"I am alone, and miserable." How does this quote from Chapter 16 link to the theme of isolation?

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We see, in the novel, that isolation is bad for everyone, emotionally and sometimes physically, as well.  Captain Walton tells his sister in one of his earliest letters,

You may deem me romantic, my dear sister, but I bitterly feel the want of a friend.  I have no one near me, gentle yet courageous, possessed of a cultivated as well as of a capacious mind, whose tastes are like my own, to approve or amend my plans.  How would such a friend repair the faults of your poor brother!

Walton is sad that he lacks a friend to whom he might tell his plans, his hopes; he wishes that he had someone with whom to commiserate, who might share his passions and interests, who could help to improve him as a person.  He is lonely, and his loneliness causes him sorrow.  When his crew finds Victor on the ice, Walton believes that this man could have been the friend for which he's been hoping, but he's aware that Victor is not long for this world.

Likewise, Victor suffers from his lack of companionship when he's in Ingolstadt, working on his project.  He's been away from home for several years, and there is no one near him in whom he can confide or who can provide comfort and succor to him as he becomes more and more ill.  He says, "Every night I was oppressed by a slow fever, and I became nervous to a most painful degree; the fall of a leaf startled me, and I shunned my fellow creatures as if I had been guilty of a crime."  Finally, his best friend, Henry Clerval, arrives, and Victor credits him with nursing Victor back to health.  In order to recover, then, Victor required a friendly soul who cared for him.  Something similar happens later in the story when Victor's father comes to be with him in jail, after he's been accused of murdering Henry.

This actually seems to be one way to confirm the creature's humanity: he requires companionship, as does every other major character in the novel, in order to be healthy and happy.

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The first poster fully articulated the isolation of the monster in the novel, so I'll give you some other instances.

Victor's quest for ultimate knowledge leads to isolation from his family and friends. Indeed, he does not correspond with them for 6 years, devoting his entire life to the study of reanimation. He locks himself in his apartment, refusing to acknowledge those around him. This is similar to Walton's quest-another search for ultimate knowledge that necessitates self-imposed isolation. Both men come from stable childhood homes, with very loving and devoted parents. But their desire for scientific discovery leads them into their own alienation.

At the time this novel was written, Romantic poets were espousing the virtues of, essentially, being alone. The common theme was that nature would reveal secrets and truth if one existed in solitude. Yet Shelley inverts this, as in her novel isolation...

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leads only to despair.

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There are plenty instances, as one of the main themes in the story is isolation.

On Ch. 16, the complete sentence reads:

I am alone, and miserable; man will not associate with me; but one as deformed and horrible as myself would not deny herself to me. My companion must be of the same species, and have the same defects. This being you must create."

The monster had been wondering for a while, after realizing his isolation is not only from society, but from humanity. He is depressed because, like he says after inhabiting the cottage, and experiencing the beauty of women, not being able to do anything about it, and experiencing human emotion while trapped in the body of a monster:

I felt emotions of gentleness and pleasure, that had long appeared dead, revive within me. Half surprised by the novelty of these sensations, I allowed myself to be borne away by them; and, forgetting my solitude and deformity, dared to be happy. Soft tears again bedewed my cheeks, and I even raised my humid eyes with thankfulness towards the blessed sun which bestowed such joy upon me.

The realization of needing a partner, namely a female, shows the human need of connection, communication, and emotion. It also reveals his own capacity for it, and it shows the inner conflict of the poor monster who finds himself a lonely wanderer.

The story of Frankenstein begins with Walton, the explorer to whom the story was conveyed, who is-himself- isolated and lonely as he explores those faraway lands. He finds Victor who is, at that point, a lost man also as lonely and left by society as can be.  It is a series of lives touched by all forms of isolation not only from others, but from their sense of self.

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