Just when I thought I was going to get some sleep. Oh well.
Indigo, those words may be Greek to me too, but they're supposed to be Greek (or Latin). That's medicine for you.
How can I help? I measure exhaled CO2 every day on patients. That's part of what anesthesiologists do. On the other hand, I'm not an exercise physiologist, so I only look at patients whose CO2 production is less than normal, not increased. On the other hand, their CO2 elimination is compromised by their decrease ventilation, so I see elevated CO2 levels in virtually every patient. Anyway, I digress.
As far as your questions are concerned:
1.) It is certainly OK if your experiment disproves your hypothesis. There is a reasonable school of thought that the BEST science fair experiments produce results different than expected. And as far as real science is concerned, advances come from looking into unexpected results. If we always knew the answers, why do the experiments.
2.) CO2 production is related to a number of factors. First your muscles need energy to do their work, and generally they obtain energy by breaking down molecules of glucose. Glucose is a sugar that can be obtained from food and can also be created from other chemicals in the body. Glucose contains chemical energy that is useful to cells, and thus is rather like a fuel. In order to obtain the energy from glucose, the muscle cells need oxygen to help them break down the glucose molecules, and the oxygen is brought to them by the red blood cells. When glucose is broken down in the presence of oxygen, it releases energy for use by the cells and at the same time several additional products are formed. These are: carbon dioxide, water and heat.
Carbon dioxide is toxic to cells if it stays around, so it is carried away by the blood and removed from the body by being passed into the air we breathe out.
The process by which muscles obtain energy from glucose in the presence of oxygen is called aerobic metabolism. In certain types of exercise, as for example in sprinting or weight-lifting, the muscle cells can turn briefly to another type of energy production that does not require oxygen at that time. A waste product called lactic acid is formed, and when this accumulates it will stop the muscles from continuing to work until it is removed. This special type of energy production is called anaerobic metabolism, and can only be used for short spurts of intense activity. When the lactic acid is broken down later, oxygen is again required, and carbon dioxide is produced as in aerobic metabolism.
Your body has a basal metabolic rate (which consumes a baseline amount of O2 per minute, and exhales a proportionate amount of CO2). It is affected by body temperature and body surface, among other factors. It goes up 6% per degree Celsius increase in body temperature, for example.
Second, you have the metabolic rate associated with additional activities (such as exercise). Also, when the anaerobic threshold is reached (during near maximal exercise), the body uses anaerobic metabolism (no oxygen used) to produce energy, which produces different amounts of CO2 that aerobic energy(normal oxygen utilizing metabolism).
3.) Why are you assuming that a non-athlete would produce CO2 faster than a conditioned athlete? The second that you start metabolizing substances in your both to produce work (energy) you immediately start producing CO2 in that chemical reaction. So if both athletes are the same mass, and are producing the same amount of work, they will both produce the same amount of CO2. Now the rate at which they exhale that CO2 is an interesting question.
This google article talks about the basal metabolic rate, and introduces the concept of the respiratory quotient (the ratio of carbon dioxide to oxygen used by the body.)
http://en.wikipedia.org/wiki/Basal_metabolic_rate
When the body us utilizing glucose for energy, the overall equation for this reaction is:
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O
Because the gas exchange in this reaction is equal, the respiratory quotient for carbohydrate is unity or 1.0:
R.Q. = 6 CO2 / 6 O2 = 1.0
When the body is using fats for energy (palmitic acid in their example) the overall equation for the substrate utilization of palmitic acid is:
C16H32O2 + 23 O2 → 16 CO2 + 16 H2O
Thus the R.Q. for palmitic acid is 0.696:
R.Q. = 16 CO2 / 23 O2 = 0.696
Lastly, proteins can be utilized for energy production. The equation for this, using albumin as an example, is:
C72H112N2O22S + 77 O2 → 63 CO2 + 38 H2O + SO3 + 9 CO(NH2)2
The R.Q. for albumin is 63 CO2/ 77 O2 = 0.818
So different fuels in the body produce different relative amounts of CO2.
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The first article that ghariman referenced won't help your point. It mostly relates to the bodies response to lack of oxygen during exercise. It's an interesting point while climbing Mt. Everest, but shouldn't help you here. And it showed no difference in ventilatory sensitivity of athletes to non-athletes during hypercapnia (think that athletes and non-athletes repond similarly when they put a plastic bag over their heads. Again not helpful for your question.)
Now if athletes initially metabolized differently than non-athletes (utilizing carbohydrates instead of fat initially), I would think you might see a CO2 production difference. But both should preferentially use carbs as their initial fuel, so I don't think you'd see a difference. Pulmonary capacity and maximum oxygen utilization ratios will be different, but not CO2 production.
This may again be Greek to you, but much of what I'm saying is that I would think you would see a difference between conditioned athletes and slugs at or beyond the anaerobic threshold (during near maximal exercise), but not necessarily with lesser exertion.
BTW, feel free to ask for any of the medical definitions if you can't understand them from the dictionary.