters, he notices the nonfunctioning bell pull. He observes

that it is fastened to a hook just above where the little opening for the ventilator is.

He easily sees that it is used to create an opening in the room—an opening large enough for the snake to enter.

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I want to talk about four clues that seem important here.

First, you have the fact that Dr. Roylott has moved Miss Helen Stoner into the room that used to be her sister's room.  This suggests that there is something in particular about that room that helps him kill people.

Second, you have the fact that Roylott put the bell pull in without Julia asking for it.  Why would he do that if it did not have to do with her death?

Third, the bell pull is not attached to a bell -- just to a hook in the vent.

Last, the vent leads to the next room, not to the outside.  It would make more sense and be easier for a vent to hook up to the outdoors.

So the vent and bell pull are weird and they are put in this room where Roylott wants Helen to sleep.  Very suspicious.

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