There's a reason you feel sluggish and awful after you've been sedentary at work all day: your body is designed to be moving throughout the day, primarily staying active. In fact, it's not just that inactivity makes you feel sluggish and awful; according to the World Health Organization, inactivity is the fourth largest killer of adults and is responsible for 9% of premature deaths.
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Sitting curves your spine and often contributes to slouching that puts added pressure on your spinal cord and prevents your lungs from expanding fully. If your lungs aren't inflating properly due to slouching, your muscles not only aren't getting enough oxygen, but they are also stressed from being in one position too long without moving.
When inactive, your body also slows down the rate at which you burn calories and your insulin effectiveness rate drops, in turn increasing your risk of type II diabetes and becoming obese. Also, the number of lipids and triglycerides that help your body process fat intake take a plunge, which can cause your "good cholesterol" (HDL cholesterol) to fall.
The American Cancer Society conducted a study of men who spend 6 or more hours a day of their leisure time sitting and concluded the test subjects had a 20% higher death rate than those that spent less than 3 hours sitting. The death rate for women was even worse at 40%. On average, it's estimated that people who sit too much shave a few years off their lives.
You may be thinking, "No problem, I work out and go to the gym." The reality is, you're what many call an "active couch potato" and that isn't enough to compensate for spending a majority of your day being inactive. It's much better than nothing, and we applaud your motivation to work out, but it isn't enough on it's own.
You might be asking yourself what you can do. The answer is switching your position at work regularly. If you're sitting, work standing part of the day. Take breaks that bring a little motion with them, such as a short walk. Even a short walk to the water cooler is a step in the right direction. Making sure you change positions several times throughout the day will help make sure you can counteract the negative effects of sitting all day.