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Ok about a month ago I developed some awkward knee pain when training for my first marathon, I tend to be one of those stubborn individuals who doesn't stop when I know I should. However, I continued running out the rest of training for this day. It was painful to move my knee correctly and by roughly 6-8 hours later I had full function in my knee again. However, the pain originates to the right of my right knee cap, it can be kind of dull pain, I don't have any pain when setting down, bending my knees, going up and down stairs, this tends to flare up just when I run and it can bounce around when it flares up. While the pain did resurface .2 miles into my marathon, it did not stop me from completing it. The following week I completed a Spartan Race and the pain didn't show up until 3 miles into this race. I have taken ~3 weeks off to allow this to possibly heal. I am a flat foot runner which unfortunately could be some of this culprit, I have since gotten some orthotics to try and help this, however going to the doctor at this time is out of the question, I just wanted to see if anyone has had any issues with something similar to this. I have to guess it's either ITBS or PFPS.
Brandon, when going to the doctor is out of the question, overtraining should also be out of the question. Awareness of this responsibility is one reason why you are required to sign a waiver before participating in every sporting event. I'm not sure why you competed in a race a week after your first marathon, especially if you were feeling the beginnings of an injury before that marathon. I know you mentioned being stubborn. I've been stubborn too, as have a lot of us runners... but I would like a commitment from you that you will only follow good examples and good advice from now on, so you can enjoy this running thing a lot longer - and feel better doing it. Deal?
I would also like to know that if it was painful to use your knee correctly, that you will not use it incorrectly in order to avoid pain or continue to train. It may seem that pain showing up at three miles is progress, over pain at .2 miles. That is only true if something else isn't getting wrecked in the process, the pain of which my not be evident at this time.
I am glad that you are looking at the flat foot issue, since it may be a source of further damage and pain going forward, if left uncorrected. I wish I could agree that off-the-shelf "orthotics" are a positive step in that direction, but you can't be assured of this unless a competent and qualified professional signs off on it. There is a lot you can learn about the biomechanics of flat feet, overpronation, problems with muscle function and bone structure in a runner's foot, but you may not have time for that in a few weeks of downtime. It is a lot for the average runner to absorb. The most important thing to remember now, is that a temporary fix like an orthotic does not solve the real problem with your foot. It is only a quick fix, a crutch.
An arch is formed from bones of lengths that vary between individuals, held together by ligaments and fascia of varying flexibility, and shaped by muscles and tendons that do not function the same way in all runners. There can be deficiencies in tone or rigidity that result in abnormal arch height. Some of these factors can be controlled or corrected, and some require work-arounds. Muscles that fail to properly control and maintain the arch can be treated and retrained, but anatomical realities like bone length can be impossible to change. In addition, other predisposing factors like leg-length discrepancies further complicate the correct operation of your foot in the gait cycle.
You may be an overpronator, which can contribute to knee pain, among other problems. This dysfunction is not necessarily as permanent as some of the anatomical contributions may be. Muscles such as the Tibialis Posterior can be strengthened to increase the height of your arch, even when a short 1st metatarsal may induce the inward rolling of the foot we call pronation in order to compensate and increase stability. A small thin pad under the ball of the foot can help reverse this compensation in such cases.
The dorky video below discusses the tiring of muscles related to arch height, how to massage them (not too sure about techniques shown), and how to engage proprioception to begin retraining them. I'm sure there are other ways and better ways to do this, but I did not have time to find an example. What is important to show is the movement of the arch up and down in response to activation/relaxation of the appropriate muscles, how to isolate and stimulate their action.
Ok, with that out of the way, I did find an interesting jock-oriented discussion of other factors that can influence how you stand, and how your posture may influence how your foot adapts to this. The language is a little rough, but it is well-intended and aimed at highly motivated athletes like yourself.
If the previous video was over the top, here's another angle to consider. While I am aware of yoga, I do not practice it, and believe that stretching exercises are not for everyone, or appropriate under all circumstances. Yoga is not all about stretching though, and can be helpful for correcting postural issues.