Actually the method you have devised for measuring CO₂ output is a clever one. The more CO₂ you add to water, the more the pH will indeed fall. However your teacher makes a valid point in that while this relationship is true, it may be difficult to measure what you are trying to measure in this manner, for two reasons. First, it is very difficult to use an approach like this in a way that is consistent. For example, you can never control how hard a person blows over the thirty second time period, and the CO₂ will also quickly escape from the water and equilibrate into the air! Second, even if you could control for those things you may be trying to measure a very small change that could be difficult to see in pH.

Unfortunately, the best way to measure the CO₂ content that is being out gassed in an experiment like this is probably with a professional device that will likely be expensive (such as a gas chromatography machine or the like). There are certain to be several commercial kits for this purpose-- for example, air pollution monitoring kits-- or you may be able to borrow a device from somebody who uses such a tool regularly (such as the rebreather/analyzers used by exercise physiologists, or a gas analyzer from a heating and air conditioning professional). There are also several chemical methods that you could try, but these would most likely also be subject to the same problems as your current method.

I'm guessing here, but I think your teacher is afraid that you won't see much difference in the pH of the water before and after exercise. You have the right idea. CO₂ does dissolve in water to form a weak acid, so more CO₂ bubbled through water means lower pH. But even all the CO₂ in the atmosphere only drops the pH of rain from 7 to 6.5 or so. (That's pristine rain, without the extra acids from smog.) The change in the CO₂ concentration in the air we breathe out is tiny. You may not be able to measure the tiny drop in pH you'll get with a pH meter. Then again, you may.

Quick and dirty:
- Measure a change in the person's respiration rate. This is the number of breaths a person takes per minute. This will give you some idea of the increase in the person's respiration due to exercise, but of the change in CO₂ concentration in the air they exhale. Typically, we inhale air with 20.84% O₂ and 0.04% CO₂ and exhale air with 13.6% O₂ and 5.3% CO₂. I'm not an exercise physiologist, but I'm guessing that during exercise, these numbers probably don't change much. What does change is the number of times we breathe in and out and the amount of air we take in and expell with each breath. This is how we rid our blood of CO₂ faster and get more O₂ to our cells: we breathe faster and deeper, not more efficiently. (Plus changes in heart rate and volume.) (As a side note: marine mammals remove much more O₂ from the air than we do with each breath: there is a greater difference between the O₂ concentration of air going in the lungs and coming back out. This is ONE thing that enables them to go longer between breaths.)If you have a budget:
- Add a pH indicator to the water. Perhaps this is what you suggested to your instructor already. The pH indicator will change color as the pH of the water changes color. Here's a description from a I found on the web: "To compare your CO₂ output under different conditions, you will exhale through a tube into a bottle partly filled with the pH indicator solution. The CO₂ that you exhale will dissolve in the water, and gradually acidify it. You'll be able to see the pH indicator change color as this happens. By measuring how long it takes for the pH change to occur (and always exhaling at the same rate), you will have a relative measure of the amount of CO₂ in your breath. The less time it takes for the color change to happen, the more CO₂ there was in your breath."

science_b
- You can buy carbon dioxide sensors that measure CO₂ concentration in the air. I'm not sure how expensive these are. Again, remember that the concentration of CO₂ in the breath won't change, it will be the overall amount of CO₂ exhaled (lung volume x number breaths).

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- The way excercise physiologists measure an athlete's performance during exercise it is open-circuit spirometry: they collect the air athletes exhale while they are exercising at a specific intensity over a specific time and then "scrub" the CO₂ out of the air and measure it. You'd have to have a re-beather system for this, which delivered clear air, recovered expelled air, and then ran the old air through a filter with soda lime. This is kind of similar to the way re-breathers work for SCUBA divers.