Predisposition to obesity, BMI, and other measures of adiposity are highly heritable, but I don't think there is much evidence that this related to what is commonly called metabolism. The primary mechanisms seem to implicate biological processes involved in appetite and satiety, and dysfunction in homeostatic mechanisms intended to preserve fat stores. However, there is definitely strong evidence that individuals differ in response to positive or negative energy balance. This was known since earlier studies on identical twins:
http://www.nejm.org/doi/full/10.1056/NEJM199005243222101
The critical issue was within-pair similarity in contrast to between-pair variability in response to overfeeding which was used to infer genetic mechanisms. The findings are similar with negative energy balance. However, this does not appear to be caused primarily by differences in slowing of metabolism in response to calorie reduction, as findings generally show any changes in metabolism were accounted for by weight change :
http://jn.nutrition.org/content/127/5/943S.short
The interesting thing is there has been progress since then in identifying some genes involved.
It's been a long while since I have read up on the literature, and using Google for these sorts of things is....dubious at best.
But from what I understand, your basic metabolic rate has to do with everyday bodily activities (such as breathing, digesting, heart beat, etc.)
Inevitable, people have different lung capacities. Yes, you can train-up your individual lung capacity through vigorous exercise. (Cold-weather exercise is particularly good at beefing up your lung capacity.) But not everyone is going to be a Michael Phelps or a Lance Armstrong. Very few people could even train at their intensity level, or as often as they could. And even if they could, they still would not necessarily get to the same level of lung capacity as those two athletes.
And if (when) they stop training, their lung capacity will not decrease to as low as most people. They will always have a higher lung capacity than most people. Therefore, their base metabolism will always be higher than more people for that very reason.
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Digestion is also a large factor in metabolizing calories. That's why your metabolic rate tends to drop if you were to attempt to "starve" yourself as a poor "solution" to losing weight. That;s why you do need to eat on a regular basis, and a minimum number of calories in order to lose weight efficiently.
Now, when it comes to digestion, just like with lung capacity, some people have more and stronger stomach acid than others. (I have acid reflux. There is an excess amount of acid and other chemicals in my stomach. It is also stronger than normal. My body has to work a lot less to break down foods. This is a very simplistic explanation of this health issue.)
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3097951/
The above link describes acid reflux, and the compares and contrasts that with metabolic syndrome.
According to that paper, acid reflux (gastro-esophageal reflux) is not very well understood. There does seem to be a strong correlation between the disease and obesity, but the evidence is inconclusive.
I've always had issues with getting sick on certain foods growing up. (Incidentally, my niece goes through the same things I did. It was much worse when I was really young, just like with her. I couldn't eat pizza at all, until I was about 10 years old. My 11 year old niece refuses to eat pizza. The thought of it makes her want to puke.)
Then you throw in the ****** diet that parents all too quickly and easily throw into their kids' meals these days without much thought, which establishes bad habits and really can screw up an individual's bodily chemicals and how their body processes foods.
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Sorry, lost my train of thought. I thought of something funny: Conservatives love to talk about "all those lazy fatasses out there." One solution the Democrats have come up with, was limiting junk food in schools. Conservatives turned about and cried about "freedom of choices!" I dunno. I thought of that for some reason as I was typing. Anyway.
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I guess what I was trying to get at, is the fact that while you can control your metabolic rate to some degree for your individual self through exercise and proper nutrition.....you cannot control who you are. Other people's bodies do, in fact, tend to burn more or less calories, simply because no two human bodies are the same. Lungs could be a little larger or a little smaller. Some people will be genetically predisposed to having more or less muscle mass (another contributor to base metabolic rate.). Stomach acid content is totally different from individual to individual, which can also contribute to base metabolic rate. I cannot believe that everyone would naturally have the same metabolism, given the same environmental conditions, exercise, and nutrition.