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I have heard that isolation exercises are pointless by some, and that total body workouts are to be abided by. I must digress as, for example, what if supporting muscles are strikingly weak?

I have noticed with me personally that during squats I feel like I have to "bounce" a little fast on the bottom because my hamstrings seem to "burn up" and get sore/painful if I don't.

Some have said, "Just do more squats!", but it hasn't made all the difference. That's why I figured, what can be bad about routine isolation every now and then? Why do some trainers rarely isolate and do workouts in packed "units" of muscle groups, rather than tackle weaker areas directly? How is that harm?

Anyways, is isolation "good" in any sense, and would it benefit me in my insufficiently muscle-activated squats?

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To start, if you notice that you feel pain rather than a burn or soreness in your hamstrings, it may have to do with your squat stance, rather than lagging hamstrings. However, the hamstrings are more often underdeveloped compared to their quad counterparts found in front of them for most trainee's, so a muscle imbalance isn't out of the question. And while explaining proper squat form doesn't organically relate to the rest of your questions, I am just mentioning this because while the squat can be absolutely draining and downright brutal, it shouldn't feel painful.

To understand how and if isolation exercises should be implemented into your training program, I'll go over the advantages and disadvantageous of them compared to compound exercises. But first, what is an isolation exercise?

Isolation Exercises include all exercises or movements that affect only one joint. For example, the movement of the bicep curl involves only the elbow joint as the forearm move over the arm, making it an effective isolation exercises for the biceps. Now, as for why and why not you'd want to include them in your own training.

Why Not

  • Isolation exercises recruit muscles less powerfully than compound exercises.
  • Isolation exercises are generally less effective than multi-joint exercises in increasing strength and size.
  • Muscle recruitment in isolation exercises does not increase as it does in compound exercises, as you increase repetitions.

Why

  • Isolation exercises use less strength and energy, making them less physically exhausting then compound exercises.
  • Isolation exercises target muscles better than multi-joint exercises. This allows for the trainee to develop a better "feel" for working that particular muscle.
  • With compound exercises, certain muscles will take precedence over others (such as in the squat) and isolation exercises can help you maintain muscular balance.

    With your situation in particular, muscular imbalance can develop between the muscles that make up the hamstring (the biceps femoris, semitendinosus, and semimembranosus) in two popular ways as described in The Strength Anatomy Workout II:

1) The physical structure of your personal bones pushes you to use the inner or outer hamstrings more than the other.

2) Faulty motor recruitment due to an inability to feel your hamstring muscles working. To improve motor recruitment, vary the (isolation) exercises you use to target the hamstrings. Hamstring exercises can be divided into 4 categories depending on the angle in which the muscle is working. - The first are exercises that bring the feet toward the butt (ex: lying and standing leg curls) - The second are exercises that lift the torso (ex: dead lifts and good mornings) - The third are exercises that contract the upper part of the hamstring and stretch the lower part (ex: sliding lunges) - The fourth are exercises that stretch the upper part and contract the lower part (ex: seated leg curls)

The book also mentions that by changing the position of your feet, you can try and change the recruitment of your hamstrings. By turning your feetoutward, it will involve the biceps femoris more, and inward will work the semi muscles. It also recommends to warm up your hamstrings before doing compound exercises for the legs (such as squats) as working cold hamstrings can cause pain in the knees and back during the exercises.

I also wanted to note that by doing more squats, you will only compound the problem at hand. Your only repeating something that isn't working for you and expecting it to create different results, which no offense, but according to Einstein, would be considered crazy. Now a final summary of everything:

Compound exercises target and work more muscles than isolation exercises, and allow more weight to be used per exercise, making them essential for a muscle building program. However, because they recruit multiple joints and muscle groups, the possibility of a one muscle group taking over and doing more of the work is very, very real. By including isolation exercises, you can bring up lagging muscle groups so that when you return to the essential compound lifts, the muscle imbalance is gone, which results in more weight lifted. Additionally, isolation exercises are less exhausting which means you'll be less tired after doing them, compared to compounds. Finally, they can also help you learn to develop a feel for working that muscle, meaning you'll be able to recruit it later on.

Hopefully now you can see there is no "harm" in including isolation exercises in your own training program. If I was unclear at all, please let me know.

Sources

1] Delavier, Frédéric, and Michael Gundill. The Strength Training Anatomy Workout. Champaign, IL: Human Kinetics, 2011. Print. http://www.amazon.com/Strength-Training-Anatomy-Workout-The/dp/1450400957

2] Delavier, Frédéric, and Michael Gundill. The Strength Training Anatomy Workout II. Champaign, IL: Human Kinetics, 2012. Print. http://www.amazon.com/Strength-Training-Anatomy-Workout-The/dp/1450419895

3] Bompa, Tudor, Pasquale Mauro. Di, and Lorenzo Cornacchia. Serious Strength Training.3rd ed. N.p.: Human Kinetics, 2012. Print. http://www.amazon.com/Serious-Strength-Training-3rd-Tudor-Bompa/dp/1450422446/ref=sr_1_1?s=books&ie=UTF8&qid=1388116631&sr=1-1&keywords=serious+strength+training

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The trouble with using a large amount of isolations, is that after doing an isolation (hamstring, for instance) you won't be able to hit squats at full weight right after. Now the rest of your development suffers. Rather than using isolations, stick to compounds and the weaker muscles will shape up. Also: isolations are better for bulking muscles that (like the bicep) don't necessarily get very large from compounds. –  Chris Dec 27 '13 at 17:57
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Development will not suffer by including isolation exercises. Its the compound movements that are compounding the problem :) and increasing them will increase the problem. You could always do the isolation exercises after the compounds as well, to avoid any fatigue before. I'm not sure exactly what a bulking muscle is, but while curls are great isolation for the biceps, the stimulus they get from helping out in the heavier compound lifts (ex: rows and pull ups) definitely aids in growth. Since rows do not target the biceps specifically, adding curls is a more efficient way of targeting them. –  Anabolic Animal Dec 27 '13 at 23:13
    
Outside of a laboratory, NO exercise "isolates" one muscle. A specific muscle group may be the emphasis of the exercise, but you cannot isolate a single muscle or muscle group (Such as biceps) –  JohnP Feb 25 at 14:43
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