Sunday, 10 July 2011

Debunking Corner: Prothero Review Reviewed

One of our forums has been having fun over the past few weeks taking apart a piece written by Marc Surtees of the Edinburgh Creation Group.

Marc did respond to some of the points made, but to be perfectly honest none of the responses really seemed of any substance.  By all means read the full thread if you want to. 

Well done Dannyno.

Marcsurtees vs Prothero 

On Haeckel
I've been reading the review of Prothero by Marc Surtees which has been posted here.

The third paragraph of Surtees' review says:

Surprisingly we find a copy of Haeckel’s drawings of embryos (p.110) and the statement that although Haeckel may have been over‐enthusiastic with his diagrams  he was essentially right.  
Prothero completely overlooks work published by Richardson et al (1997) which demonstrates that the embryological differences are much more significant.  Then, as if to clinch the argument and close down any remaining opposition, Prothero provides us  with a picture of a human embryo at five weeks (p.111) and states that, “You still had many fish‐like structures, such as a well‐developed tail and the embryological precursors of gill slits,”  which is simply not true.
To take the points in order, Prothero reproduces George Romanes' drawings (the citation is clear), "after Haeckel" (, rather than copies of Haeckel's original drawings, as Surtees states.

What Prothero says about Haeckel is rather more nuanced than Surtees admits. He actually goes back to von Baer's earlier work on the commonalities of embryonic development. As for Haeckels's notion that "embryonic development... repeats... evolutionary history" (p.108), Prothero says:
To the limited extent that von Baer had shown 40 years earlier, this is true. But embryos also have many unique features... that have nothing to do with the evolutionary past and are adaptations to their developmental environment. Thus it is dangerous to overextend the evolutionary implications of the stages in an embryo, but they are useful guides nonetheless.
Richardson et al (1997) is an interesting piece of work. Their conclusion is this:
Haeckel’s drawings... have been used to substantiate two quite distinct claims. First, that differences between species typically become more apparent at late stages. Second, that vertebrate embryos are virtually identical at earlier stages. This first claim is clearly true. Our survey, however, does not support the second claim, and instead reveals considerable variability – and evolutionary lability – of the tailbud stage, the purported phylotypic stage of vertebrates. We suggest that not all developmental mechanisms are highly constrained by conserved developmental mechanisms such as the zootype. Embryonic stages may be key targets for macroevolutionary change.
Prothero is in explicit agreement with this point, as ought to be clear from his reference to "adaptations to their developmental environment".

Notice that Richardson et al (available online here: do clearly state that species differentiation becomes "more apparent at late stages". Richardson et al are actually addressing a very specific point. They do not deny that pharyngeal pouches are seen in embryos, they only question whether there is such a thing as a common pharyngeal stage (p.92):
The phylotypic stage in vertebrates has been defined as the pharyngula stage, after the series of pharyngeal pouches seen in embryos (Ballard 1981). However it is not clear precisely which stage of development this represents, since pharyngeal pouches appear over an extended period of development.
Thus, Richardson does not support Surtees at all.

- - -

On fish and gills

Surtees claims that Prothero says: "You still had many fish‐like structures, such as a well‐developed tail and the embryological precursors of gill slits” at five weeks. Surtees says this is "simply not true".

Well, what is "simply not true"?

Surtees quotes the text around the image, but not the explanatory text in the main part of the book, where Prothero is much clearer:
If you had any doubts that you once had ancestors with fish-like gills and a tail, Figure 4.11 shows what you looked like five weeks after fertilisation. Why did you have pharyngeal pouches (predecessors of gills) and a tail if you had not descended from ancestors with those features?
What's "not true" about that? Is that not what we look like at five weeks, or does the picture not show what Prothero says it shows, or are pharyngeal pounches not the predecessors of gills? 

Surtees is not specific.

- - -
On the fossil record
In paragraph 4 of his review, Surtees comments on Prothero's section about "systematics and evolution":
Prothero then goes on to remind his readers that this is not a problem for an evolutionist because they know the ancestors existed, and it is dishonest for a creationist to claim that the ancestors are missing.   He also insists that we have to understand that “evolution is a bush not a ladder” (p.125) as if that resolves all the problems with the fossil record.   It does not explain why we only ever see the twigs and tips and almost never the hypothetical common ancestor. This is a litany that he repeats quite often (see pp.221, 263, 280), as if that will somehow prove that evolution is true, whereas creationist biologists are perfectly aware of the bushiness of the fossil record and find this supports a biblical view of biology.
The section referred to here is not doing what Surtees claims it is doing. It is clarifying what the debate about ancestry, is really about, contra creationist claims.

The point is not that "it is dishonest... to claim that the ancestors are missing", but that it is dishonest to present the debate about systematics to be about whether evolution happened or not. Rejecting the concept of ancestry is not a rejection of the concept that living things must have had ancestors. Prothero also makes the point that the incomplete fossil record makes it "highly unlikely that any particular fossil in our collections is the remains of the actual ancestor of another taxon." (p.134).

On p.125 Prothero does not say that "evolution is a bush not a ladder" as if that "resolves all the problems with the fossil record"! He repeats the phrase in order to drive home the point that the search for "missing links" is misconceived. It's not any kind of attempt to "prove that evolution is true" in isolation.

- - -

On Life's Origins

Says Surtees:
Prothero states that Miller was able to produce “molecules of biological relevance and complexity”, which is strictly speaking true, as he was able to produce amino acids. He goes on to state that, “Even though amino acids are much more complex than the chemicals he started with, Miller showed they were remarkably easy to produce.” This ignores the fact that the next steps to functional proteins do not occur spontaneously and are much more difficult, yet Prothero states repeatedly that it is very easy to get biologically complex molecules. 
The quotes above are both on p.148 of Prothero.

However, only the second is actually Prothero's words. The line about "molecules of biological relevance and complexity" is actually a quote by Prothero from Andrew Knoll's "Life on a Young Planet: the first three billion years of evolution on Earth" (2004). Odd for Surtees not to notice that, but I guess par for the course so far.

Surtees goes on to claim that 
He leaves the reader with the impression that life gets started because the simple building blocks “link up” and form functionally useful polymers, which is not true.
This is a bit vague: what's not true? 

That the "simple building blocks" do not "link up" into "functionally useful polymers", or that the linking up isn't how life gets started? It's important to be clear what the objection is before trying to address it.

Anyway, Prothero actually says things like this (p.152):
For origin of life research, the biggest challenge is how to assemble longer and more complex polymers, especially the long proteins that are so important for life. Most of the primordial soup chemical experiments have produced only shorter proteins.
and, after reviewing some approaches (p.153):
Naturally, these highly speculative ideas are very controversial...
So I think the reader does come away understanding that the work in this area is highly experimental, but also promising.

Surtees' review has a specific complaint about a particular reference by Prothero:
Prothero claims that, “In the 1950s Sidney Fox showed that splashing amino acids on hot dry volcanic rocks produced most of the proteins found in life instantly.” Unfortunately, no references are given so it is difficult to check this. 
It's true that Prothero doesn't cite Fox's work directly (and that it would have been more helpful if he had), but it is not true that "no references are given", and it's not true that it is difficult to check. 

The “Further Reading” on pp.158-159 includes several titles which discuss the work of Fox (and not uncritically, either, for Fox seems to have been a self-publicist who made increasingly wild claims about his findings), including Fry (2000), Hazen (2005), Shapiro (1986) and Wills (2000). 

To quote Hazen (p.199):
He imagined a hot primordial Earth where amino acids from the soup dried and baked on cooling volcanic rocks. He mimicked these conditions in his lab, drying amino acids on a hot surface at 170 deg C, and found that his chemicals quickly polymerized into a lumpy substance he called “proteinoid” This discovery, announced in 1958, would shape his checkered three-decade career in origins research.
Fox later became scientifically isolated, but the original work still seems to stand up, according to the above literature. 

However, a literature search yields a couple of papers by Sidney Fox and co‐workers.
Only a couple? Using Scopus, I found quite a few, from the 1950s onwards. 

The original paper appears to be: Fox, S. W., and Harada, K., 1958, Thermal copolymerization of amino acids to a product resembling protein: Science, v. 128, p. 1214-..

A few pages later we have another outrageous claim that, “All it would take is a few zeolites in a primordial soup, and the amino acids could be lined up into much more complex proteins.”
I don’t know about “outrageous”, but this sentence appears in the section, pp.152-153, in which Prothero clearly states that 
These highly speculative ideas are very controversial but not impossible...
Here we do not even get a name to help us try to find the original research that shows this. We have to take Prothero at his word.
Again, although Prothero doesn’t cite anyone in the text (after all, this is admittedly speculation), there is the further reading at the end of the chapter. And we find that zeolites are discussed in Hazen (2005 – Hazen discusses and cites the ideas of Joseph Smith, p.160), which is cited there.
And so it goes on, the whole chapter on the origin of life is full of similar assertions, until we arrive at the end, where we read that, “In most cases, each step can either be simulated in the lab or seen in examples of the process” (p.158). This statement is seriously misleading.
Again, this chapter is full of statements – which I’ve quoted - emphasising that we are at a very experimental stage. On pp.157-158, Prothero says, clearly:
Not every problem has been solved or every answer revealed, but the research on the origins of life is a relatively young, healthy field of science with much more to learn and much more to do.
Prothero’s line about “each step” has been ripped out of context (so yeah, it is misleading!). At that point in the text, Prothero is directly concerned with the creationist challenge. He points out that it is possible to construct a plausible (not proven) series of steps “that show us how to gradually build life” (p.158). He’s just done it, indeed, in this book! To put the sentence taken out of context back into context:
None of the steps require extraordinary conditions, and none are outside the realm of plausibility. In most cases, each step can either be simulated in the lab or seen in examples of the process (such as endosymbiosis) still working in nature today.
One might get the impression from Surtees that the chapter ends with the sentence about “each step”. But it doesn’t. The final paragraph of the chapter begins:
If the reader still feels uncomfortable with the speculative nature of the research into the origins of life, we can put the whole issue aside for now.
In other words, no fair minded reader (which Surtees is not) would come away from the chapter thinking that Prothero was trying to say that the origin of life was a solved problem. 

- - -

On the Cambrian Explosion

Surtees (from his review):
Prothero tries to prove that there was no Cambrian explosion (his term is “slow fuse”). His case stands or falls on whether or not he can show that there are earlier fossils that could have given rise to the Cambrian creatures.
Well, not really. Recall that Darwin said that the apparent non-existence of pre-Cambrian fossils was a possible objection to his theory. So the first important question is: are there fossils before the Cambrian? 

There is no theoretical reason to expect that the earlier fossils must necessarily include samples of creatures which are the direct ancestors of the Cambrian creatures. Perhaps none of the direct ancestors were preserved as fossils. No, the most important thing to establish is the existence of fossils earlier than the Cambrian. Are there fossils before the Cambrian? Yes, there are. 

Another point is that “Cambrian explosion” is taken to imply that all of a sudden vertebrates appear in the fossil record, unprecedented and at once. This is false. As noted, they are not unprecedented. Also, the Cambrian fossils appear over a 80 million year timespan, not all at once. 

Therefore the picture is not of an “explosion”, but of, as Prothero says (p.161), a “long slow build up to the first appearance of typical Cambrian shelled invertebrates.” 

Says Prothero (p.165):
advanced multicellular life... was on Earth 600 million years ago (more than 50 million years before the Cambrian), and possibly as early as 900 million years ago.
Prothero tries to suggest that the Ediacaran fauna are possible ancestors, but the only problem with this argument is that they are completely different and none of the experts on the Ediacarans believe these creatures to be the ancestors of Cambrian creatures.
“Completely different”? What’s that supposed to mean?

What Prothero actually says is this (p.163):
some palaeontologists have suggested that the Ediacara fauna was made by organisms unlike any that are alive today. They... argue that they are an early failed experiment in multicellularity.
So Prothero does not suggest that the Ediacara are “possible ancestors” (or if he does, and I’ve missed it, perhaps Surtees can tell us where?) of Cambrian life. He actually spends some time recording the controversy over whether Ediacara are related to Cambrian or existing life. He concludes (p.165):
Whatever the biological affinities of the Ediacara fauna, it is very clear that they are multicellular organisms, whether animals, plants, fungi, or some early experiemental kingdom not in any living group.
Surtees misleads in trying to suggest that he, Surtees, is overturning Prothero by referring to “the experts”. Prothero discusses the issue clearly himself. 
But by making light of the differences and stating that they are intermediates between single‐celled organisms and the more complex and varied Cambrian creatures, Prothero tries to persuade us that the Cambrian explosion is a creationist illusion.
Prothero makes no such statement, so far as I can see (reference?). 

He says only that multicellular life existed at least 50 million years before the supposed “Cambrian explosion”. And that does mean that the “explosion” is an illusion.

Here he uses terms likely to confuse by suggesting a link between the “small shelly” organisms and “large shelly” organisms like the trilobite.
Prothero introduces the “little shellies” (p.165) as the third stage of the Cambrian “slow fuse”.

The “little shellies”, says Prothero, appear during the Nemakit-Daldynian and Tommotian stages of the Cambrian, from 520 to 545 million years ago.

I’m not sure what Surtees thinks is confusing, exactly, or what the “link” is that he is objecting to. I can make no further sense of this.
The problem with this is that trilobites were not shelly creatures, they had exoskeletons like those of arthropods.
The problem with what? It’s not clear.

The book continues the review of the evidence of evolution by looking at the invertebrate fossils before bringing in the vertebrate fossils from fish to human. Here we find some examples of nice transitions in shell morphology, which are not going to convince anyone either way.
Surtees neglects to supply an actual argument here, apart from his own incredulity.

This is followed by discussion of the various transitional forms that supposedly link worms to “shell‐less” worm‐like molluscs, segmented molluscs and unsegmented molluscs. These forms (some of which are living today) are regarded as transitional because they have a mixture of features or a mosaic of characters. The best example is perhaps the velvet worm, with its segmented worm‐like body and, according to Prothero, “jointed” limbs like an insect.
Here we are on p.192-193 if you’re following at home.

Prothero compares the velvet worm to “arthropods” generally, not just to insects specifically, it should be noted. 

But again the details of how exactly these creatures demonstrate the evolution of worms to insects is unclear
I think Surtees needs to read the book again and then come back and tell us exactly what is unclear.
and the story starts to fall apart when examined closely because we find that velvet worms do not have jointed limbs and the “segmented” mollusc Neopilina is not considered to be truly segmented.
For some reason, Surtees earlier strict line on referencing doesn’t apply to his own assertions. I’ve had to go and check these claims about velvet worms and Neopilina without any assistance. 

As it happens, a quick literature search on this question is inconclusive, because some sources say velvet worms do have jointed appendages. Others say they don’t. This probably boils down to a question of definition. Same goes for Neopilina and segmentation.

If Surtees could share his sources on this, we could do some more chasing down of references and double check the state of opinion. As it stands, it looks to me like Prothero is within his rights.

- - -

On Jaws

In the chapter on fish we are simply told that jaws “appeared”.
What Prothero actually says is this (p.210):
One of the great evolutionary breakthroughs in vertebrate history was the origin of jaws. Before jaws appeared, vertebrates were severely limited in what they could eat...
The evolutionary issues are then discussed.

The fossil evidence is conspicuous by its absence.
Incorrect. Prothero cites the fossils of sharks as evidence (p.211-212).
This lack of evidence illustrates one of the major gaps in the evidence for evolution: there is no evolutionary explanation for the appearance of jawed creatures in the fossil record.
I don’t understand how Surtees can say this. Clearly any structure which enabled vertebrates to do more than just filter feed would convey an advantage and be preserved.

- - -

On Land

Prothero moves quickly on to the transition to land.
This is the subject of a whole different chapter, in fact.
There are claims that the fins of amphibious fish like mud skippers are “jury‐rigged” and “suboptimal” without any evidence to show that this is the case.
Prothero’s point about mud-skippers is not just about their fins, but about their entire adaptive approach to living on the edges of water. If you were designing them from scratch for their niche, would they look like that?

Prothero goes on to talk about aquatic (as distinct from amphibious) creatures with “fin fingers” (p.224):
these “fin fingers” are not robust or muscular or as flexible as tetrapod fingers, so they cannot manipulate objects with them. They are jury-rigged features built out of another structure (ray fins) and suboptimally modified to be “semifingers”
The claim that the pelvic (hind) fin of Panderichthys is foot‐like is demonstrably false, while the case could be made that the pectoral (front) fin is more fin‐like than foot‐like.
If it’s demonstrably false, where and how has it been demonstrated false?

The evolution of life adapted to land is presented as having occurred but the evidence is again not readily apparent. (In fact the evolutionary scenario involving Pandericthys and Tiktaalik, has now been shown to be wrong by the recent find reported by G Niedźwiedzki et al. Nature 463, 43‐48 (2010).
Notice that Surtees neglects to tell us what Niedźwiedzki et al actually says, or what implications that has for the “evolutionary scenario” in question. I imagine this is because what Niedźwiedzki et al actually say doesn’t help Surtees at all. Assuming Surtees actually read the article. 

What the authors discovered were tetrapod tracks which are about 18 million years older than the earliest known tetrapod fossils, and 10 million years older than the earliest known examples of creatures like Pandericthys and Tiktaalik. Presumably Surtees accepts the accuracy of this dating, if he is making claims based on the research?

Here is what Niedźwiedzki et all say about the implications of the find:
Until now, the replacement of elpistostegids by tetrapods in the body-fossil record during the mid–late Frasnian has appeared to reflect an evolutionary event, with the elpistostegids as a short-lived ‘transitional grade’ between fish and tetrapod morphotypes. In fact, tetrapods and elpistostegids coexisted for at least 10 million years. This implies that the elpistostegid morphology was not a brief transitional stage, but a stable adaptive position in its own right.
The environment of the area is not, we are old, conducive to fossilisation, but nevertheless the fossils that have been found still make it look as though elpisostegids preceeded tetrapods. Why that is, is one of the things that Niedźwiedzki et all try to address.

It’s certainly an interesting paper, and it could lead to the current hypothesis (that reported by Prothero) being overthrown. But as other commentators note, other interpretations are possible and more research is needed. Because of Niedźwiedzki et al, paleontologiests are looking in different places to where they were looking before, and in time this will advance our knowledge further and either support or discomfirm Niedźwiedzki et al’s hypothesis.

However, the lack of evidence does not stop Prothero making unsubstantiated claims like, “Internal fertilization evolved more than once of course” (p.234).
Well, if you have both spiders and sharks internally fertilising, that’s a reasonable conclusion.

The evolution of life on land is supposed to be another good example of evolutionary transition, yet when we examine the examples provided (pp.235‐234),
We have to read this backwards?   

we have only a confusion of “primitive” and “advanced” features that appear to come and go at random.
I think Surtees must be referring to pp.235-236. There are references here to “a mosaic” of primitive and advanced characteristics, but Surtees doesn’t explain what the problem with this is, exactly. 

Then there is the amazing transition of land reptiles to marine reptiles. The fossils presented as evidence for this transition are again not convincing, but rather show a variety of marine creatures with reptilian features (p.240).
“Not convincing” is not an argument I can do much with. Surtees is here referring to a diagram showing the evolutionary transformations of ichthyosaurs. Surtees describes them as merely “a variety of marine creatures”, but palaeontologists have identified them as ichthyosaurs.

This is just one of five examples of the supposed evolution of land creatures to sea creatures. Even though Prothero admits that it is amazing to believe that five different types of creature made the transition from land to sea, this just shows us the power of natural selection.
This is not what Prothero says (not “admits”). What he says is (p.238):
The most amazing thing about all three groups is that they were clearly reptiles, so they were descended from terrestrial creatures that developed a land egg, yet theses all three independently returned to the ocean... This seems amazing in itself, yet the fact that it has happened many times shows how powerful the selection forces for this lifestyle must be.

- - -

On Gaps


In the chapter on dinosaurs, Prothero goes to great lengths to discredit Gish by bringing forward evidence that is supposed to fill in all the gaps in dinosaur evolution.
We're now up to chapter 12. In Chapter 12, he does discredit Gish but not in the way you suggest. He's not trying to fill in "all the gaps" at all. He's addressing some of Gish's specific claims.

Yet in doing so he fails to address some key problems associated with dinosaur origins. The earliest dinosaur was the bipedal Eoraptor, but we are not told how such an evolutionarily advanced biped arose.
Prothero mentions "the earliest known dinosaur Eoraptor on p.251, and elsewhere. It is described by him as "the earliest and most primitive" known dinosaur (colour plate 4, note), not as "evolutionarily advanced". I'm not sure what you can possibly mean by "we are not told how" it evolved. By natural selection!

Later we are told that it is wrong to reject the evolutionary account of the horned dinosaurs, as there are many examples of similar dinosaurs that lack the frills and horns typical of well known creatures like Triceratops. A more likely interpretation is that these “transitional” forms merely show different varieties of ceratopsian dinosaurs (the created group that Triceratops belongs to). (This view has also received recent support form work published by Scannella and Horner (2010).
Prothero mentions Gish's use of Triceratops on p.254. The "varieties" referred to by Surtees occur millions of years apart, which is why they are regarded as transitional. You don't see Protoceratops fossils with the same dating as Triceratops fossils. In that kind of context, what could "created" mean?

I don't have access to Scannella and Horner (2010), but the abstract from Informaworld merely suggests that they have reclassified Torosaurus as a different growth stage of Triceratops, i.e. the same "variety", not a different "variety". As figure 12.5, p.256 of Prothero shows ,Torosaurus and Triceratops occur in the same timezone.

Then we are told that the controversy over the evolution of birds from dinosaurs was quickly resolved, yet it appears from the main protagonists that it is still ongoing.
This hugely misleading comment baffled me somewhat, since the "main protagonists" include TH Huxley, who proposed that birds were descended from dinosaurs in 1863 and has been dead since 1895; Harry Govier Seeley, who challenged the theory, and who died in 1909; and Gerhard Heilmann, who died in 1946.

The breakthrough by John Ostrom (who died in 2005) took place in the 1970s (in other words, the debate was already over a century old - hardly "quickly resolved"!), after which Prothero says:
Since Ostrom's initial papers, the controversy over the "birds are dinosaurs" hypothesis raged for several years but quickly resolved because the evidence soon became overwhelming. Hundreds of specialized shared-derived characters support the hypothesis, and there are no competing hypotheses with even a fraction of that support. All but a tiny minority (less than one percent) of paleontologists are convinced by the data...
Prothero proceeds to explain why the minority position doesn't stand up. Surtees seems to be implying that Prothero doesn't discuss any of this at all. In fact, Prothero even makes the deadliest accusation of all against the minority - he says they "resemble the creationists."! (p,259). Ouch!

- - -

On Mammals

Next Prothero treats us to a tour of the fossils that are said to demonstrate the evolution of mammals. For instance, the dog, cat, elephant, horse, rhino and camel fossils that creationist biologists would interpret as evidence of post‐Flood diversification. 
Surtees skips the rest of chapter 12 and so here we are at chapter 13 which is all about the "mammalian explosion". 

Why would any of this be interpreted as "evidence of post-Flood diversification"?

There is no convincing evidence that these creatures descended from a common ancestor, although Prothero attempts to persuade us that they all descended from a synapsid ancestor. 
There's that argument from personal incredulity again. The evidence, of course, is the "almost continuous series of well-preserved fossils" (p.271) referred to by Prothero, which is what you would expect to find according to evolutionary theory.

We are shown representative fossils that are supposed to demonstrate the gradual evolution from pelycosaurs to therapsids to cynodonts to mammals. 
There are three diagrams which do this: 13.3, p.274 (skulls); 13.4, p.275 (skeletons); and 13.5, p.277 (jaw bones).

However, there is a significant discontinuity between these groups, which is not so obvious when only the skulls are shown.
Which implies that only the skulls are shown. Not so, see above.

But of course there is "discontinuity", this is how fossils work. This really seems to be a big mental block for Surtees.

There is a lot of discussion of the jaws and ears as this is an important change from the synapsid middle ear with only one bone (the stapes) to the mammalian middle ear with three bones (the incus, mallus and stapes). There is a lot of detail that rather obscures the fact that the obvious gradual transition would be from one to two to three middle ear bones. 
Prothero discusses jaw/ear bones from p.277.

Surtees comment about the "obvious" transition being 1-2-3 is silly, overlooking the physiological starting points and the evolutionary pressures. You might as well argue that the obvious transition is from 2 legs to 3 legs to 4 legs (or vice versa) and so where are the three legged fossils? Prothero talks about all of this, and Surtees just ignores it.

There are no creatures with two middle ear bones which the evolutionist ought to expect.
Prothero notes that the articular bone hinged against the quadrate bone, both abutting the stirrup bone. The stirrup is the stapes, and the quadrate turned into the incus/anvil while the articular turned into the malleus/hammer. Surtees seems to be imagining that we ought to expect fossils where the quadrate is still a quadrate but the articular is a malleus! 

The evidence that we are presented with consists of a reduction in size of the bones that make up the synapsid jaw joint, a claim that the bones are in contact with the stapes and that sound is transmitted through the jaw bone. Here, Prothero's argument becomes a little confusing, because his supporting evidence is the fact that snakes hear through their jaws which often rest on the ground (p.279). 
Granted Surtees is confused, but not because Prothero is confusing.
However, snakes are not synapsids and, furthermore, the synasipds walked around on four legs so their jaws would only be on the ground when resting. Thus, it is very unlikely that synapsids had a similar sound transmission system.
Surtees has forgotten that snakes evolved from lizards, which gradually lost their legs. He's also apparently never watched snakes move. Because if he had he would know that snakes do not go around dragging their face through the dirt the whole time. Their jaws only touch the ground when they are resting, too. And of course, since skin, muscles etc vibrate, jaws can pick up vibrations felt by the rest of the body. So Surtees' argument here fails.
The clinching piece of evidence (p.279) is said to be that, when we were embryos, our ear bones were cartilages in the lower jaw and skull; but this is pure fiction.
On what grounds (no citation this time?) do you say it is "pure fiction"?

He then goes on to claim that the recently discovered fossil of Yanoconodon shows the ear bones attached to the jaw (p.279), even referring us to a colour plate of the fossil. However, he does not reproduce the photos of the jaw and supposed ear bones which show that they are separate from the jaw; they are only connected in the diagrammatic reconstruction of the jaw and ear (Nature 446, 288‐293 (15 March 2007), supplementary information).
The supplementary information cited is available here:

It contains extra photographs and very detailed anatomical description. I've been through all of it and I can't see what Surtees is getting at. See p.6 of the supplementary information for relevant photographs, plus descriptive notes. 

Then we are presented with the evolution of the whale (p.318), with a diagram (p.319) of highly stylised transitional forms that is misleading.
"Then" as in 30 pages later, he means 

Alright, so now we're looking a whales. Prothero provides a diagram showing evolution of whales from land creatures (figure 14.15, p.319)

In this diagram we are shown a hippo as the closest sister group. However, in the text we are told that Pakicetus is intermediate between mesonychids (carnivorous hoofed creatures) and fossil whales, and also that Pakicetus is related to the artiodactyla (a group which includes hippos and pigs but is completely unlike the mesonychids).
I find it hard to make sense of the above paragraph. 

What Prothero actually says is this:
most scientists would agree that whales are a group that evolved from the hippo-pig lineage within artiodactyls and that mesonychids are the distant relatives of both whales and artiodactyls. (p.320)
Pakicetus... with teeth intermediate between those of mesonychids and archaeocetes... The skeleton of Pakicetus is still quite wolf-like, with long slender limbs and a tail, so it still resembes a mesonychid in most features. (p.320)
Not sure what the problem with this is supposed to be?

Furthermore, Basilosaurus does not belong in the series as it is not transitional (even by the definition provided in this book). At best Dorudon might possibly be an ancestor of toothed whales, but we are not told how these creatures evolved the highly sophisticated adaptations such as the sonar system and the ability to suckle their young underwater.
Surtees does not explain why Bailosaurus should not be considered transitional.

Hippos can suckle underwater. 

No, Prothero does not explain the evolution of all these adaptations. So what? 

The origin of the baleen whales is also unexplained.
So? One reason why Prothero doesn't talk about them much might be because baleen fossilises only exceptionally, so they wouldn't be an obvious choice in a book about fossils. He does include mysticetes in his diagram 14.16.

Instead Prothero states that the final clinching proof is that modern whales have vestigial leg bones embedded in their abdominal muscles. Unfortunately he fails to point out that the musculature and connecting nerves, and the fact that these bones are part of the reproductive system, disqualifies them from being vestigial leg bones.
How does their use in reproduction disqualify them from being vestigial, exactly? And don't mammals use their legs in reproduction too?

The final statement of this section about all the fossil and molecular evidence also glosses over the fact that these pieces of evidence do not give a consistent picture.
I'm not sure what Surtees is referring to here. What section is he talking about, and what are the inconsistencies?

- - -

On Human Evolution

In the chapter on human evolution Prothero uses the argument that evolution is bushy (p.336), in this case “very bushy”, therefore we are unable to trace ancestor‐descendant relationships. However, we are told that is not important because the “amazing quality of the hominid fossil record is an objective fact”. That “fact” notwithstanding, there is no convincing story of how we are supposed to have evolved.
Prothero "uses" no such "argument". What he actually says on p.336 is this:
dozens of human species and genera are now known, forming a very bushy family tree that spans almost 7 million years of human evolution, mostly in Africa. The exact details of how all these fossils should be named or how they are interrelated is always controversial because many of the specimens are incomplete, and anthropologists are famous for being argumentative and contentious. But no matter how the arguments swing from year to year, the amazing quality of the hominid fossil record is an objective fact, not someone's interpretation or guesswork.
Supporting evidence is marshalled from DNA studies and observations of human “tails”. The most astonishing thing is the fact that Prothero cites the evidence from DNA hybridisation studies published in 1984 and claims that the temperature of separation is directly proportional to the number of genes in common. This is not the case, yet we are told that the chimp and human DNA has been proven to be 97.6 % identical. For some reason Prothero ignores all the DNA sequence data that was available when he wrote his book. He also assumes that the 97.6 % of the DNA that is the same are the “structural genes” which is inconsistent with the fact that the genes only make up a small percentage of mammalian DNA.
It's very frustrating when Surtees makes statements that something is "not the case", while neglecting to tell us how he knows this, so we can go and check. Help us out a bit, eh?

You do have to be careful about statements about identical DNA, and it's a complex subject I cannot get my head around at this time of night in order to address adequately.So far as I can tell more recent research has revised the estimate downwards, but not by very much. Suffice it to say that Surtees objections above sound like special pleading. Is it not extraordinary, if evolution is not true, that such huge similarities exist at all? 

We've covered the point about "junk DNA" previously. Surtees appears not to have understood it, because he confuses structural genes with regulatory genes. On this point, Prothero says (p.344):
Although there are many different ideas suggesting what is going on here, the basic idea is that the 1-2% of the genome that differentiates us from chimps must be the regulatory genes that turn on and turn off the structural genes (which make up the 97.6% that is the same). We have the genes for most parts of the ape body, and the monkey body too, and every once in a while there is a genetic mistake or atavism, and humans express the long-repressed genes that we still carry to make a tail.
Prothero also tries to use the existence of pseudotails as proof that humans have the genes for tails. However, he does not call them pseudotails. He presents three pictures as if they all come from the same paper (p.345) and suggests that this proves that we have the genes for tails. Reference to the original paper (Bar‐Maor et al, 1980) shows that Prothero has put a gloss on the findings to support his claims. The paper reports an observation of a deformed unfused coccyx, which is not a tail, and furthermore the article does not include the two pictures of what are soft boneless tissue protuberances in two subjects both with a normal coccyx.
We've covered this in detail previously in this post.

- - -

In Conclusion

The last chapter of the book (‘Why does it matter?’) is arguably the worst. For example, we are told that there “are a significant number of extreme creationists (including an entire Flat Earth Society) who believe that the Bible teaches that the earth is flat and that all those NASA photos of the earth from space are hoaxes.”
This is an example of why it's "arguably the worst" chapter? How so?

He mentions Flat Earthers just to make the point (p.352) that they would be entitled to equal time too, if that was adopted as a general principle.

Much of this chapter deals with the peculiarities of the situation in the USA and the various attempts to get equal time for creationism in the classroom, which are not so relevant to Europe. Prothero also seems to blame creationism for most of the problems of American scientific under‐achievement!
Well, he is an American author.

He sees creationism as part of a wider scientific illiteracy, so his point is perfectly arguable.

There is even an attack on ex‐president Bush and the “oil industry flunkies”, and the outlandish assertion that creationism is bad for your health (p.356) because it stops medical advances
This is what Prothero says (p.357):
the Bush Administration has been well documented... as interfering with legitimate scientists... Already the stem-cell research program in the United States has been set back compared to that in other countries, as our best scientists go to countries with less political oppression. Likewise the foot-dragging and denials of global warming by the Bush Administration and the flunkies of the oil industry in Congress...
Is he wrong?

Surtees conclusion:

In conclusion, this would have been a much better book if Prothero had spent less time preaching and more on careful analysis of the evidence and what that evidence actually shows. On the positive side there is much useful evidence for the potential of great diversification within the created kinds.
There are many interesting examples where the evidence for evolution is weak, especially when looking at the origin of life and the origin of new body plans. It also highlights a few cases where we as creationists have gone wrong and need to handle the evidence more carefully. All creationist biologists should read this book because it gives a great overview of the evidence and will prepare the reader for continuing the debate.
Surtees' review would have been much better had he not ignored, misunderstood, or misrepresented most of the evidence in Prothero's book.

The End. Phew.

Look forward to Surtees' retractions.

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