Our philosophers are fond of pointing out that the ceremony of the red heifer is above reason. Why would one person become tameh (unclean) and another person become tahor from the same object (the red heifer). However, this is the nature of the universe. Electrons are always being transferred from one atom to another, and one becomes possitive and one become negative. There is nothing irrational about it.

Aryeh Shore

I just saw an interesting article on the subject last week. heres the link : http://www.israelnationalnews.com/article.php3?id=5296
The Rabbi distributes an interesting troah thought weekly via email. He cna be reached (for joining or questions) at YYJacobson@aol.com.
I think footnote 4 is (somewhat) relevant to this disscussion.
Firstly it would be worth pointing out that this question wuould only follow the opinion of Rabbi Akiba (Yoma 14a) but not that of the Rabbi whom explain the enigma somewhat differantly.
I can however see some differance between the 2, ie. Red Heifer and Proton/electrons. For one the transfer between Proton and electron would be of equal quantity and just of differant quality (not knowing much about pyshics that really a wild guess) whereas in with the red heifer the transfered Tuma is not of the same strength of that od the original.
Secondly, and more importanly, why is the red heifer differant than any other temua where we dont find a proton/electron type transer of Tara/Tuma.

I think we have semantics problem here. The laws of tumeh are not logical. I could not derive such laws from first principles. Although R. Hirsh developed a system of degrees of death and tumeh, it is not a complete system. The question is it irrational? Nothing in the torah is irrational. We are not told that standing on ones head will cause the blood to flow to ones ears or that it is cold in Tamuz. (The importance of this is in polemics with the christieans as three can not equal 1 and 1 can not equal three.) Similarly in the Talmud we say that the Rabbis do not argue about reality. It is not irrational to say that tumeh can be transferred in two directions as this is what occurs in reality and it is part of the nature of universe. Time slowing down as one approaches the speed of light is illogical but not irrational.
Why the red heifer works two ways as opposed to other tumehs, I have not seen. But I think since the other case, the sending of the scapegoat where the sender also becomes tumeh would indicate that sacrifices brought outside the temple cause tumeh as one is lowering his level of kedushah. Similarly the Nazir brings a sin offering because he is lowering his level of kedushah (Arbarbanel).

Aryeh Shore