I love putting science into the training I do with my athletes. We know what works and what doesn't based off of years of laboratory testing, studies, and research. A coach who blindly follows a training program without knowing the science is the same as closing your eyes while riding a bike. Sure, you will get somewhere, but the end result probably won't be that noteworthy (for the good reasons!).
That being said, show me a coach who has been around kids even just a couple of years and I will show you a person who understands that the human body doesn't perform the way science always says it will. Psychological factors should be considered in training because an athlete doesn't always have the same level of desire to execute workouts in the manner it is prescribed. This obviously has to be worked out by the coach, and hopefully that athlete will come around, but we all understand it is an issue at least occasionally. If an athlete looks to be "hurting" in a workout on a day they should be fine, you need to understand something else may be going on there, and forcing the issue to continue isn't always the best choice.
The big one on my mind right now, though, is stretching. Now of course, by today's standard you have tons of different techniques such as static, dynamic, active isolated stretching, etc. If you wanted to right now, you could go on Google and find research that both supports and rejects all types of stretching. Nothing is exactly clear cut once you start looking into the studies, so what do you do? Well, I've done simple trial and error, not only with myself but with my athletes, and I know what helps me and them feel prepared to run well in a workout, or what helps us feel more recovered after a run. Sometimes it is a static stretch, sometimes a dynamic. You get the picture. Use the science as a guide, because it is usually founded in some good research, but you can't trust everything because not all studies even work with athletes. What is good for a sedentary population may have no effect on an athlete. Be mindful of what you do, but use your intuition where the lines of science are grey.
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