ENV editor David Klinghoffer has already drawn our attention to the new book by Ann Gauger, Douglas Axe and Casey Luskin on Science and Human Origins.
Although intelligent design is not committed to a particular view on whether our species Homo sapiens shares a common ancestor with other primates, the new book, published by Discovery Institute Press and aimed at the popular level, offers a thoughtful and timely evaluation of the scientific evidence bearing on the question of human origins.
Science and Human Origins, and Darwin’s Little Engine That Couldn’t
In Chapters 1 and 2, Ann Gauger and Douglas Axe respectively argue that serious caution is warranted when it comes to inferring common ancestry on the basis of similarity alone. As they show in their 2011 paper in the journal BIO-Complexity, even a relatively trivial change in function from Kbl to the function of its closely related homolog BioF requires a timespan that far exceeds the age of the earth.
Ann Gauger writes,

My colleague Douglas Axe and I took two bacterial proteins that look a great deal alike, but have distinctly different functions. They are thought to be evolutionary cousins, descended from a common ancestor millions of years ago, because of their similar structures. […] Kbl and BioF are not directly descended from each other; nonetheless, a functional shift from something like Kbl to something like BioF must be possible if neo-Darwinism is true. Functional shifts like this one are found everywhere in families of related proteins, and so should be relatively easy to achieve.
Yet when we experimentally determined how many mutations it would take, we found that it would take at least seven mutations to evolve one enzyme into the other — too many mutations to have occurred by an unguided neo-Darwinian process.

Gauger concludes that “similarity of structure is not enough to establish that there is an adaptive path between two proteins with distinct functions.” Of course, similarity can be adequately accounted for within the paradigm of common design. From her research, Gauger considers the implications for the evolution of humanity:

Let’s begin by considering what distinguishes us from great apes. What are our distinctive characteristics? There are significant anatomical differences, of course: Our upright walking, longer legs, and shorter arms, changes in muscle strength, our significantly larger brains and skulls (three times bigger than great apes), and our refined musculature in hands, lips and tongues. There are also our relative hairlessness and changes to our eyes. More importantly, there are whole realms of intellect and experience that make us unique as humans. Abstract thought, art, music and language: These things separate us from lower animals fundamentally, not just in degree but in kind.

Furthermore,

Chimps are suited for life in the trees. Humans are suited for life on the ground, walking and running. The anatomical changes needed to move from tree-dwelling to complete terrestrial life are many. To walk and run effectively requires a new spine, a different shape and tilt to the pelvis, and legs that angle in from the hips, so we can keep our feet underneath us and avoid swaying from side to side as we move. We need knees, feet and toes designed for upright walking, and a skull that sits on top of the spine in a balanced position. (The dome of our skull is shifted rearward in order to accommodate our larger brain and yet remain balanced.) Our jaws and muscle attachments must be shifted, our face flattened, and the sinuses behind the face and the eye sockets located in different places, to permit a forward gaze and still be able to see where to put our feet.

Varki and Altheide (2005) document hundreds of phenotypic traits that differ between humans and great apes.
Gauger goes on to consider whether there has been enough time (roughly one and a half million years) to render plausible the number of instances of anatomical novelty that are required to change an Australopithecus afarensis into a Homo erectus. Citing Durrett and Schmidt (2007, 2008), Gauger draws on their conclusions that “for a single mutation to occur in a nucleotide-binding site and be fixed in a primate lineage would require a waiting time of six million years” and that “it would take 216 million years for the binding site to acquire two mutations, if the first mutation was neutral in its effect.”
Since the transition from our last common ancestor with chimps to modern humans is only about six million years, argues Gauger, the time allowed is nowhere near enough to accomplish such a feat of genetic and anatomical re-engineering, especially since “many of the anatomical changes seen in Homo erectus had to occur together to be of benefit.”
Douglas Axe concurs. In Chapter 2 of the book, he writes,

So, if this humanity thing is on a level of its own, how reasonable do you suppose it is to chalk it up to Darwin’s little engine? It’s one thing to say that chimps and humans are similar enough that their likeness calls for careful explanation (few would argue with that), but as we’ve now seen it’s quite another to say that they are similar enough for Darwin’s engine to have traversed the gap between them. To insist on that is to ignore the evidence. A comparison of the complete human and chimp genomes has identified twenty distinct gene families, each with multiple genes, that are present in humans but absent from chimps and other mammals. That’s a huge gap when you compare it to the single in-family gene transition that we examined.

Human Origins and the Fossil Record
In Chapter 3, Casey Luskin weighs the evidence from the fossil record that bears on humanity’s origin. Luskin skeptically examines a number of fossils that have been thought to connect humans with other primates. Among these are the early hominin fossils of Sahelanthropus tchadensis (also called the “Toumai skull”), Orrorin tugenensis (“Orrorin”), and Ardipithecus ramidis (“Ardi”), in addition to the later Australopithecine fossils such as Lucy.
The problem with Sahelanthropus tchadensis is that the reconstruction is based on only a single skull and some jaw fragments, thus difficult to be reliably classified as a hominin. Orrorin tugenensis is also of a highly fragmentary nature, its remains being composed of some teeth, pieces of the lower jaw, arm and thigh. The evidence for the species’ mode of locomotion is thin and, even if it was bipedal, this can hardly be used as a litmus test for its hominin status. As Luskin explains, “the fossil record contains bipedal apes which evolutionists recognize were far removed from the human line.”
The bones of the famous Ardipithecus ramidus (“Ardi”) fossil, which made media headlines in 2009, were found in the early 1990s in a crushed and fragile state, perhaps having been trampled by hippos.
Luskin notes that there is also significant question regarding whether “Ardi was necessarily ancestral to humans.” He quotes Wood and Harrison (2011), who note that the fossil, if indeed it is a hominin, exhibits “remarkably high levels of homoplasy among extant great apes.”
Luskin goes on to a discussion of the Australopithecines, beginning with Australopithecus anamensis (which is thought to link Ardipithecus to the australopithecines). He asks,

What exactly was found? According to the technical paper reporting the find, the bold claims were based upon a few fragmented canine teeth that were said to be “intermediate” in size and shape. The technical description used in the paper was intermediate “masticatory robusticity.” If a couple of four million-year-old teeth of “intermediate” size and shape make “the most complete chain of human evolution so far,” then the evidence for human evolution must indeed be quite modest.

Luskin discusses the notorious Lucy fossil, which is similarly problematic because of its highly fragmented state. As Luskin notes,

Only 40% was found, and a significant percentage is mere rib fragments. Very little useful material from Lucy’s skull was recovered, yet she is one of the most significant specimens ever found.

Furthermore, Luskin notes, the claim that Lucy’s mode of locomotion was bipedal has been challenged by many scientists. Indeed, Collard and Aiello (2000) argue on the basis of Lucy’s hand-bones that she “knuckle-walked.” Moreover, they consider much of Lucy’s body to be “quite ape-like” with “relatively long and curved fingers, relatively long arms, and funnel-shaped chest.”

[M]any have challenged the claim that Lucy walked like we do, or was even significantly bipedal. Mark Collard and Leslie Aiello observe in Nature [see the paper here] that much of the rest of her body was “quite ape-like,” especially with respect to the “relatively long and curved fingers, relatively long arms, and funnel-shaped chest.” Their article reports “good evidence” from Lucy’s hand-bones that her species “knuckle-walked,” as chimps and gorillas do today.

Luskin concludes by arguing that the hominin fossil record is “marked by incomplete and fragmented fossils” where species continually appear in an abrupt fashion.
Francis Collins, Junk DNA, and Chromosomal Fusion
Chapter 4, also written by Casey Luskin, addresses the arguments advanced by Francis Collins and others regarding “junk DNA” and the fusion-origin of human chromosome 2. The first half of the chapter discusses the wealth of literature that has been published over recent years documenting a plethora of important functions for non-protein-coding DNA, thus rendering appeals to supposed “junk DNA” as an argument for common ancestry dubious.
The second half of the chapter discusses the argument, with which readers of ENV will be well acquainted, from the fusion origin of chromosome 2. Luskin points out that even if chromosome 2 did result from a fusion event, it does not demonstrate common descent since the fusion took place within our lineage after the supposed split from chimpanzees. While the evolutionist might respond that the banding patterns of chromosome 2 match two of the autosomes in chimpanzees, this only brings us back to the argument from similarity.
Luskin also points out that the evidence for the fusion origin of chromosome 2 is not entirely conclusive. In reference to the 2q13 interstitial telomeric sequences (ITS) which, in chromosome 2, are found in the middle of the chromosome, he cites Farre et al. (2009). These researchers documented that, though there are many known instances of these interstitial telomeric sequences in the genomes of humans and chimps, the 2q13 interstitial telomeric sequence is the only one that is potentially to be associated with an evolutionary breakage point or fusion. The other ones fail to line up with primate chromosomal breakpoints.
Although Luskin doesn’t address the other evidence for the fusion event, these are in my judgment similarly inconclusive. For example, with respect to secondary alpha satellite DNA on chromosome 2 (which evidences the presence of two centromeres), one interesting study, from Baldini et al. (1993), reported the presence of secondary alpha satellite DNA on human chromosome 9. To further complicate matters, Luke and Verma (1995) subsequently reported on the occurrence of secondary alpha satellite DNA in all primates.
The Science of Adam and Eve
The final chapter of the book, by Ann Gauger, explores the implications of population genetics for scientific claims made by evolutionary biologist Francisco Ayala and the BioLogos Foundation that modern biology refutes the possibility of a first human couple, “Adam and Eve.” Although the research program associated with intelligent design does not encompass this question, and though it is only one chapter in a longer book, this is a profound subject with undeniable theological implications. The chapter itself does not take a position on the historicity of Adam and Eve. Nor does it delve into any related theological or historical issues. It merely offers a critique of a widely touted objection to the historicity of the traditional first couple.
Ayala and his supporters make a scientific claim, to which Ann Gauger offers a scientific rebuttal. Unless Ayala’s original research is held to be “religious” in nature, then it must be recognized that Gauger’s conclusions are not “religious” either but instead are based squarely and exclusively on scientific considerations.
Specifically, she offers a critique of the claim that “there is too much genetic diversity to have passed through a bottleneck of just two individuals.” Gauger lists five assumptions that undergird “the equations used to reconstruct these trees, and to calculate ancestral population sizes.” These assumptions are:

• Fixed population size.
• No migration.
• Random mating.
• Constant mutation rates.
• No selection.

Using a case example of the HLA-DRB1 histocompatibility antigen, Gauger shows how assuming these factors can yield misleading results. She replies to the argument put forward by Francisco Ayala:

…Ayala calculated that there were thirty-two separate versions of the entire HLA-DRB1 gene present at the estimated time of our last common ancestor with chimps four to six million years ago (also not a sure thing — these estimates keep changing). In order for all those variant alleles to make it to modern times, he further estimated that the minimum size of the ancestral population was no fewer than 4,000, with a long-term average effective population size of 100,000. […] Because of this minimal estimate of 4,000, Ayala claimed that at no time was it possible for the human population to have passed through a bottleneck of two. In his view, there is just too much ancestral diversity in HLA-DRB1.

The problem? Ann Gauger explains that Ayala “inadequately controlled for two of the above assumptions,” i.e. the assumption of no selection and a constant background mutation rate. Furthermore, she explains, using a different portion of the gene which does have a “mutation rate close to the genomic background,” yields a different result — 7 alleles as opposed to Ayala’s 32 and an estimated population size of 10,000 as opposed to Ayala’s 100,000.
Gauger also discusses some interesting gene phylogenies that are difficult to account for within the paradigm of common descent. Many critics will, of course, ignore the fact that Gauger’s argument is purely scientific and conflate the theological implications of her argument with the argument itself.
There is a lot more detail given in the chapter. But I’ll not give away any more. I instead encourage readers to purchase and read the book.
Conclusion
To conclude, I would echo the sentiments of Douglas Axe:

As someone who loves science, I have to say that I can think of no conclusion in the whole history of the discipline that is so firm and so profound and so original that it should cause every human being to stop and rethink what it means to be human. Most simply aren’t that profound. I happen to think that Darwin was that profound, but thankfully, also profoundly wrong.

Science and Human Origins is a book that I would highly recommend, in particular for those with an interest in the current debate over origins but without the necessary expertise to dig deeply into the technical literature. Go ahead and pick up your hard or electronic copy from Amazon.