Boyle first realized his concept when he saw physical therapist blaming the same limited set of culprits for injury. Injuries seemed to be caused by a weak stabilizing muscle shifting stress to another muscle. The weakness of stabilizing muscles in the hip, spine, or scapulo-thoracic joint generally seemed to be the culprit. Specifically, the deep abdominal muscles (transverse abdominus and internal oblique), hip stabilizers (gluteus medius, adductors and quadratus luborum and hip external rotators) and scapula retractors (lower traps and rhomboids) were to blame.
And in a call back to last week's joint by joint approach article, issues in one joint were usually caused by weakness in a neighboring joint- weak deep abdominals causing low back pain, weak hip stabilizers causing knee pain, and issues with scapula retractors and stabilizers leading to rotator cuff injuries.
Functional training seeks to address these issues by shifting the focus to including the various stabilizer muscles. However, as Boyle takes pains to point out, it is not remotely clear that we need to isolate a muscle or one joint in order to reduce injuries. It seems to be far more helpful to practice movements that are related to what one is training, but in a way that incorporates as many of the relevant muscles and joints as possible.
For example, runners should focus on muscles and motions similar to actual running if they want to improve their running ability and reduce injuries. Machine assisted motions wouldn't be particularly functional (as in specific to the purpose of developing running), unless it was to develop muscle awareness or create additional safety for an injured athlete. Two-legged squats would be more functional because they use similar muscles.
Single legged squats, however, are very relevant to running because only one foot is on the ground at a time in that activity. The muscles that support the leg in that stance are all active in running as well. And the need to balance involved the stabilizers of the hips. If the stabilizers need more help, then additional challenges to balance such as standing on an unstable platform can be added.
An emphasis on functional training is also important because it guides us towards what sorts of exercises are most relevant to our needs. If the sport is running, then we must know what muscles are used in running, and then strengthen those- including the smaller stabilizing and neutralizing muscles.
This article will link to many future articles that expand on this, but for those who want to have a theoretical understanding I think this will will help. Be sure to check out my hip strengthening routine and my article on using the glutes and hamstrings in running.