They were using Claire as a "Control" subject.
Imagine a pharmecutical company testing the effectiveness of a new pain reliever. They have 100 test subjects total and they give 50 of them the new pill. The other 50 are the Control subjects and they get a placebo. Then the company can confirm that any improvent in the actual subjects not shown in the control group is due to the new pill and not due to other factors.
Regarding Rousseau, either she conceived Alex before coming to the island, or she has the same "understanding" with the Island that Locke does. It's certainly an easy way out for the writers if necessary.
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Building an artificial intelligence that appreciates Mozart is easy. Building an A.I. that appreciates a theme restaurant is the real challenge - Kit Roebuck - Nine Planets Without Intelligent Life
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