I thought I would jump in here belatedly and toss out a few more comments. First of which would be to thank @John_Harshman for a nice review of the first several parts of Darwin’s Doubt.
I hadn’t picked up the book for many years, and re-reading it was interesting. On a positive note, I believe this book is a reasonable summation of the progress, as it were, of the ID movement over the decades. It seems as if Meyer wanted to pull together most of the cogent arguments that ID proponents had raised against evolution over the years, and to tie these together into as coherent a train of thought as possible. I believe he did a credible job in this book.
Of course, in so doing, he has summarized, in one place, all of the time-worn and refuted arguments that has shaped the core of ID thought over the decades. The strange obsession that the ID camp has for the Cambrian Explosion is presented in full display, and the problems with their arguments are being hashed out quite nicely in this thread. I have nothing to add, mainly because better-qualified persons are doing such an excellent job here. My own interest has to do with molecular genetics and the like, which are subjects of Chapters 8-12 in this book. I won’t post a lengthy review of these chapters, since most of the issues raised are familiar and can be summarized fairly succinctly.
The title of Chapter 8, “The Cambrian Information Explosion”, is pretty self-explanatory, and tries to make the case that the Cambrian Explosion must have been heralded by some massive increase in information. This is a theme that recurs in the book. I believe this assertion has been discussed by others in this thread, and I don’t need to add anything.
The title of Chapter 9 is “Combinatorial Inflation”. A centerpiece of the chapter is the “legendary” Wistar Institute Conference of 1966, and deliberations that started to get at the matter of the ratio of functional sequences to all possible sequences. (One subsection is aptly titled “In Search of the Ratio”.) Favorable mention is made of the simplistic view (1/20^n) as well as some estimates borne out of sequence alignments that still yield vanishingly small numbers. To Meyer’s credit, though, some shortcomings are acknowledged, and he frames the work of subsequent ID proponents as seeking to address some of the problems with this naïve approach.
The title of Chapter 10 is “The Origin of Genes and Proteins”. The centerpiece of this chapter is Doug Axe, and his work that sought to better define the ratio mentioned in the preceding paragraph, namely that of function to all possible sequences. Put in this light, I would offer that Axe’s work was and is laudable. Other subjects are touched upon, but the emphasis is on the implications of Axe’s work, namely that protein function is rare in sequence space.
The title of Chapter 11 is “Assume a Gene”. The point of this contention is the matter of the origins of the many new genes assumed to be necessary for the appearance of new animals in the Cambrian Explosion. Initial focus is placed on a review article by Manyuan Long et al. entitled “The Origin of New Genes: Glimpses from the Young and Old”; this focus seems to derive from favorable mention of the review, and of the various mechanisms for the origins of new genes, by three thorns in the side of the Discovery Institute – Alan Gishlick, Nick Matzke, and Wesley Elsberry. These mechanisms deal with various ways by which gene duplication, exon shuffling, and other rearrangements might give rise to genes whose protein products encode novel activities. The feasibility of these mechanisms is argued against on largely theoretical grounds, based on ideas concerning protein folding, domain structures, and the like. (Ann has raised some of these issues in other threads.) Subsequently, Meyer raises the problem of the origins of so-called ORFans – genes and proteins with no apparent evolutionary ancestor. The likelihood that such genes might arise is discounted at least in part on the basis of Axe’s work.
The title of Chapter 12 is “Complex Adaptations and the Neo-Darwinian Math”. The general gist of the chapter is the need for complex adaptations, and therefore complex protein structures, during the unfolding of the Cambrian Explosion. These complex adaptations will require numerous coordinated mutational events, and thus run up against conceptual problems outlined in, among other places, a paper by Behe and Snoke and Behe’s book entitled “The Edge of Evolution”. Additional mechanisms involving co-option of extant proteins for new functionality are confounded by, among other things, research conducted by Gauger and Axe.
As John Harshman’s more extensive review here and the discussion show, there is a lot to talk about in this book, and this certainly holds for these four chapters. However, rather than a laborious (most here might prefer the descriptor excruciating) point-by-point takedown, I will try to convey my own overview and summation. As I stated above, this book is a reasonable overview of ID thinking circa 2013, something that (IMO) hasn’t changed much in 5 years or so. In the four chapters I have briefly described, Meyer lists several of the key pieces of research upon which are (still) based the core of Intelligent Design. Among these are:
Axe (Axe DD. Estimating the prevalence of protein sequences adopting functional enzyme folds. J Mol Biol. 2004 Aug 27;341(5):1295-315.) – the seminal study that purports to prove that functional sequences are impossibly rare in sequence space.
Behe and Snoke (Behe MJ, Snoke DW. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 2004 Oct;13(10):2651-64.) – the study that claims to have established that impossibly long times are required for even the simplest of mutational pathways to be “enacted”.
“ The Edge of Evolution: The Search for the Limits of Darwinism ” by Michael J. Behe – the book in which Behe immortalizes the number 10^-20 as a value representing the rarity of occurrence of appearance of a new protein functionality.
And Gauger and Axe (Gauger AK, Axe DD (2011) The evolutionary accessibility of new enzyme functions: a case study from the biotin pathway. BIO-Complexity 2011(1):1-17.) – this study has been discussed by @Agauger elsewhere in this forum, and she is welcome to briefly summarize its implications here. They basically have to do with the difficulty (impossibility?) of extant proteins acquiring new functionality by mutation.
(I would include here parts of Chapter 11 that, as far as I know, have not been formally published anywhere. These parts deal with objections to several of the specific mechanisms laid out in Long et al. that concern the evolution of novel function via gene duplication, domain addition or swapping, exon shuffling, and the like.)
This is a useful summary that Meyer gives us, as it connects some oft-discussed (and debated) studies with a foundational core of ID thought – namely, that macroevolutionary processes (as represented by the Cambrian Explosion) are beyond the reach of evolutionary processes. I would go so far as to say that the body of work given us by Meyer in these 4 chapters is central, foundational, essential to the ID movement. This was the case in 2012 (when, I suppose, Meyer was wrapping up the writing) and is, in my estimation, true today.
Which brings me to my point. ID proponents today treat this body of work as the last and final word on the matter of gene and protein evolution. However, as has been seen in this forum and elsewhere, each and every one of these works is fundamentally flawed, and in fact do not lead to the broad, sweeping generalizations and conclusions that are seen in the ID literature. What Meyer has in fact shown us is that the anti-evolution arguments that are part and parcel of the ID movement are based on studies that are fundamentally (I would argue fatally) flawed. Along with the service Meyer provides regarding the overview of the history of the ID movement, this latter outcome is one for which Meyer might be thanked.
(The review by Long and colleagues that occupies part of Ch. 11 - Long M, Betrán E, Thornton K, Wang W. The origin of new genes: glimpses from the young and old. Nat Rev Genet. 2003 Nov;4(11):865-75.)