What do most scientists think causes Bovine Spongiform Encephalopathy (Mad Cow Disease) ?

Most scientists believe that it is caused by an abnormal protein in brain tissue, called a prion, that can cause fatal disease when eaten.

Additionally, these types of proteins, as mentioned above, are caused by mutations in its actual production. Because all proteins have a specific shape, if one protein's shape is damaged in some way, then they will not be able to fulfill their purpose. In this case, the brain disease you mentioned has mutated and malformed proteins that are normally found to begin near the blood vessels in the neck.