By default, the Beaglebone Black with Debian as of this writing doesn’t have packages like
python-scipy in the repositories.
This is simple to fix by enabling the “backports” repo as follows.
On the Beaglebone
/etc/apt/sources.listuncomment the line
deb http://ftp.debian.org/debian wheezy-backports main contrib non-free
on the Beaglebone
and then you may find the packages you wanted.
Note: Some of the Python packages might be of versions older than you’d like (e.g. Scipy 0.10).
pip install --update scipy
may help those particular cases.