Disclaimer: I'd like to add my $0.02, but I need to be very upfront and honest before I do. Without meaning any offense to anyone here, and with the deepest and most sincere respect for those who hold different views, I want to make it clear that I do NOT believe in 'chi', or meridians, or auras, or bio-force fields affecting our physical bodies or mental states. With that said, if you're still at all interested in some input from a skeptic who approaches meditation from an entirely physiological perspective, here goes:
Now back to my regularly-scheduled post: The autonomous nervous system regulates many important functions subconsciously. Critical fuctions that must continue at all times, such as breathing, are controlled without conscious thought, so that they continue even while sleeping, or under extreme duress (such as survival situations). Your body regulates all such functions through the complementary interaction of the two main components of the autonomous system: the sympathetic nervous system, and the parasympathetic nervous system.
The sympathetic nervous system is your body's primary defense system for high-stress survival situations. It is responsible for the so-called "fight-or-flight" response. When faced with life-threatening crises, this autonomous system kicks into gear without conscious thought and prepares you to respond to critical danger. Immediately, adrenaline and other corticosteroids are dumped into your bloodstream. These raise your heartrate, reduce your fine-motor coordination in favor of greatly increased gross-motor ability, constrict your pupils, raise your blood pressure, increase rapid, shallow respiration, make available a host of other steroids and hormones (including opium-like substances that assist in pain-tolerance), and generally prepare you to fight for your life or flee.
The parasympathetic nervous system is the counterbalance to the sympathetic system. After the danger has passed, this autonomous system automatically releases hormones that counteract and reduce the level of adrenaline and corticosteroids in your bloodstream. Blood acidity goes down, as CO2 levels are reduced, heart rate diminishes, blood pressure is lowered, pupils dilate, muscles relax, and respiration subsides to slower, deeper breaths.
These two systems work together to balance all the systems they affect (heartrate, breathing, blood pressure, blood pH level, hormonal levels, etc). If either system is overactive for too long, a dangerous health situation can result, and in our tensed-up, caffeinated, high-stress culture, generally, the sympathetic nervous system is running on continual overload. In order to restore a healthy balance, stimulation of the parasympathetic system is desireable.
Notice in the (rather long) list of physiological features that these two systems affect subconsciously, the breath rate is the only one that can also be controlled consciously. Experimentation has shown that the parasympathetic nervous system can be stimulated by simply breathing slower and more deeply (as the sympathetic system can also be stimulated by rapid, shallow breathing). Thus, the result of focussed, deep, slow breathing is reduced heart rate, lowered blood pressure, reduced blood acidity, higher blood oxygen content, decreased stress hormone levels, etc. etc. etc.
Now, for those who look to the 'chi' model in meditation, you might choose to view the parasympathetic and sympathetic systems as part of the 'yin and yang' of chi. For me, I know that the controlled deep breathing works, and I have physiological evidence to back up the 'why' and 'how' of it. If my model is accurate, then the breathing involved in meditation is more important than the subject matter thought about (or not thought about) during meditation - at least for this particular laundry-list of benefits.
Your thoughts?