Scientists say Alzheimer’s might not be a brain disease after all: The common theory that Alzheimer's disease is caused by the buildup of beta-amyloid plaques in the brain is now being challenged by a new theory. Scientists say Alzheimer's may be an autoimmune disease. This theory is based on 30 years of research. It suggests that beta-amyloid, rather than being an abnormal protein, is actually a component of the brain's immune system. Its role is to protect the brain from injury and infection,