Challenging the Precious Pharyngula - Evolution News & Views

Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

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Challenging the Precious Pharyngula

This series began when ENV writer Jonathan M. asked some tough questions of PZ Myers about evolution and embryology at a Skeptics event in Glasgow, Scotland. As a recap of this series, below are links to ENV articles which have appeared on this topic:
Part 1: Colliding With the Pharyngula: My Encounter With PZ Myers: Jonathan M. gives his firsthand account of what happened at PZ Myers' lecture.
Part 2: Rate My Professors: P.Z. Myers: David Klinghoffer asks whether PZ Myers should be bullying undergraduate student Jonathan M. simply for asking some hard questions of evolutionary biology.
Part 3: Revisiting Those Early Developmental Stages: A Response to PZ Myers: Jonathan M. responds to PZ, reiterating that he isn't simply critiquing Haeckelian capitulation, and re-explains why the evolutionary funnel model of vertebrate development is wrong.
Part 4: How P.Z. Myers' "Incendiary Rhetoric" and "Class-War Claptrap" Shocks His Fellow Evolutionists (Prelude to a Rebuttal): Casey Luskin investigates PZ Myers' heavy use of personal attacks, and why they expose PZ's lack of scientific rebuttals.
Part 5: Demystifying the Debate with PZ Myers Over Evolution and Embryology: Luskin breaks down the embryology debate between Jonathan M. and PZ Myers into three simple points and counterpoints, revealing that PZ is not responding to our arguments.
Part 6: Haeckelian Recapitulation Is Not the Issue: Luskin explains, for the Nth time, that PZ Myers is wrong to consistently misrepresent ID arguments as only attacking Haeckel's recapitulation model.
Part 7: Caught in Contradictions, PZ Myers Claims "Evolutionary Theory Predicts Differences as well as Similarities" (and Therefore Predicts Nothing: Luskin discusses three contradictions in PZ's arguments, showing PZ has changed his tune over what evolution says about vertebrate embryos.
Part 8: PZ Myers Replies With Incendiary Rhetoric Instead of Scientific Arguments: After PZ writes a name-calling filled reply, Luskin explains that PZ uses personal attacks instead of scientific rebuttals.
Part 9: Challenging the Precious Pharyngula: Luskin discusses mainstream scientific papers which challenge the existence of the idea which gives PZ's blog its name--the "pharyngula".
Part 10: Three Flawed Evolutionary Models of Embryological Development and One Correct One: Luskin recounts various models of embryological development which have been discussed during this debate, concluding that evolutionary biology has failed to explain the data.
We've seen that at various points in this debate over evolution and embryology, PZ Myers has disavowed that evolutionary processes should necessarily lead us to expect similarities between vertebrate embryos in their early stages. Thus, PZ has said things like "Neo-Darwinism does not predict that early development will be conserved" or "evolutionary theory predicts differences as well as similarities."

But at other times he has seemingly contradicted himself, claiming that evolutionary theory does lead us to expect certain similarities in early vertebrate embryos. As PZ has argued, "[v]ertebrate embryos at the phylotypic or pharyngula stage do show substantial similarities to one another that are evidence of common descent. That's simply a fact."

Likewise in response to Jonathan M., PZ has argued that "there is an interesting and real convergence on the broad, general outlines of the body plan at one point in development that needs to be explained." In another post, PZ claims that only common ancestry can answer the question: "Why should animals that differ in appearance as adults exhibit similarities as embryos?"

PZ tries to answer that question in response to Jonathan Wells, where he makes an evolutionary argument for why the phylotypic stage must be conserved by evolution:

The specific morphology of the phylotype really does represent a literal foundation upon which the rest of development proceeds, and is resistant to evolutionary change, because there are too many later events that are dependent on it.

After discussing some shared similarities between vertebrate embryos, PZ contends that "[t]he best explanation for these phenomena is that they are a consequence of a common heritage." But does this pharyngular, or phylotypic stage exist?

The Phylotypic Stage: "Fact" or "Controversial"?

PZ is known for casting his vitriol at those who would cite scientific papers questioning the existence of the pharyngular (or "phylotypic" or "tailbud") stage. Yet a number of scientific papers by leading embryologists have recognized challenges the existence of the pharyngular stage. In fact, a paper in Nature from just last year, co-authored by 9 biologists, acknowledged that:

both the model and the concept of the phylotypic period remain controversial subjects in the literature with some studies of heterochrony in vertebrates indicating that divergence peaks at the phylotypic period or that there is no temporal pattern of phenotypic conservation.

(Kalinka et al., "Gene expression divergence recapitulates the developmental hourglass model," Nature, Vol. 468:811 (December 8, 2010) (emphasis added).)

As we've seen, PZ simply asserts that the existence of a conserved pharyngular stage is "a fact," yet this Nature paper says that the "concept" of the pharyngula is a "controversial subject in the literature." Who is correct: PZ writing on his blog, or these 9 biologists writing in Nature?

In 1997, a research paper was published by 7 biologists, including leading embryologist Michael Richardson, in the journal Anatomy and Embryology with the title "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development." Seeking to combat a PZ-like "pharyngula is 'a fact'" mindset, Richardson et al. write:

One puzzling feature of the debate in this field is that while many authors have written of a conserved embryonic stage, no one has cited any comparative data in support of the idea. It is almost as though the phylotypic stage is regarded as a biological concept for which no proof is needed. This has led to many problems, not least of which is the lack of consensus on exactly which stage is conserved. The phylotypic stage in vertebrates has been defined as the pharyngula stage, after the series of pharyngeal pouches seen in embryos. However it is not clear precisely which stage of development this represents, since pharyngeal pouches appear over an extended period of development.

(Michael K. Richardson et al., "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development," Anatomy and Embryology, Vol. 196:91-106 (1997) (emphasis added) (internal citations removed).)

The authors observe that biologists like PZ treat the phylotypic stage "as a biological concept for which no proof is needed."

Likewise, in a 1999 BioEssays paper, Richardson argues that "[t]he phylotypic stage is often discussed in terms that emphasise conserved features, and ignore variable features." He further contends that "the phylotypic stage is assumed to be particularly resistant to the action of natural selection. But I suggest that the phylotypic stage is a misleading concept that needs to be reassessed." (Richardson, BioEssays, Vol. 21:604-613 (1999).) This argument directly contradicts PZ's claim that "[t]he specific morphology of the phylotype really does represent a literal foundation upon which the rest of development proceeds, and is resistant to evolutionary change, because there are too many later events that are dependent on it."

Empirical Problems with the Pharyngula

Richardson et al. (1997) discuss striking differences among various vertebrate embryos in what they call the "purported phylotypic stage of vertebrates":

We find that embryos at the tailbud stage - thought to correspond to a conserved stage - show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phylogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype.

(Michael K. Richardson et al., "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development," Anatomy and Embryology, Vol. 196:91-106 (1997) (emphasis added.)

The paper ends by explaining the differences between embryos in the early stages which demolish claims of a conserved pharyngular stage:

Contrary to the evolutionary hourglass model, variations in the adult body plan are often foreshadowed by modifications of early development. A good example is the aortic arch system in the rat that, even during the pharyngula stage, begins to presage the adult pattern of arteries. Thus the first arch has already broken down completely by the 25-somite stage in the rat (de Ruiter et al. 1989). In summary, evolution has produced a number of changes in the embryonic stages of vertebrates including:

1. Differences in body size
2. Differences in body plan (for example, the presence or absence of paired limb buds)
3. Changes in the number of units in repeating series such as the somites and pharyngeal arches
4. Changes in the pattern of growth of different fields (allometry)
5. Changes in the timing of development of different fields (heterochrony)

These modifications of embryonic development are difficult to reconcile with the idea that most or all vertebrate clades pass through an embryonic stage that is highly resistant to evolutionary change. This idea is implicit in Haeckel's drawings, which 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.

(Michael K. Richardson et al., "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development," Anatomy and Embryology, Vol. 196:91-106 (1997) (emphases added).)

A 2004 paper by Poe and Wake in The American Naturalist undertook a quantitative study and corroborated the findings of Richardson et al. (1997):

Our quantitative analyses suggest that no such trend in event heterochrony exists and support the qualitative studies that have questioned the existence of especially constrained stages in development such as a "phylotypic" stage (e.g., Richardson et al. 1997).

(Steven Poe and Marvalee H. Wake, "Quantitative Tests of General Models for the Evolution of Development," The American Naturalist, Vol. 164 (3):415-422 (September 2004).)

Similarly, an earlier paper by Richardson focused on the "pharyngula" or "phylotypic" stage and found it to "poorly conserved":

The "pharyngula" stage. This is when a paired series of pharyngeal arches and pouches is present. The total number of pharyngeal pouches varies between species, but if embryos with four pouches are compared, it is seen that the degree of development of organ Phyloprimordia differs between species. In the lungfish, for example, the heart tubes have appeared by this stage but the fin buds have not; in Xenopus, neither heart nor limb primordia have appeared; and in the lizard Lacerta, both are present.

(Michael K. Richardson, "Heterochrony and the Phylotypic Period," Developmental Biology, Vol. 172:412-421 (1995) (internal citations removed).)

This particular paper concludes, "The data reveal striking patterns of heterochrony during vertebrate evolution. These shifts in developmental timing have strongly affected the phylotypic stage, which is therefore poorly conserved and is more appropriately described as the phylotypic period."

Also, a 2003 paper in Proceedings of the Royal Society, B argues that the phylotypic or pharyngular stage--commonly cited as evidence for common ancestry--does not exist in vertebrates:

[T]he phylotypic stage has never been precisely defined, or conclusively supported or disproved by comparative quantitative data. We tested the predictions of the 'developmental hourglass' definition of the phylotypic stage quantitatively by looking at the pattern of developmental timing variation across vertebrates as a whole and within mammals. For both datasets, the results using two different metrics were counter to the predictions of the definition: phenotypic variation between species was highest in the middle of the developmental sequence. This surprising degree of developmental character independence argues against the existence of a phylotypic stage in vertebrates. Instead, we hypothesize that numerous tightly delimited developmental modules exist during the mid-embryonic period. Further, the high level of timing changes (heterochrony) between these modules may be an important evolutionary mechanism giving rise to the diversity of vertebrates. The onus is now clearly on proponents of the phylotypic stage to present both a clear definition of it and quantitative data supporting its existence.

(Olaf R. P. Bininda-Emonds, Jonathan E. Jeffery, and Michael K. Richardson, "Inverting the hourglass: quantitative evidence against the phylotypic stage in vertebrate development," Proceedings of the Royal Society of London, B, Vol. 270:341-346 (2003) (emphases added).)

None of this is to say that there are no shared similarities among vertebrate embryos, nor would this challenge the notion that some similarities appear in general patterns--in some cases even hourglass patterns--across various vertebrate types. While there is no doubt that some noteworthy morphological and transcriptional genetic similarities appear throughout vertebrate development, there are also considerable differences, and they don't always fit with a conserved pharyngular stage. These articles thus argue there are too many differences in vertebrate development to accept a PZ-like claim that the pharyngular or phylotypic stage is "a fact." In fact, Richardson suggests that biologists like PZ "emphasise conserved features, and ignore variable features," cherry-picking data to make the case for the pharyngula. These papers make it clear that there are significant challenges to the existence of the pharyngula, a crucial piece of evidence bolstering PZ's arguments.

Losing the Pharyngula?

The pharyngula is important to PZ Myers that he named his blog after it. The tagline of "Pharyngula" reads: "Evolution, development, and random biological ejaculations from a godless liberal." On the about Pharyngula page on his blog, he states that the "Pharyngula" is "an evolutionarily conserved period when vertebrate embryos of all species are most similar to one another." Clearly the pharyngula is very important to PZ when he evaluates the evidence for evolution. So what does PZ think when he reads articles by leading authorities in scientific journals with titles like:

  • "There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development"
  • "Inverting the hourglass: quantitative evidence against the phylotypic stage in vertebrate development"
  • which make conclusions like:

  • differences in body size, body plan, growth patterns, and growth timing show "wide variation in morphology among vertebrate embryos," which "is difficult to reconcile with the idea of a phylogenetically-conserved tailbud stage."
  • "These modifications of embryonic development are difficult to reconcile with the idea that most or all vertebrate clades pass through an embryonic stage that is highly resistant to evolutionary change."
  • differences between vertebrate embryos "argu[e] against the existence of a phylotypic stage in vertebrates"
  • "The data reveal striking patterns of heterochrony during vertebrate evolution. These shifts in developmental timing have strongly affected the phylotypic stage, which is therefore poorly conserved..."
  • Indeed, we even saw that a 2010 paper in Nature observed that "both the model and the concept of the phylotypic period remain controversial subjects in the literature." As this post has reviewed, there are serious challenges to the pharyngular, or phylotypic, stage and the notion that it is highly conserved, thereby providing evidence for common ancestry.

    How will PZ respond? As we've seen, PZ Myers uses name-calling and personal attacks to prevent people from challenging him. Typically, when someone resorts to bullying, that's an indicator they cannot defend themselves through arguments and must instead use other tactics. Since PZ uses name-calling and personal attacks most of the time--including in this exchange with Jonathan M.--what does that say about the evidence?

    There's a reason why PZ concluded, "I was not rude enough to MacLatchie." In an unintended sense, PZ was correct: PZ wasn't rude enough to successfully intimidate Jonathan M. from speaking out and thereby exposing weaknesses in his arguments. His attempt to intimidate Jonathan M. into silence failed. Indeed, as of this writing, PZ has written two invective-filled responses to Jonathan M. and one to me, but has yet to respond to Jonathan M.'s discussion of the data which challenges the existence of the pharyngular stage. How will he respond to this one?

    In a final article, I will compare the models of embryological development we've discussing in this series, and explain why one is right and the others are wrong.


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