I assume you'll ignore my last post, where I posited that stretches are the first warning of injury and provide a very slow way to fix the problem if done correctly. If that was the "the engine's making more noise than it usually does," than this post is about the warning light going off on the dashboard. The next step is breaking down on the side of the road, which is too late.
I went to a track meet last summer and saw one of my old nemeses racing. His usual fluid movements had become herky-jerky and I thought "I could beat him now" (though I couldn't in actuality run a step at that point). Having had an injury, his body adapted and allowed him to run, but not quite the way he had... and he probably wasn't even aware of the difference. The problem was one of mobility, the inexorable slowing that comes with slight adjustments to avoid pain. You can tell when looking at older runners how long they've run and what order they'll finish in, just by looking at how odd their motions while running are; the more injuries, the slower and more idiosyncratic their actions.
Muscles and tendons should not hurt if you press on them. By that standard, two years ago, I had more than 30 and possibly as many as 45 injuries - and I was a mess. Among the dozens of treatments I needed were a variety that are all variations of the same idea - try to break up the adhesions, the cross-hatching, that the body does to compensate for tearing. Sports massage, rolfing, deep tissue massage, cross-frictional massage, active release therapy, graston technique - all are ways of having someone else do to you what you can, with difficulty, do to (for) yourself.
The foam roller, if nothing else
Most runners have at least a passing familiarity with foam rollers, which are used the same way as the two-person techniques, to bring back mobility. People tend to go with the easiest, most comfortable roller they can, but it is the one time when "no pain, no gain" actually holds true. What you're doing is tearing muscle (or tendon) fibers, which hurts. The real problems tend to be deeper and harder to access than I think rollers can manage. I find that a golf ball and a softball work well (and are cheap and easy to find), the latter when you need to spread weight over a larger area; you need to put a great deal of pressure on the area you're working, which generally means body weight (or part thereof) and a golf ball gives a very small area and is hard enough. Even better than a golf ball, though, is to use your thumbs, but it's often very hard to reach where you want and your thumbs will get sore quickly; there's a high incidence of thumb injuries among sports masseuses.
Starting with your feet and working up, press with your thumbs at all the muscle attachments - if you don't know your anatomy, most are right at joints. You'll probably find many spots that are sore if you press hard and you may think it's normal for them to hurt if you press on them, because that's what you've become accustomed to. If nothing else, you'll get a comfortable massage out of it.
For example, since I mentioned hamstrings in the last post, almost everyone, and especially runners, have tight hamstrings. You might not be able to stretch them as far as some, but it doesn't necessarily lead to a problem. With this step, you might find that you have spots in your hams that are sore if you press on them very hard. The semitendinosus will hurt near the medial (inside) side of the knee; the semimembranosus, which has a long wide attachment, a more diffuse area from the inside of the knee to the middle of the thigh; the biceps femoris on the outside of the knee; all three attach near each other at the hip, where you might also find a sore spot or two.
It can take months of daily work before these spots will not hurt, no matter how hard you press. Even then, there's another step that needs to be taken, because for every muscle that's tight, there's one that's weak. That's what I'll try to cover next.
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