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The AMNH has already a long history in graduate level education through its join programs with Columbia University, NYU, CUNY and Cornell University. Many courses are already taught right in situ by the Museum's curators, and the students enjoy use of the various resources for their research (besides the collections, there are molecular laboratories, digital imaging with a SEM facility, and the fastest computer clusters for phylogenetic analysis ever assemble, just to name a few). However, further governing autonomy will surely create a more cohesive atmosphere and save a few headaches to its students. Nevertheless, as far as I know, the AMNH will keep its join programs with the universities.
This post was prompted by the launching of the new Ph.D. program website. The application deadline is December 28, 2007. I highly recommend anyone interested to contact some of the curators and apply for this or subsequent academic years.