Pruning has been the subject of hundreds of studies for 2 centuries.  In spite of some people saying that the branch collar should not be cut, the recommendations have been to cut branches as close as possible to the joining stem - a flush cut-and then paint the wound with some material to prevent rot.  Although this has been the recommendation, many people did not follow it because they felt that the "shoulder wood," or "heal collar" should not be injured and removed.  Many people over the last 50 years, at least, have questioned the benefits of wound dressing.

When the hand saw was the major tool for pruning, most cuts were proper.  It was much faster and took less work to cut the branch at its smallest point, which was the position where the branch met the branch collar.  The real troubles started when small power saws were used for pruning.  The raised ridge within the branch crotch just made a natural fit for the powerful saws.  But, this was good, they thought, because now the old recommendations were being followed.  And, the flush cut did stimulate rapid growth of callus that "healed" the wound.  So, all this was thought to be good.  Of course, we know that it was anything but good.

Flush cuts and cuts that leave stubs are major starting points for many tree problems: discolored wood, decayed wood, cavities, resin pockets that do not accept preservatives in wood products, circumferential cracks (ring shakes), radial cracks and seams (frost and sun cracks), wetwood, a host of different cankers, energy depletion about the wound that invites insects, and dead strips on the trunk that may continue downward to roots.  This information is not new to many people who have worked closely with trees for years.