The majority of the book focuses on criticizing neo-Darwinian evolution (and some materialistic alternatives to it that have been suggested as well) as an explanation for the origin of new animal life (focusing particularly on the Cambrian Explosion). So far as I am competent to judge (which is only to a limited degree), I think Meyer does a fantastic job here. His critique is extremely thorough and detailed, apparently leaving no stone unturned (at least of all the stones we currently know about). He does a wonderful job of being fair in stating as strongly as possible the opposing points of view and the arguments used to support them before offering a fantastically detailed rebuttal of them. The book has definitely reinforced my suspicion that neo-Darwinism simply doesn't and can't work as a mechanism for explaining the forms of life that exist.
The last part of Meyer's book is devoted to defending Intelligent Design as the best explanation for the origin of the Cambrian forms of life and new animal life in general (his book assumes a standard mainstream scientific view of the age of the earth and the fossil record). I think he makes a very worthwhile case in this part as well. However, I would like to offer some further thoughts on and even some criticism of Meyer's positive case for ID.
Meyer affirms that ID is the best explanation for the Cambrian animals, and animals in general, arising in history, on the grounds that while we never see materialistic (unintelligent) causes producing complex specified information such as we see in living things, we often see intelligent agents producing such information. Thus, Meyer believes he can make a pretty straightforward uniformitarian-type affirmation: We should look for causes operating today to explain past events. Only intelligent causes can be seen acting today to produce new complex specified information (such as is found in buildings, computers, etc.). Therefore, it makes the most uniformitarian sense to invoke intelligent causation as the best explanation for new animal life. This argument definitely has some significant plausibility. It is certainly a scientific argument worthy of careful consideration.
However, I have a few concerns with the argument:
1. First of all, it is certainly true that non-intelligent processes are not known to be able to produce the kind of complex specified information seen in living things. In fact, as Meyer has shown well (so far as I can tell), they seem utterly inept at producing such information. It is also true that, in our regular experience, only intelligent agents are known to be able to produce such complex specified information. Meyer compares his inference to ID to explain animal life to the inferences to humans in the past archaeologists often make when explaining various ancient artifacts (like the Rosetta Stone).
However, in my opinion, Meyer does not take adequately into account a significant difference between the inferences of archaeologists to earlier human conscious activity and his inference to an intelligent designer to explain aspects of living systems. In the first case, everyone agrees that there were conscious agents living in the past who were humans like us who tend to produce things like the sorts of artifacts we often find buried in the ground. We all accept previous human history before our time, so we all acknowledge that there were humans in the past we can draw on to explain artifacts that appear to have been intelligently designed. In addition, the artifacts archaeologists typically find are obvious built for use by human beings, and often for purposes that are at least somewhat apparent. For example, if an archaeologist finds a necklace buried in the ground which could fit around a human neck, it is not a big jump to assign the creation of that necklace to a human being living in the past. Or if we find pottery, it is not a big jump to recognize that humans often make containers to put things in and therefore to assume that that sort of activity explains the pottery. Or when we find writing, we know that we ourselves use writing to communicate and so it is natural to assume that previous humans produced the writings we find in the ground (and this is augmented when we can read the writings and see that they deal with subjects we modern humans are quite familiar with).
When it comes to life, however, it is evident that human agency cannot be the explanation for its existence. We ourselves are a part of the group of "living things" that needs to be explained. Therefore, in this case, we have no known agents acknowledged by everyone to exist that can be appealed to to explain the origin of living things. To appeal to intelligent causality to explain the origin of living things, we have to bring in more controversial beings such as advanced aliens, gods, God, etc. The fact that such beings are more controversial makes the inference to their agency significantly more of a stretch than an archaeologist's appeal to ancient human agency to explain pottery, etc. This additional stretch weakens, to some degree, the force of the argument. It may still be the case that ID is a better explanation than non-intelligent material explanations, but the argument is nowhere near as evident or strong in this case than it is when archaeologists appeal to human agency.
Bringing in non-human intelligent causation requires the raising of a whole host of new questions and issues that have to be addressed, such as the question of the plausibility of there being non-human intelligent agents capable of supplying the agency required to produce the information in living things. For example, let's look at the idea that the non-human agency involved in producing living things on earth may have been supplied by advanced aliens. Positing such a thing requires an appraisal of the probabilities involved in the idea of alien life visiting earth and producing living things on it (and doing this perhaps a number of times over billions of years in a systematic sort of way, considering that--assuming a mainstream scientific view of the age of the earth and the fossil record--various living things have appeared in history at different times over very long stretches of time). How plausible is it that advanced alien intelligent life exists in the universe? How plausible is it that such beings would have been able to get to earth? How plausible is it that they would have even wanted to get to earth (motivation is a relevant and unavoidable issue when appealing to intelligent agency)? How plausible is it that these beings would have been able to produce living things on earth? Why would they do this over perhaps a period of billions of years, without showing any other signs of their existence? And so on. I do not point to these and other such questions to suggest that they cannot in principle be answered, but to point out that they have to be asked. An ID proponent cannot simply shrug these questions off for further research, for the plausibility of the ID argument to a significant degree depends upon the answers to these kinds of questions (assuming that advanced alien life forms were the intelligent designers).
2. If the intelligent designer of life on earth was advanced aliens, then it is a safe inference that these aliens, being physical, material, finite beings like us, would exhibit the same basic sort of complexity that life on earth exhibits and which requires us to seek an explanation for it. In other words, if life on earth had to have been designed by a prior intelligence, that prior intelligence (if it fits in a category like "advanced aliens") would also need to have been designed by another intelligence prior to it. And that prior intelligence (assuming more "advanced aliens") would need to have been designed by another intelligence prior to it, and so on and on ad infinitum. But an infinite regress of intelligences creating future intelligences leaves us with no ultimate explanation for intelligence at all, for infinite regresses do not explain the origin of anything but simply keep pushing the problem back forever without ever resolving it. So it would seem that the logic of the ID inference would preclude advanced aliens from being the final explanation for the origin of the information in living systems on earth. Therefore, the logic of ID inherently requires something beyond advanced aliens.
In fact, the only way to avoid such an infinite regress attaching to the ID inference is to end up positing the classical theistic God. Only such a being has the properties necessary to avoid having to be traced back to a prior explanation. (See my book, Why Christianity is True, and particularly the chapter on "God", for arguments to that effect.) What causes Meyer and others to see a need to appeal to intelligent causation to explain living systems is their specified complexity--that is, the fact that they are complex, information-rich systems with parts geared towards functioning together to support the common system, systems of such complexity and possessing such highly specified information that it is not realistic to expect blind processes to hit upon them. Intelligence is appealed to because intelligent agents have the ability to envision such systems and then to manipulate the physical world to instantiate in it the systems they envision in their minds. Intelligent agents can provide complex specified information.
The real issue here is the unified diversity of living systems. Whenever there is a system--that is, a unified whole made up of interacting parts, such a system must be explained by reference to a prior more unified reality from which it is derived. This is a key argument in a case for the existence of God:
The material universe appears as an interacting system, and therefore as a unit, consisting of several parts. Hence there must be a unitary Agent that mediates the interaction of the various parts or is the dynamic ground of their being. (Louis Berkhof, Systematic Theology [Grand Rapids: Eerdmans, 1941], p. 26--referring to an argument by B. P. Bowne)
God is the most simple being; for that which is first in nature, having nothing beyond it, cannot by any means be thought to be compounded; for whatsoever is so, depends upon the parts whereof it is compounded, and so is not the first being: now God being infinitely simple, hath nothing in himself which is not himself, and therefore cannot will any change in himself, he being his own essence and existence. (Stephen Charnock, The Existence and Attributes of God, 2 vols. [1853; repr., Grand Rapids, MI: Baker Book House, 1979], I: 333--quoted in this article)
(See also the aforementioned chapter on "God" in my book, as well as this earlier blog post.)
Atheists, obviously, don't accept the existence of God. So how do they explain the interacting diversity of parts that make up the universe? Well, they do so in different ways. One way some of them do it is to appeal to a unified reality from which all this diverse reality is derived. This unified reality differs from the classical theistic God in that it is deemed to be impersonal rather than personal. In short, what is envisioned is a single, undifferentiated, indivisible, impersonal (that is, not possessing consciousness) reality from which all is derived. This is thought to explain the diversity-in-unity of the universe.
I would argue, as I do in my book, that such an impersonal unified reality is not sufficient to explain the universe we live in because our universe is full of consciousness and there is no explanation for consciousness in a non-conscious ultimate reality. Thus, to explain the unity-in-diversity as well as the existence of consciousness in our universe, we must posit an ultimate, supreme being who is both absolutely unified and indivisible (simple) as well as conscious--namely, God. Therefore, the ID inference ultimately requires and leads to the idea of the classical theistic God.
3. The reason this is a problem for ID argumentation is that ID proponents typically want to say that the ID argument is distinct from "religious" arguments for the existence of God. They want to distance ID from being just a particular instance of a larger battle between theism and atheism. They want to say that the ID argument is a scientific argument and not a philosophical argument, and that one need not be a theist to accept the reasoning of the argument. But it is impossible to separate the ID inference from this larger theist-atheist argument.
For example, take the atheist argument mentioned above--that the universe can be explained by appealing to a non-conscious, unified ultimate reality. While I would argue that such an explanation fails because it does not account for consciousness, this argument of mine as well as the atheist response to it are philosophical in nature and not scientific (assuming a view of things that sees these two methods of inquiry as distinct). If we assume a naturalistic philosophy, there is no problem explaining the universe by means of an ultimately impersonal reality. And this allows the naturalist to escape the force of the ID inference. If Meyer argues that living systems require an intelligent designer because of their specified complexity, an atheist/naturalist could respond in this way: "The entire universe is full of complex specified information. The universe is a system of interacting parts which requires a single, unified source to explain it. That explanation is the single, undifferentiated, impersonal reality (perhaps the state of the universe before the Big Bang) that gave rise to everything else. The real issue is explaining systems that have parts that are oriented towards each other to function together as a complete system. Explaining such systems doesn't require intelligence; it simply requires that a system be derived from a more ultimate unified reality. Living systems are just one example among many of specified complexity in the universe. If the entire universe as a whole does not need an intelligent designer, but simply an impersonal unified source, then life can be explained the same way. Living systems are simply one aspect of the diversity-in-unity of the universe that is explained by tracing the universe back to a more ultimate, unified, impersonal state."
Such an explanation is certainly not Darwinian. Darwinism assumes that life is not pre-programmed into the universe, but has to evolve by means of chance events combined with orderly processes like natural selection. This alternative atheist argument I've just articulated assumes, rather, that life is pre-programmed into the universe, so that the origin and development of life is not due to chance, but it denies the need to explain such "pre-programming" by means of intelligent agency. Instead, it explains the pre-programming by means of an ultimate, unified, impersonal state of reality from which the diversity of space and time are derived. An analogy may help here: Imagine a pattern etched into a rock by non-intelligent forces such as wind, rain, etc., acting over time. If that rock were to be broken into pieces, the pieces would still fit together. They would be oriented towards each other, not by chance, but by a "pre-programming" originating in the fact that the rock was once whole. We need not bring in intelligent agency to explain the fact that the parts go together and form a unified system that transcends what chance could produce. We need only appeal to the unified origin of the parts of the rock. Similarly, an atheist could look at how the universe exhibits diversity-in-unity that transcends what chance could produce, and he could see life as a built-in manifestation of that diversity-in-unity, "pre-programmed" into the universe, and explain it all not by reference to intelligent agency but to the universe being derived from an impersonal, unified, ultimate reality. In fact, he might argue on philosophical grounds that the idea of God is highly implausible or even impossible, and thus that some impersonal ultimate reality is either necessary or at least highly likely.
As I mentioned earlier, I think there are fatal flaws in this way of explaining the universe, but my arguments here would not be scientific but philosophical. There is no way to make a non-philosophical, scientific argument that exposes the flaws in this reasoning. Therefore, while I think that Meyer has (so far as I can tell) successfully made a good scientific case against neo-Darwinian mechanisms and other materialistic mechanisms relying to a great degree on chance being able to explain the specified complexity of living systems, I don't think he has made a truly compelling scientific case for ID as the best explanation for such specified complexity. His case begs the question, because it assumes a theistic rather than an atheistic philosophical system and is dependent on theistic philosophy for its strength without acknowledging this assumption and dependence. Meyer cannot fully establish his ID inference without delving into the broader philosophical arguments between theists and atheists, and so since his argument is presented as a scientific and not a philosophical argument, it is ultimately question-begging. (On the other hand, if it were presented as a philosophical argument, it would reveal itself ultimately to be simply another example of classic argumentation for the existence of God such as that of historic monotheistic theologians and philosophers.)