Dear Mr. Harpaz,
thank you for your letter of April 17 regarding AM98029R. In response to it I should let you know that the material you enclose can not be sent out to referees.

No explanation why not.
What I can send out to referees is a re-revised version of your manuscript. Such a revised version should address the concerns raised by previous referees. I do not think that your comments accomplish this goal.
I think it is unlikely that he actually have read them.
I can also assure you that referree #1 is an eminent professional neurobiologist.
Most likely a lie. This referee showed ignorance not only of the stochastic connectivity, which may be just a pretension to reject the paper. He also gave as an example of synapses in the brain synapses in the spine (here, referee 1), and the superior colliculus as as an example of connectivity in the cortex (here).
If you were to allow me to offer a suggestion I would say that the referee in question seems to me much less hostile towards your paper than you think. My interpretation of his comments is that he would want you to rephrase your statements (admittedly several of them). He seems to say that the author (meaning yourself) claims that connections in the brain are stochastic. Further he seems to say that the author does not offer any evidence in favor of his claim but that is O.K. The author should simply refer to some previous work where such evidence is provided (meaning previous papers by experimentalists which should be included in the list of references). Failing this the author should simply state his claim as an assumption and proceed from there. If I may say so, what he proposes is standard practice when it comes to scientific papers.
Note that he didn't bother to refer at all to what I say in the first paragraph of the letter, and completely ignore my comments on the review.
As I said before I expect to receive your revised manuscript within 6 months. If I do not hear from you before then I will withdraw your paper and any later submission will be considered a new submission.
A.K. Moschovakis, M.D., Ph.D.
Professor of Physiology