I'll start with the disclaimer that I'm not any kind of medical or training professional. Everything I say here is based on my research (lots of it) and personal experience.
You say you're working at 85%-90% of your heart rate ... which I'm assuming you're basing on the whole 220-[your age]=[your max heart rate], right? Or you're using the numbers on the machine, which is based on that figure.
But the thing is that those numbers are GUIDELINES. If you are in good enough shape that you can work out at 90% of that figure for an hour, then you're probably not working out at what is high intensity FOR YOU. (The *for you* part is really important.)
When I first started working out, I couldn't handle 85% of my calculated heart rate for more than a minute. I remember trying the interval program on the elliptical and collapsing in tears after 5 mins because I couldn't breathe during the high interval parts.
Now? I can do the interval program on the machine for an hour and no problem. When I do intervals, I have to time them myself because the machines don't take into account that I'm in much better cardio shape than the majority of average gym-goers.
Now, FOR ME, "high intensity" is not 90% of 180 (which is my calculated maximum at 220-40 (my age) which would be a heart rate of 162). For me, in the shape I am now, "high intensity" is closer to between 175 and 180.
This is where the "perceived exertion" scale comes into play. This is where you judge your intensity by how hard the exercise feels and how well you can breathe/talk while you're doing it.
I hope all of that makes sense - it's hard to explain when typing it out.
So ... ultimately here, if you are able to work out at a certain level for an hour (or close to an hour) then you're probably working at what is medium to medium-high intensity for you. If you kick it up to where you cannot sustain the level and still breathe (but not talk) for more than 1 or 2 mins, then you're kicking it up to high intensity, for you. (All the "for you" is important.)
Working at medium intensity will burn more calories immediately. Alternating medium with high intensity will burn calories for longer as it raises your metabolism for longer.
Either way, when you burn calories, you burn a combination of fat and muscle. Always. Which, as I said above, is why it's a good idea to include muscle building exercises *and* cardio ... to help sustain and rebuild the lean muscle tissue you lose when you lose weight.
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