Calories Eaten ≠ Calories Absorbed
It is very possible (and for CFers, very common) to eat many more calories than we are actually digesting, absorbing, and utilizing for our nutriment. When our digestive faculties are impaired (as with CF) or when we have a food sensitivity or a gut flora imbalance that causes GI distress which leads to inflammation, malabsorption, diarrhea and/or constipation, we are essentially wasting a lot of the calories that we put in our mouths. I like to say, food waste doesn't just happen when you throw half your sandwich in the trash, it can happen if you can't digest the half that you did eat and so it passes right through you! But more than just passing through you without being absorbed, ingesting unhealthy foods or foods that we can't digest well can actually damage the tissue of our digestive tract and inhibit our abilities to digest and absorb the other foods we ingest before or after that ill-fated meal.
This happens in a few ways. First, foods that we cannot digest well - that we are intolerant or allergic to, or that are in bad combinations with other foods - can cause distress and inflammation in the stomach, the small intestine, and the colon that make absorbing the nutrients (macro- and micro-nutrients) inefficient or impossible. If the stomach is inflamed or cramping it will not do a proper job crushing, churning, and mixing the proper amount of hydrochloric acid with the food to begin the digestive process. This is a particularly important step for protein digestion, which occurs largely in the stomach. Secondly, inflammation can actually cause the gallbladder and pancreatic ducts connecting to the small intestine to swell shut, preventing bile and/or pancreatic enzymes from moving into the small intestine to mix with the food exiting the stomach. Bile is critical for fat digestion and absorption, and inflammation in the small intestine may be one of the reasons why CFers can experience both acholoric (clay-colored) stools and greasy stools. From there the intestines may start to think that the food you ate is too inflammatory and irritating to spend any more time in the GI tract, wreaking havoc on its way through. So it may start the evacuation process, speeding up the transit time and causing diarrhea or loose stools. If this is the case (like what happens when I eat a big piece of cheddar cheese) the food that was eaten before that irritating meal and that still resides in your body lower down in the GI tract is also going to be hastened along, reducing the time your body needs to digest and absorb its nutrition too. So you've now not only wasted the calories and nutrition from the irritating food, but also part of the calories that you would have absorbed had there not been as much irritation and/or diarrhea caused by the offending food.
A Real Life Illustration
A friend of mine experienced this reality in a very extreme way. He has CF and at age 19 he took a dive in his health. His lung function declined and he started dropping weight quickly, probably related in part to developing CF-related diabetes. He followed the standard CF protocol and did everything his docs told him to do. He had a G-tube put in and started eating 5,000 calories a day, of all the typical junk food (and I consider the modern Western diet and commercial nutritional supplements junk food) that CF docs tell us to eat. He continued to decline and to lose weight.
What his docs were telling him to do wasn't working, so he decided to take matters into his own hands. He changed his diet to emphasize whole, natural foods. He cut out junk food and nutritional supplements and cut back on sugar. His lung functions began to improve and he started to gain weight. His docs couldn't believe it. He had his G-tube removed and still improved. He was now eating 2,500-3,000 calories a day and still gaining weight. How did this happen?
How to Heal
Based on what I have studied, a large part of his improvement may be due to the reduction in GI inflammation - and thus improved absorption capacity - that he experienced by cutting out hard-to-digest and inflammatory foods. In his case, as in many other cases (including cases where people want to lose weight) calorie counting has very little to with healing. If calories (foods) are of low quality and are inflammatory, they can cause weight gain or weight loss, depending on the person. This is why so many non-CF people can lose weight on a whole-foods diet like Paleo without calorie counting and often without even increased exercise! And CFers who improve their digestive capacity by eating a healthier diet full of natural, nutrient-dense, easy-to-digest foods - like the Paleo or GAPS diets - can actually gain weight! Eating a healthy diet can help the body balance itself out when there are extremes on either end. In herbalism, we call herbs that can heal two opposing conditions amphoteric. I believe, just like certain healing herbs, an ancestral diet like the Paleo diet is amphoteric because it provides the body with the medicine that we've evolved to need over 1.3 million years of hominid evolution - real food!
So while it is proven that CFers need more calories than non-CFers for a variety of different reasons, it is not helpful or acceptable to only rely on calorie counting to try to maintain or gain weight, or to maintain or improve our health. Healing is largely about calorie quality NOT quantity. So in my own healing regime I try to eat as many calories in as I can, but this is secondary to the quality of my food, where it comes from, how it was grown/raised, how nutrient-dense it is, how I combine it with other foods, how well I digest it, and how it makes me feel emotionally, physically, and spiritually. Holistic eating is a medical art in and of itself. Let's practice it!