There are three generations of "they will become one in My hand."
The first generation is E and J, the Tree of Life. Which is on top, E or J? J is on top.
The second generation is D and P, the rabbinical part of Torah, an approximation of the Tree of Knowledge. This part is Pagum, and must be repaired. Which is on top, D or P? Due to the Mishnah and the Talmud, P is on top.
The third generation is the completion of the Tree of Knowledge. It has Science on one hand, and Torat HaMoshiach on the other. Torat HaMoshiach has three phases, starting with the Kabbala of Arizal/Rashbi, and the Kabbala of the GR"A/Ramchal. In the last phase, it will incorporate Science. Which will be on top? Torat HaMoshiach will be on top.
However, the "cycle" is kind of closed, as Torat HaMoshiach is also akin to the universal aspects of E and D.
