There's growing evidence that the difference involves the fibers that carry information from one part of the brain to another. Brain scans of people with autism show a lack of synchrony between different areas of the brain.
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The story about Autism research that has a breakthrough information by Western Psychiatric Institute at the University of Pittsburgh. It's astory about an Autistic man, Hudale, who has done for the past 25 years is help scientists understand autism by letting them study his brain. The research described in this article is a good start but that's all. It's a start.