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So recently I was diagnosed with lumbar disk degeneration. The discs between my L4&L5 and L5&S1 have no fluid left and are bulging. So no more sit-ups, squats or deadlifts for me. Planks and crunches are painful. I'm trying to figure out exercises to keep my legs strong and core strong so I can still keep fit. I'm .mil and a 3-gun guy so I'm trying to keep that in mind.
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Did the doc say crunches are ok? If he did, that right there would negate anything he says to me about how to keep my back strong and from getting worse. When you squat properly, there will be almost no movement of the vertebrae, allowing all the muscles that support it to contract isometrically and get/stay strong.
When you do crunches, you are in spinal flexion over and over, which is worse for your spine health (especially with what you have) than a squat at reasonable weights.
If it were me, I would squat and maybe deadlift at nice light weights and work up over time and see how it feels.
You are right though, doing nothing and letting everything get weaker isn't the answer.