Sean B. Carroll has an analogy to tell you about, and this book is how he is going to do it. Essentially, it is this: life has basic rules for how it keeps a complex system more or less in balance, even when it is perturbed, and they are very similar at the level of a single mammal or an entire ecosystem. We maintain our blood pH, internal temperature, and many other things with a narrow band, so long as we are alive, and in spite of many changes in climate or diet. If any of these depart from that narrow band, for example if our blood pressure is too low or our sodium levels get too high, it can be a very bad sign. Carroll's assertion is that ecosystems do the same thing, and that the systems it uses to do it are very similar. I'm not sure that Carroll would even use the term "analogy" for this, he might say they are fundamentally of the same type.
One of the basic principles that recurs in this book is the idea that nature uses push and pull to control things, like a driver that drives with the gas pedal down, and controls the speed by pushing down more or less on the brake pedal. Thus, our DNA may have a gene for making a particular protein, but normally this is suppressed by another molecule (e.g. one that clamps onto that portion of the DNA and prevents it from serving as the template to make the protein in question). When the cell needs to make that protein, a third molecule disrupts the suppressor, and the protein gets made in abundance. This is, for example, how we can have the same DNA in every cell, but proteins only get made in the cells where they're needed.
This is, needless to say, a bit more complicated to think about than a simple set of on-off switches. It is as if in order to turn on the lights we need to short circuit the light-circuit-breaker. Perhaps for this reason, it took quite a while for biologists to figure out what was going on here. Carroll takes us through the history of it for a few chapters, introducing us to a number of historical figures from all around the world who figured it out. Once it was known, it was possible to start putting it to use in the field of medicine. Many of our modern pharmaceuticals work on the principle that it is not just the gene that makes a protein which can go wrong; it can also be the other gene that is supposed to (but sometimes fails to) suppress the first.
There is also a discussion of a similar phenomena in recent cancer research, where it has been discovered that cancer requires not only a carcinogen, but also the failure of the several genes that normally help to suppress cancer. Once again, the malfunction may not have begun in the obvious place (the carcinogen), but in the failure of the suppressor (in this case, genes for natural cancer-fighting proteins). There are a number of good stories here, of great minds motivated to understand how our bodies work and how to make them right again when they start to fail. In particular, hearing about how even these great minds struggled and stalled for a time on the way to their eventual breakthrough is always more interesting than presenting them as having the right idea from the get-go and just confirming it with an experiment. Real science has a lot of hard work and puzzle-solving involved. It also has to be carried out in between the times when real life intervenes, as when Jacques Monod was working inside France as a member of the French Resistance, using several different names and coordinating sabotage. Carroll is a good storyteller, and he weaves the science and the history together well.
Next, it is on to ecosystems. Here, we discover odd facts like the fact that more wildebeest on the Serengeti can result in more giraffes. Why? Well, if the wildebeest have died off to lower numbers (e.g. by a disease, rinderpest, that was a great problem in the early 20th century), then the grasslands will not be grazed as much, and there will be more tinder in the dry season for fires. These fires can kill off the new trees which grow up to become giraffe food. The links between rinderpest in wildebeest, grassfires, trees, and giraffes has a daisy chain of positive and negative feedback in it, which can resemble our own internal metabolism.
Thus, the normal (and often quite chaotic, in the mathematical sense) variation of a given species population can get moderated, by things such as a reduction in prey leading to a reduction in predator numbers, or a shift by them to an alternate food source. Carroll takes us through a number of examples, some of them closer to home in the fishing lakes of the northern Midwest (where the loss of a link in the food chain can result in algae mats choking a lake). I quite enjoyed this part as well, since it was telling me more about ecology than the standard "oh we have sinned and if we don't repent soon it is DOOM for us all!" that so many with concern for the environment concentrate on (which is both depressing and uninformative, and also by the way not very likely to convert anyone to your cause who wasn't already on board).
The very last part of the book is an attempt to make the case that, just as we were able to solve problems in medicine using our knowledge of how the interrelations of molecular biology worked, we can solve problems with our environment by using what has been learned in recent decades about how ecosystems work. Some of it, like the case study of Gorongosa Park in Mozambique, is quite good. Towards the very end, Carroll gets a bit carried away with an analogy between the effort to eradicate smallpox and the need to restore ecosystems. I'm not sure that this part holds up to close scrutiny, since the competition between manufacturing in different countries to have the lowest cost has a tendency to drive everyone together towards lower environmental standards, and smallpox didn't face a similar pressure on countries to NOT vaccinate their population. But it's a small blemish on an otherwise excellent book, and in any case the story of how smallpox was eradicated is in itself interesting enough.
When the book was finished, I wished there were more of it to read.