I just had a look at this theme. thehealthyskeptic, study your theme more closely. What do you see in index.php? I see this at the top …
<?php if(is_single() || is_page()) { // Single entries and pages ?>
<-------code------------->
<?php } else { ?>
<?php include(TEMPLATEPATH.'/loop.php'); ?>
<-----more code-------->
What does that say? It says if we are on single.php or page.php DO THIS. In this case THIS being the_content
otherwise (ELSE) call <?php include(TEMPLATEPATH.'/loop.php'); ?>
The changes you want to make are in loop.php