<p>I'm trying to run a shell command using the backtick operators, but the fact that the child process inherits php's open file descriptors is problematic.  Is there a way to keep this from happening?</p>

<p>I'm running PHP 5.1.2</p>

The only way I really know of is to have the children open up their own resources after forking.
There is a fairly decent tutorial on pcntl here:
http://www.hackingwithphp.com/16/0/0/miscellaneous-topics
http://www.hackingwithphp.com/16/1/4/duplication-of-resources-when-forking