I think he sums up the book quite nicely actually in the introduction. "A single meal can flood the body with thousands of compounds, many of which have never been isolated or identified."
This sentence alone points out the obvious misnomers associated with 'Nutrition-ism,' the flaws of Nutritional research and the importance of eating whole food. It is a strong indication, before he even discusses the various myths/facts of compounds we do know of, that it is impossible to assume that certain 'base chemicals' like Omega-3 fatty acids (to which there are actually 3 different types) are actually responsible for contributing to good health.
The truth is we really don't know if it is these Fatty Acids alone that contribute to good health, or if it's the interaction of those fatty-acids in conjunction with other compounds in fish oil for example that actually contribute to good health. How they interact with other aspects in our diet is also unknown. It could be their interaction with other compounds in our body or in other types of food that contribute to good health. Is the relationship between Omega-6 and Omega-3 consumption what is truly important?
The second most important aspect of the book, is that the 'poisons' we so aptly refer to when discussing things that are supposedly 'bad' for us (think lactose, gluten, fluoride, artificial sweeteners, etc...) are actually largely dependent on dosage to become toxic in the body and cause damage. Our bodies are in fact quite good at clearing up harmful chemicals that appear in even our most natural/organic of foods. Apple's for instance (and not many people would know this) contain formaldehyde, acetone (paint thinner) and cyanide (a known poison) in trace amounts, yet eating 2 or 3 apples a day will certainly not kill us. Toxicity is an important factor that many people miss in their assumption of the micro-nutrient content of food.
I think the introduction gives a good indication that this is what he believes as an eater: that whole foods are what is most important (not the molecular make-up) and that most of our food consumption is dependent on quantity or dosage, not what the specifics of the molecular make-up actually are.
As a food chemist, he also indicates that he is publishing a book based on the real science and not the interpretations of certain radical groups. He took a bunch of things that appear to be almost nutrition lore and looked at the actual data to support it. He never really appears to to offer strong support for one notion or the other, but rather attempts to let you come to your own conclusions.
The rest of the book, was a scientist's view on the chemistry of food. It also indicates that nutrition is highly individual and there are a lot of unknown's to this day. The question that he mostly poses is not whether any singular particular thing is good for you, but rather, will it actually harm you based on dosage?
Overall, I would say he wrote the book with a rather un-biased point of view. He points out some key flaws in certain types of rationality with regards to food from a purely scientific view point. The notion that artificial sweeteners turn to formaldehyde in the body, for example, is a ridiculous assumption, but he makes no such claims that consuming them is actually good for you, rather points out that they went through rigorous testing and the evidence was never conclusive that they cause any 'harm' at this point. That is not to say, that we won't in future, discover harm either.
I think you must read this book with an open mind. If you have already convinced yourself that lactose is bad, gluten is bad, trans-fat is bad, fluoride in water is bad, then you won't get anything from this book because you will not allow yourself to deviate from your previous beliefs about those minute details of the human diet.
When the truth is, as this book points out, that the consumption of certain types of foods is largely individual and 'it depends' on a variety of circumstances, many of which are unknown. If you have a gluten/lactose intolerance, then gluten/lactose is bad, but if you don't, then milk and grain products can contribute to overall health and well-being. If you are predisposed to tooth decay than brushing your teeth with a flouride based tooth-paste is probably a good idea. There is some research now finding naturally occurring trans-fat that might actually be good for you health believe it or not, though that is too recent to have been published in this book (maybe in a future edition you will see it).
We as a society like the good vs evil approach. Each of us have our beliefs about the good foods and the obvious counter-balancing evil foods. We can't have good without evil, right? It appears though that these beliefs are constantly changing as new research is done (in limited context and applicability I might add), which leads to more and more confusing data on a wide variety of foods and food compounds.
There are, however, two-sides to every story and I think as a general whole, Dr. Swartz does a fairly good job of citing both sides of these stories in a concise fashion.