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Just rambling. Maybe this very basic info will help someone, or maybe the resulting discussion will teach me something I didn't know. Nothing earth shattering here, basic exercise physiology.

Machines
The main advantage of resistance machines is that they force you to perform a movement using, more or less, the correct motion. Thus, even someone with very little knowledge of how to do strength training movements correctly can use machines without having to worry about injuring themselves.

The main disadvantage is that the limited ranges of movements don't necessarily transfer well into the real world. In sports, martial arts, etc., the ranges of movements you use are varied and random. Relying too much on machines when your intent is to put your fitness to functional use can in fact make your more prone to injury. They are better suited to those who are simply trying to burn calories or target very specific muscle groups, or as a supplement to those also on other fitness routines.

Free weights
The biggest disadvantage to free weights is probably the knowledge required to perform the movements correctly. And let's face it, most people simply do not make an effort to learn this information before jumping right into it. A bench press junkie who has not suffered a rotator cuff injury as a result of either incorrect posture, or overexercising one muscle group while neglecting another, is extremely rare.

The advantage applies primarily to those who are more interested in functional fitness than making themselves pretty (though it works just as well for the latter as machines do, assuming you know what you're doing). The simple fact that the movements are not guided forces you to balance the weight yourself, which incorporates the use of smaller, less obvious muscle groups that would probably be neglected when using machines that do not require as much control.

Thus, it is not advisable for someone to base their entire fitness routine on machine based exercise, and then jump into an activity requiring extremely varied ranges of motion like football or combat sports. If a movement doesn't end up going exactly as you have trained for, you will probably end up getting yourself injured.

Calisthenics
This is my favorite. Not necessarily because it is superior to free weights, but because it is more convenient for someone who is either always on the go, or simply doesn't like the gym atmosphere.

Aside from convenience, the primary advantage of calisthenics is the versatility that can be incorporated into the exercises. A combination of pushups, hand stand pushups, squats, piston squats, gymnastic and wrestling bridging, and a pull-up bar or some portable gymnastic rings (or anything you can grab onto and pull), can hit any muscle group that machines or free weights can hit. And though it might require some creativity, weight can be added to increase the challenge fairly easily. I personally use a V-Max weighted vest, but as mentioned in another thread, a backpack full of little sand bags works almost as well. I can carry my entire "gym" up a hill with me while going for a morning hike, do my workout at the top, and then hike back down. Makes me feel a little less like a hamster than running on a treadmill or something.

Endurance
Regardless of which types of machines or weights are used, the principal is the same. Any resistance based movement which you can perform more than around 20 times before muscle failure improves your endurance.

Hypertrophy
Hypertrophy, to put it simply, is making your muscles bigger. This is the primary concern for most people who are interested in body building. Any movement which you can perform 8 to 12 times before muscle failure is going to be most efficient in increasing your muscle size. Those interested in sports where endurance is more important than maximal strength may actually want to avoid too much of this. A boxer, for example, does not want unnecessarily heavy arms because the second they fatigue and drop, the fight is over.

Maximal strength
High weight, very low repetitions. This will also cause some degree of hypertrophy, as will endurance training, but not nearly as much as sticking to the previously mentioned 8 to 12 range. Maximal strength exercises, incidentally, also tend to be more effective in developing fast twitch muscle fiber, which makes them particularly attractive to those interested in combat sports or martial arts.

Isometrics
This can best be described as infinite resistance. You can push as hard as you want on a wall, for example, and it will never move. Also useful for developing fast twitch muscle fiber and maximal strength, though it might require a bit of creativity to work a full range of movement using isometric exercises. Bruce Lee is said to have developed his devastating strikes, such as his 1 inch punch, utilizing isometrics.

Calories out
Though I don't really agree with the conventional concept of calories out, I will use that concept to explain this. Running, or your basic treadmills, elliptical machines, etc., are performed primarily to simply burn calories. While they may be efficient at this during the exercise itself, interval training has been gaining popularity lately for its efficiency at burning calories even after the workout is over. Theoretically, a shorter, more intense workout, as opposed to a longer, less intense workout, though it might burn less calories during the workout itself, will continue to consume energy for long after the workout is finished as your body continues to repair itself. The same principal can be applied to resistance training. A muscle might take one to several days to repair itself, and will continue to consume energy during this process. Stronger muscles, once repaired, will continue to be less efficient in terms of energy usage as well (i.e. they burn more calories simply by existing).
 
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