You have to compare intensity over time. Exercising at 70% of Max Heart Rate for 30 minutes will burn more Total calories than 30 minutes at 50% heart rate. The percentage of fat burned at each intensity for the different exercises depends on different variables including; conditioning level, age, diet, body composition, etc. While training at higher heart rates may burn less fat for fuel during the exercise, you will burn more total calories per training period and during the post-training period.
A highly conditioned swimmer will be able to maintain a higher-heart rate over a longer period of time and therefore burn more total calories than say a unconditioned runner over the same period of time. And the swimmer will lose weight as long as his total calorie intake is less then his expenditure.
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