Javascript yes, but PHP, no. It's too much of a security hole - anyone who got into a teacher account could potentially do a lot of damage to Moodle and the server it's running on.
There was some talk a while back about a new resource type called "PHP code" which WOULD parse the documents for PHP. I think this could be a good idea as long as it was an option controlled by the admin.
Teaching with Moodle
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