Intelligent Design

The man who mistook himself for a fish

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Over at Pharyngula, PZ Myers (who is a cladist) has written an entertaining but misguided post titled, Yes, you are a fish. In today’s post, I’ll argue that the key to classifying organisms correctly isn’t phylogeny, anatomy or genetics; it’s embryology. Only embryology can tell us something specific about an organism’s past and present characteristics, as well as resolving disputes about taxonomic categories.

The importance of taxonomy to biology cannot be overstated. To put it bluntly: you cannot hope to understand organisms properly unless you know how to classify them. During the past few decades, there has been a move away from the traditional approach (favored by Linnaeus and later by Richard Owen) of classifying living creatures on the basis of their morphological characteristics, towards a phylogenetic approach (also known as cladistics) which arranges organisms in an evolutionary tree, classifying them on the basis of their ancestry. (There are, however, subtle differences between cladistics and evolutionary systematics.) I believe that Intelligent Design can make a major contribution to biological thinking, by proposing a way of classifying organisms which “carves nature at the joints,” as the philosopher Plato memorably put it. The classification I am proposing here, far from being anti-evolutionary, attempts to identify those traits of organisms which have been conserved over the course of their evolution, because of their essential role in organisms’ development. It turns out that many of these traits (such as gene regulatory networks) are precisely those features of organisms which are most likely to have been intelligently designed.

Myers’ minority view

Biological groups. A monophyletic group (also known as a clade) includes a common ancestor and all of its descendants. A paraphyletic group consists of a common ancestor and some but not all of its descendants. A polyphyletic group contains no common ancestor, and consists only of a few distantly related organisms. Image courtesy of Wikipedia. [Unfortunately, I am unable to correct the mis-spelling of “polyphyletic” in the image. My apologies – VJT.]

The claim, “You are a fish,” certainly makes for good headlines. The only problem is that the vast majority of biologists would never make such an outlandish claim. PZ Myers is one of a very few scientists who does.

Almost all of the authorities I consulted online rejected the assertion that humans are fish, on the grounds that “fish” are a paraphyletic group. All fish have a common ancestor, but not all of the descendants of that common ancestor are actually fish. Four-legged vertebrates, such as amphibians, reptiles, birds and mammals, are obviously not fish.

For precisely that reason, the University of California Museum of Paleontology defines “fish” in its glossary as a paraphyletic group, and the Berkeley University Website article, What is a fish?, declares that fish do not form a clade (i.e. a monophyletic group), because a non-fish lineage (four-legged vertebrates) is nested within the group that includes lobe-finned fish. Dr. Steven M. Carr (Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland), describes fish as a paraphyletic group in his article, Concepts of monopoly, polyphyly, & paraphyly, while British paleontologist Dr. David Hone, (Queen Mary College, University of London), expresses the same view on his blog site: fish, he says, are obviously paraphyletic, since all vertebrates share a single common ancestor, but no-one would call mammals or birds fish. Associate Professor Stanley Rice (Dept. of Biological Sciences, Southeastern Oklahoma State University), in his Encyclopedia of Evolution (Facts on File Science Library, 2007, New York), is of the same view, bluntly declaring in his article on Cladistics (p. 75): “Fish is a paraphyletic category,” which entails that from a strictly cladistic standpoint, there is no such thing as a fish. Finally, Associate Professor Steve Mount, (Dept. of Cell Biology and Molecular Genetics, University of Maryland), has written a blog article titled, Can we not speak of fish?, in which he declares that when he speaks of fish, he means “vertebrates that are not tetrapods,” although he acknowledges that some of his scientific colleagues prefer not to use the term “fish” at all. Standard references also support the view that fish are a paraphyletic group. Wikipedia, in its article on fish, matter-of-factly states: “Because the term ‘fish’ is defined negatively, and excludes the tetrapods (i.e., the amphibians, reptiles, birds, and mammals) which descend from within the same ancestry, it is paraphyletic, and is not considered a proper grouping in systematic biology.” The online dictionary, Dictionary.com, explicitly refers to fish in its definition of “paraphyletic.” Even the BBC refers to fish as a paraphyletic group, on its 2014 Nature Wildlife page on fish.

PZ Myers grudgingly acknowledges at the end of his post that if you wish to define a fish as a craniate [i.e. a vertebrate with a skull] that is not a tetrapod, and if you use that definition, then we are not fish. Nevertheless, he rejects this definition as “willful” and “annoying,” because in his view, it arbitrarily excludes tetrapods and thereby turns fish into a paraphyletic group. However, the problem with Myers’ reasoning here is that it could be used to bludgeon any scientist who objected to using a common term (e.g. “reptile”) as a biological clade, on the grounds that the term, as it is normally used, denotes a paraphyletic group, rather than a monophyletic group: “You’re being willful!” The end result would be that all paraphyletic groups would end up getting redefined as monophyletic, because it suits cladists better that way. How convenient!

Indeed, I was not able to find a single scientist online who supported PZ Myers’ view that fish are monophyletic and so constitute a genuine clade. The only author I could find in Myers’ camp was science writer Brian Switek, who wrote an article for Wired titled, I’m an Ape, and I’m also a Fish (March 21, 2012).

It seems to me that Professor Myers could have saved himself a lot of trouble if he’d simply said, “Yes, you are a vertebrate.” (Hagfish, which lack a vertebral column, appear to be degenerate vertebrates.)

Myers’ cladistic approach to taxonomy – and what’s wrong with it

I’d now like to discuss Professor Myers’ cladistic approach to classifying organisms (bolding mine – VJT):

A taxonomic clade is a “grouping that includes a common ancestor and all the descendants (living and extinct) of that ancestor”.

So, for instance, humans belong to the mammalian clade, which includes mice and cats and cows…

We’re also members of multiple clades. For example, the tetrapod clade is the group that descended from a 4-limbed ancestor, an early amphibian, so it includes frogs and salamanders, and also reptiles, mammals, and birds, and the fact that we’re weird bipeds that have specialized our two pairs of limbs in odd ways, or that birds have turned a forelimb into a wing, doesn’t get us out of the club labeled “four footed”.

… But we belong to another clade, all the organisms descended from an ancient fish, and “fish” is the common label there…

I could say we’re all gnathostomes, and nobody would freak out because most of them wouldn’t have the slightest idea what I was talking about… But the point is that you are descended from an ancestor that was a torpedo-shaped aquatic vertebrate with gills, a fish. You can never escape your ancestry.

PZ Myers’ quip about gnathostomes is a cheap shot: gnathostomes are actually defined as jawed vertebrates. I don’t think anyone would object to being described as a jawed vertebrate. There’s simply no taxonomic justification for describing humans as fish.

But the real flaw in Professor Myers’ claim that you can never escape your ancestry is that given sufficient time, not only ancestral features, but even the anatomical and genetic vestiges of those features, may disappear. Take snakes, which have no legs but are classified in the clade “tetrapods,” on account of their having had a four-legged ancestor. Snakes arose a mere 100 million years ago, so it is not surprising that some snakes (e.g. pythons and boa constrictors) still retain vestigial legs (see here and also here). One billion years from now, they probably won’t. Genes can be lost, too: the ancestors of mammals lost many of the color receptor genes possessed by their reptilian ancestors. You might think that these genes would still survive in a broken form, in the genome. However, since broken genes are no longer subject to selection, they may end up being completely deleted from the genome. This is precisely what happened in mammalian evolution.

It is true, of course, that snakes are, and always will be, more genetically similar to four-legged vertebrates than they are to earthworms (which are also legless, but which last shared a common ancestor with snakes over 800 million years ago, compared to 355 million years ago for the common ancestor of snakes and frogs). But that information, in and of itself, tells us nothing about how the distant descendants of snakes, frogs and earthworms will look, or what anatomical characteristics they will possess. To make matters worse, we don’t even know what genes they’ll possess.

What a good taxonomic system should be able to do

I would propose that an ideal taxonomic system for classifying organisms should possess four features:

(a) it should tell us something about an organism’s evolutionary past;

(b) it should describe an organism’s present characteristics;

(c) for any set of organisms sharing a common ancestry, it should provide us with a natural way of classifying these organisms into sub-groups at the same taxonomic level, and of generating new groups at lower taxonomic levels; and

(d) the taxonomic ranks it generates should be capable of being applied across the board, to organisms in any lineage.

The phylogenetic (or cladistic) approach to classifying organisms clearly satisfies condition (a). And it is fair to say that if consistently applied to all organisms, it would satisfy conditions (c) and (d) as well. For example, one might use the concept of a “molecular clock” to define each taxonomic level according to when two sister populations at the next sub-level diverged from one another: thus the different families within each superfamily of primates all appear to have diverged around 20 million years ago, while the genera within each family diverged more recently, around 5 to 10 million years ago, and species more recently still. (In reality, of course, things are not so simple: molecular clocks are not constant at all times, and across all species.) But the real problem with this approach is condition (b): a cladistic approach to taxonomy tells us nothing specific about an organism’s physical characteristics, now. Cladistics is backward-looking: your ancestry forever defines what you are, no matter how much genetic and anatomical change your ancestors may have undergone, over the course of time.

A genetic approach to taxonomy (also known as a synthetic or evolutionary approach) might sound more promising, as genes are present-day components of an organism’s genome, which can tell us a lot about an organism’s evolutionary past. But the knowledge that organisms A and B are classified in the same taxon does not tell us anything specific about their genes, let alone their anatomy. The information it conveys is merely probabilistic: organisms belonging to the same class will have a certain degree of genetic similarity, but there is no guarantee that they will share any particular gene, let alone any particular anatomical feature. Thus it still fails condition (b).

By contrast, a morphological or phenetic approach classifies living things into different groups on the basis of their overall similarity, which is measured by cataloguing and measuring as many characteristics of organisms as possible, and attempting to identify taxonomic clusters (or phenograms). Since this approach groups organisms according to their physical characteristics, it passes condition (b) with flying colors. However, the morphological approach is achronological: it completely prescinds from questions relating to organisms’ ancestry, and thus fails condition (a). Some readers of this blog might be inclined to respond, “So what?” But if organisms do share a common ancestry, then that ancestry is surely part-and-parcel of their identity: it constrains their present characteristics as well as their future evolution, and is therefore pertinent to how we classify them.

Another problem with the phenetic approach is that although it now attempts to rigorously quantify the physical characteristics of organisms, there remains an element of subjectivity in identifying these characteristics the first place.

I maintain that only embryology can tell us something specific about an organism’s past and present characteristics, as well as resolving disputes about taxonomic categories. An embryological taxonomic scheme would group organisms according to the specific phases they pass through during the highly sensitive phylotypic stage, when genetic regulatory networks are being laid down.

An embryological approach satisfies condition (a), because the embryological features which it uses to classify organisms are very ancient, and were laid down millions of years ago. Such an approach can tell us quite a lot about an organism’s evolutionary past.

The approach also satisfies condition (b), because these embryological features are present-day characteristics of organisms, which unfold in the course of their embryonic development. Some of these features are later identifiable as morphological traits. (Please note that I am not claiming here that “ontogeny recapitulates phylogeny,” as Haeckel incorrectly proposed. All I am claiming is that morphological traits develop from embryonic traits.)

My proposal that an embryological approach to taxonomy provides us with a natural way of slicing and dicing organisms, as stipulated in condition (c), is, I realize, a highly contentious one. Below, I will be discussing a recent journal article which lends strong support to this point of view.

The article I’ll be citing below also appears to suggest a way of applying embryological data from the phylotypic stage to organisms, across the board – or at least, for all plants and animals, and possibly fungi as well – thereby satisfying condition (d). I’ll leave the question of how to classify microbes as a problem for another day.

The phylotypic stage

Before I continue, I’d like to declare my agreement with Professor PZ Myers on one fundamental point: the study of embryos yields abundant evidence for the common descent of animals (and especially vertebrates). I would refer readers who wish to review this evidence to a 2003 essay written by Myers himself, on the subject.

I’d now like to draw readers’ attention to an article by Andrew G. Cridge, Peter K. Dearden and Lynette R. Brownfield, titled, Convergent occurrence of the developmental hourglass in plant and animal embryogenesis? (Annals of Botany, Volume 117, Issue 5, pp. 833-843, March 24, 2016). A short excerpt from the abstract conveys the overall tenor of the piece:

The remarkable similarity of animal embryos at particular stages of development led to the proposal of a developmental hourglass. In this model, early events in development are less conserved across species but lead to a highly conserved ‘phylotypic period’. Beyond this stage, the model suggests that development once again becomes less conserved, leading to the diversity of forms. Recent comparative studies of gene expression in animal groups have provided strong support for the hourglass model…

The discovery that an hourglass pattern may also exist in the embryogenesis of plants provides comparative data that may help us explain this phenomenon…

Evidence of a morphological and molecular hourglass in plant and animal embryogenesis suggests convergent evolution. This convergence is likely due to developmental constraints imposed upon embryogenesis by the need to produce a viable embryo with an established body plan, controlled by the architecture of the underlying gene regulatory networks. As the body plan is largely laid down during the middle phases of embryo development in plants and animals, then it is perhaps not surprising this stage represents the narrow waist of the hourglass where the gene regulatory networks are the oldest and most robust and integrated, limiting species diversity and constraining morphological space.

Why the hourglass?

One might expect the very earliest stages of embryonic development to be the most highly constrained, as alterations early in development would be more likely to have widespread downstream effects. On such a model, the resemblances between different animals should be greatest at the beginning, and diversification should arise later. This is what the “funnel model” predicts. Surprisingly, however, animal development conforms to an hourglass model, with the greatest resemblances (and the tightest regulation) occurring in the middle stages of embryonic development. The reason appears to be that regulation in the earliest stages appears to be related to the spatial orientation of animal body axes, which is looser than the synchrony required for the development of animal body plans, which occurs later on, at the blastula, gastrula and neurula stages. Images courtesy of Wikipedia.

It is well-known to biologists that the earliest stages in an embryo’s development are not the most highly conserved: they vary widely, even across organisms belonging to the same phylum. Scientists now realize that within a given phylum, the way in which the embryos of various organisms develop is much more divergent in the early and late stages than in the middle stage. This is what is popularly known as the “hourglass model” of embryonic development. The question which naturally arises is: why the hourglass? Why not a funnel instead, where the earliest embryonic stages are the most sensitive to alteration? Cridge, Dearden and Brownfield address this question in their article, where they explain that the earliest embryonic stages are under purely spatial constraints, relating to symmetry, whereas synchrony of developmental signals is more important role during the middle stage of embryonic development, when the body plan is being laid out. It is at this stage that errors can prove particularly hazardous:

[T]he highest level of conservation occurs during the ‘middle’ stages of embryogenesis, corresponding roughly to the morphologically conserved phylotypic period

We might presume that the earliest stages of embryo development would be the most constrained, as it could be expected that alterations early in development would be more likely to have widespread downstream effects. As development progresses, alterations would then be more widely tolerated, in turn promoting diversity. This funnel-like model predicts that the highest conservation would occur at the earliest stages of development (Fig. 2) (Raff, 1996). Conservation of early embryogenesis is, however, not seen on the morphological or molecular levels in plants and animals, implying that this early stage is less constrained than the subsequent mid-embryonic stages.

…[T]he earliest periods of development are divergent in terms of not only morphology but also gene expression and protein sequence evolution. The implication is that as long as the gene expression pathways can establish the major axes of the embryo, then development can proceed. The expression, function or sequence of the early-acting genes can change, as long as the outcomes of the genetic pathways they are involved in do not. This allows the evolution of variation in early embryogenesis on which selection can ultimately be applied. Given that axes can be determined through various and subtle asymmetries in a single cell (e.g. reviewed for insects in Peel et al., 2005), it is possible that developmental drift, between a range of potential axis-forming signals, is possible.

Mid-embryogenesis is …. characterized by precise co-ordination between growth and patterning, and as such is highly sensitive to perturbations in the sequence of temporal and spatial activation of genes (Duboule, 1994). Taking a more global view of conservation, Raff argued that the complexity of interactions between genes, cells and developmental processes reaches a maximum during mid-embryogenesis when the body plan of the organism is being established (Raff, 1996).

How do we reconcile changes in the network with the conservation we observe in the developmental hourglass model? The most likely explanation is that the hourglass model represents an evolutionarily constrained central node in the ‘hierarchical’ system structure of the developmental network essential for maintaining core gene networks that regulate essential developmental outcomes, such as an antero-posterior identity of the embryo.

Is the hourglass universal across plants and animals?

Recent evidence suggests that not only animals, but also plants, and possibly fungi as well, exhibit the same hourglass pattern, in the course of their embryonic development. Cridge, Dearden and Brownfield recognize this fact, and suggest that the hourglass evolved independently in animals and plants:

The phylotranscriptomic hourglass patterns associated with embryogenesis in animals and plants are convergent as embryogenesis evolved independently in animals and plants (Meyerowitz, 2002), but may be a consequence of similar processes in developmental regulation. The hourglass pattern constrains the evolution of embryogenesis, producing a developmental stage that every embryo must pass through with reduced evolutionary, transcriptomic and morphological variation. This stage appears to evolve in both plants and animals, there is evidence for it in fungi and modelling suggests it may occur spontaneously. Despite this, the developmental hourglass must (and does) limit variation, constraining variation that can exist or survive. Variation readily evolves before and after the phylogenetic stage, providing the glorious diversity of plants and animals alive today, but constraint does seem to exist. It is an intriguing thought that the way transcription factors act to regulate gene networks may spontaneously lead to the waist of developmental hourglasses, and that these in turn constrain the morphology that can be produced, or that will be viable. Is the very nature of developmental gene regulation responsible for the production of phyla?

The authors also hypothesize that the phylotypic stage is a “frozen” (i.e. unalterable) reflection of ancestral developmental networks, in which the hourglass formed spontaneously. However, they cite only tentative evidence from a single paper to support this speculative claim. What is more interesting, however, is that the genes expressed in the waist of the hourglass, where the developmental constraints are tightest, turn out to be the oldest genes:

Perhaps the frozen phylotypic stages we see today are a reflection, probably highly embroidered, of ancestral networks that allowed the first metazoans and plants to regulate their morphology effectively. This frozen regulation, however, has consequences. The phylotypic stage must constrain the morphological space which an embryo is able to occupy; evolution beyond the phylotypic stage can cause dramatic shifts in morphology, but these changes are still based on the conserved body plan of each phyla, and are conserved by the ancient gene regulatory network lurking in the waist of the hourglass. Whether produced by selection, or as an unforeseen consequence of the evolution of gene regulatory networks, it seems that developmental hourglasses constrain variation in both plants and animals, linking their morphological range and, in turn, species diversity…

[T]here is some tentative evidence that hourglass patterns may form spontaneously due to the nature of developmental networks. Evolutionary modelling of regulatory gene interactions in simulated hierarchical gene networks can produce hourglass patterns (Akhshabi et al., 2014). This pattern is reflected both in the divergence of gene expression and, interestingly, in ages of genes, with the oldest genes being expressed in the ‘waist of the hourglass’ (Akhshabi et al., 2014). These hourglass networks are produced in situations where developmental regulators have increasingly specific functions (Akhshabi et al., 2014), a situation consistent with the biology of embryos. That simulation of random networks produces hourglass patterns indicates a propensity of all such networks to form this pattern.

Control process of a gene regulatory network. Public domain image courtesy of the U.S. Department of Energy Genome Programs and Wikipedia.

Readers of this blog will be aware that biochemist Professor Michael Behe demolished the idea that genetic regulatory networks could have arisen spontaneously, via unguided processes, in his 2007 bestseller, The Edge of Evolution (Free Press, New York). The following passage encapsulates Behe’s key argument:

Figure 9.3 is an illustration of the genetic regulatory system that turns on the genes that control the construction of a tissue called the endomesoderm in sea urchins. Notice the obvious, impressive coherence of the drawing. The figure is intended to be strikingly reminiscent of a complex electronic or computer-logic circuit, because in essence that is what genetic circuits are. The system contains a core of six genes that code for master regulatory proteins that eventually switch on scores of proteins that boast many more DNA switches, very far beyond the criterion of three proteins or switches. We can thus conclude that this system is well beyond the edge of evolution. It was very likely purposely designed. (2007, p. 197.)

What does the hourglass tell us about an organism’s evolutionary history?

In their paper, Cridge, Dearden and Brownfield argue that the oldest genes in an organism correspond to the highly constrained phylotypic stage of embryonic development, when the organism’s body plan is being assembled. Younger and evolutionarily more recent genes correspond to later stages in the development of the embryo, when “morphological detail rather than fundamental structures” are unfolding. The overall pattern for animals appears to be that “evolutionarily younger transcription factors seem to be more important in later stages of development, whereas evolutionarily older genes are prevalent in the earlier stages of development.”

Does the ‘phylotypic stage’ represent the oldest, most robust, most integrated part of a developmental system? If this were the case, then the convergent evolution of developmental hourglasses in animals and in plants might be seen as inevitable, rather than coincidence. Indeed research has identified developmental hourglasses in other analogous developmental systems (e.g. Coprinopsis cinerea) (Cheng et al., 2015)…

Analysis of D. rerio and D. melanogaster identified that evolutionarily younger transcription factors seem to be more important in later stages of development, whereas evolutionarily older genes are prevalent in the earlier stages of development.

Late embryogenesis differs markedly between plants and animals. Animal embryos at this stage build on their regionalized axes to produce limbs and organs, elaborating on body plans to produce diverse morphologies. Differences in late embryogenesis produce taxa-specific patterns and morphological variation in adult forms… At these stages, evolutionary changes in gene expression are presumably less pleiotropic, providing morphological detail rather than fundamental structures on which morphology is built.

In flowering plants, the body plan does not change dramatically during the later stages of embryogenesis, as the basic body plan is elaborated upon post-embryonically… While flowering plant embryos do not show the morphological variations in the later embryo stages that are seen in animals, a molecular hourglass pattern is observed in A. thaliana embryogenesis (Quint et al., 2012; Drost et al., 2015). The transcriptome at later stages contains both genes with a greater sequence divergence from close relatives and younger genes that are more recently evolved… The transcriptome at this stage also contains evolutionarily younger genes, which is not surprising as seeds are a younger invention, arising approx. 350 million years ago (Mya) (Linkies et al., 2010), compared with plant embryogenesis, that probably evolved as plants became adapted to land between 480 and 420 Mya (Bowman et al., 2007).

Putting it all together: how embryology provides the key to taxonomy

The overall picture which emerges from the paper by Cridge, Dearden and Brownfield is that:
(i) the embryonic features which are most critical to the development of organisms are very ancient, and were laid down millions of years ago;
(ii) these features correspond to the highly conserved phylotypic stage of embryonic development;
(iii) the oldest genes in this stage regulate the development of fundamental body plans, which vary from one phylum of organisms to another;
(iv) embryonic features which appear later in an embryo’s development are more recent, and – at least in animals – correspond to lower-level taxa.

What this suggests to me is that by carefully studying the middle and later stages of embryonic development in animals (and possibly plants and fungi as well), biologists may get a sense of which taxonomic levels in current use represent natural categories, and which are merely artificial divisions.

Problems with an embryological approach to taxonomy

This graph shows the main taxonomic ranks: domain, kingdom, phylum, class, order, family, genus, and species. Here it demonstrates how taxonomic ranking is used to classify animals and earlier life forms related to the red fox, Vulpes vulpes. Image courtesy of Wikipedia.

As I see it, the main problem with an embryological approach to taxonomy is that it is not applicable to all taxonomic levels. For instance, there is no stage in an embryo’s development which corresponds to the taxonomic ranks of a domain (eukaryotes) or even a kingdom (animals). Rather, the body plans that we see unfolding in the middle stages of embryogenesis correspond closely to the taxonomic rank of phylum (e.g. chordates). And while it is quite possible that further research will reveal that differentiation at later stages of embryonic development matches up well with the taxonomic ranks of class (e.g. mammals) and order (e.g. carnivores), it is unlikely that anything corresponding to the taxa of family, genus and species will be found. This suggests that an embryological approach to taxonomy has at best a limited application, and that it may need to be supplemented with another approach.

Another problem with the embryological approach to taxonomy is that it is unclear exactly comparisons of different taxa can be made across different phyla. Insects, for instance, are classified as belonging to a subphylum called Hexapoda, which also includes three much smaller groups of wingless arthropods. How do we know that the subphylum Hexapoda (which belongs to the phylum Arthropoda) and the subphylum Vertebrata (which belongs to the phylum Chordata) are of the same taxonomic rank? After all, it is difficult to compare the embryos of vertebrates and insects, which develop at different rates and according to different patterns. The suggestion I would make here is that although the patterns of development are quite different, correspondences can be identified across phyla, especially during the “middle” phase of embryonic development, and that if the changes in body plan which signal the development of an insect body plan are found to correspond to genes which are of equal antiquity to those which signal the development of a vertebrate body plan, then it would be fair to conclude that “insect” and “vertebrate” are categories on the same level. In the same manner, it should be possible to resolve disputes regarding classes within the vertebrate subphylum. On a conventional, physiological classification, there are seven classes: Class Agnatha (jawless fishes), Class Chondrichthyes (cartilaginous fishes), Class Osteichthyes (bony fishes), Class Amphibia (amphibians), Class Reptilia (reptiles), Class Aves (birds) and Class Mammalia (mammals). Cladists would, however, classify the last four classes within “bony fishes” – more specifically, within the class of Sarcopterygii (lobe-finned fishes).

But whatever classificatory system we come up with, it should not do violence to the meaning of everyday words such as “fish” or “tetrapod,” which the common people, and only the people, have the right to fix. To call a snake a tetrapod, or to call a man a fish, is linguistic lunacy. If we are to choose a term, then let it reflect the common embryonic features of humans and fish, or of snakes and their four-legged ancestors – features which are still found in these creatures, and which can be readily applied, when classifying them into groups.

The important point for Intelligent Design, however, is that the key taxonomic divisions that “carve nature at the joints” turn out to be complex regulatory systems, which are the product of an Intelligent Mind at work in Nature. It is for this reason that I believe that the field of taxonomy is one in which ID proponents can do some pioneering scientific research. Currently, the field of taxonomy is a mess: it is a field riven by “endless vistas of fruitless time-wasting and bickering,” as one scientist put it recently. Any team of biologists that can sort out this mess will be doing the scientific world a great favor.

At this point, I’d like to throw the discussion open. What do readers think?

10 Replies to “The man who mistook himself for a fish

  1. 1
    Mung says:

    There is no such thing as a “Fish clade”, and PZ Meyers knows this.

  2. 2
    Robert Byers says:

    I use the fish to fisherman CLAIMS of evolutionists to point out what they are saying. I understand they always have “some fishthing’ crawling onto the land and soon a hippo.
    Anyways snakes having vestiges of former legs is not evidence of anything but former legs. ITS NOT Evidence for process or common descent. a YEC creationist welcomes snakes with these vestiges as evidence of GENESIS claim snakes lost their legs. I would insist its one of the few cases in biology. Its not GOOD sampling to use them to prove evolution. naughty.

    Anyways.
    I think embryology has no evidence for evolution. it only shows life in stages of serious early development.
    Any likeness to biology out there is just because of limited options at such levels.
    What should embryology look like if evolution was not true?
    If there is a common blueprint and there is THEN it would also be that those stages have likeness because of common design.
    Why not?
    The idea that the history of creatures evolution remaining in the fetus stages is very strange and 19th century thinking.
    Its simplistic hunching.
    Comparativeness in nature must not be proof of common descent.
    There are more and better options and obviously evolutionism only can use embryology if there is no other option for looks.
    Think harder evos.

  3. 3
    bornagain77 says:

    as to this claim:

    “Younger and evolutionarily more recent genes correspond to later stages in the development of the embryo, when “morphological detail rather than fundamental structures” are unfolding.”

    and yet we find:

    Age doesn’t matter: New genes are as essential as ancient ones – December 2010
    Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”
    http://www.sciencedaily.com/re.....142523.htm

    New genes in Drosophila quickly become essential. – December 2010
    Excerpt: The proportion of genes that are essential is similar in every evolutionary age group that we examined. Under constitutive silencing of these young essential genes, lethality was high in the pupal (later) stage and (but was) also found in the larval (early) stages.
    http://www.sciencemag.org/cont.....2.abstract

    Dr. Giem has a lecture video on the subject that goes through the details:

    New Genes Are Essential 6-13-2015 by Paul Giem – video
    https://www.youtube.com/watch?v=6qgGPV1AO1E

    Can new genes arise from junk DNA? – August 2015
    Excerpt: Researchers are beginning to understand that de novo genes seem to make up a significant part of the genome, yet scientists have little idea of how many there are or what they do. What’s more, mutations in these genes can trigger catastrophic failures. “It seems like these novel genes are often the most important ones,” said Erich Bornberg-Bauer, a bioinformatician at the University of Münster in Germany.,,,
    Scientists also want to understand how de novo genes get incorporated into the complex network of reactions that drive the cell, a particularly puzzling problem. It’s as if a bicycle spontaneously grew a new part and rapidly incorporated it into its machinery, even though the bike was working fine without it. “The question is fascinating but completely unknown,” Begun said.
    A human-specific gene called ESRG illustrates this mystery particularly well. Some of the sequence is found in monkeys and other primates. But it is only active in humans, where it is essential for maintaining the earliest embryonic stem cells. And yet monkeys and chimps are perfectly good at making embryonic stem cells without it. “It’s a human-specific gene performing a function that must predate the gene, because other organisms have these stem cells as well,” McLysaght said.
    “How does novel gene become functional? How does it get incorporated into actual cellular processes?” McLysaght said. “To me, that’s the most important question at the moment.”
    http://www.uncommondescent.com.....-junk-dna/
    Original article
    https://www.quantamagazine.org/20150818-a-surprise-source-of-lifes-code/

    New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation – Aoife McLysaght, Daniele Guerzoni 31 August 2015
    Excerpt: From simple beginnings, these genes have in some instances acquired complex structure, regulated expression and important functional roles. New genes are often thought of as dispensable late additions; however, some recent de novo genes in human can play a role in disease.
    http://rstb.royalsocietypublis.....8/20140332

  4. 4
    EvilSnack says:

    Of the four features of a good features of a good taxnomic system, the first one—information about ancestry—is not really that useful. When people study lions, having some notion of what an ancestor’s qualities may or may not have been is of no real use in the here-and-now.

    * First, we don’t ascribe common ancestry until we have made a certain amount of observation and have seen a great deal of similarity, and (more importantly)
    * Having put the house cat and the lion into the same family, we do not conclusively attribute any quality observed in either to the other unless and until it is observed in that other.

  5. 5
    bornagain77 says:

    as to:

    I maintain that only embryology can tell us something specific about an organism’s past and present characteristics, as well as resolving disputes about taxonomic categories.

    One can almost hear ole Charlie murmuring, “strongest single class of facts”,

    “The embryos of the most distinct species belonging to the same class are closely similar, but become, when fully developed, widely dissimilar.” This is,,, “by far the strongest single class of facts in favor of my theory.”
    Charles Darwin – Origin of Species (1859), Letter to Asa Gray (1860)

    Haeckel’s Embryos
    Excerpt: In The Origin of Species, Darwin gave credit to Ernst Haeckel: “Professor Haeckel in his “Generelle Morphologie” and in [other] works has recently brought his great knowledge and abilities to bear on what he calls phylogeny, or the lines of descent of all organic beings. In drawing up the several series he trusts chiefly to embryological characters [to establish evolutionary sequences].”
    Based on what Darwin thought was scientific evidence concluded: “So again it is probable, from what we know of the embryos of mammals, birds, fishes, and reptiles, that these animals are the modified descendants of some ancient progenitor.”
    In The Origin of Species, Darwin wrote, “Thus, as it seems to me, the leading facts in embryology, which are second to none in importance, are explained on the principles of variation in the many descendants from some … ancient progenitor”
    http://www.darwinthenandnow.co.....s-embryos/

    Yet, Darwin’s “strongest single class of facts” was soon found to be fraudulent after Darwin published his book. Moreover, despite being shown to be fraudulent, they were, none-the-less, widely used by evolutionists in school textbooks until just recently:

    How fudged embryo illustrations led to drawn-out lies – 20 January 2015
    Excerpt: German biologist Ernst Haeckel included illustrations of the embryological stages of vertebrates in a series of books published between 1868 and 1908. Fudging the data, he placed the drawings into a comparative grid, highlighting similarities between species and blurring differences. The results are highly inaccurate.
    Haeckel wanted to convince his readers that all vertebrates share a common ancestor, and that, as he put it, “ontogeny recapitulates phylogeny” – our embryonic development repeats our evolutionary past. This aphorism was soon disproved, but the use of Haeckel’s drawings persisted, particularly in education. There were waves of criticism, from the 1870s when the drawings were published, up to 1997 as Haeckel’s “fraud” was rediscovered and exploited by creationists.
    http://www.newscientist.com/ar.....-lies.html

    Icons of Evolution 10th Anniversary: Haeckel’s (Bogus) Embryos – Jonathan Wells – January 2011 – video
    http://www.youtube.com/watch?v=lAC807DAXzY

    Failures of Evolution: Phylogeny Recapitulates Ontogeny – video
    https://www.youtube.com/watch?v=Qv1TyS09nLM

    Haeckel’s Embryos – original fraudulent drawing
    http://www.darwinthenandnow.co.....ped-II.jpg

    Actual Embryos – photos (Early compared to Intermediate and Late stages);
    http://www.ichthus.info/Evolut.....mbryos.jpg

    There is no highly conserved embryonic stage in the vertebrates: – Richardson MK – 1997
    Excerpt: 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,
    http://www.ncbi.nlm.nih.gov/pubmed/9278154

    Side by side comparison of Haeckel’s drawings to actual photographs
    http://www.ichthus.info/Evolut.....ckel-2.jpg

    Other embryo photographs by Richardson
    http://www.ichthus.info/Evolution/PICS/embryo3.jpg

  6. 6
    bornagain77 says:

    Problem 8: Differences Between Vertebrate Embryos Contradict the Predictions of Common Ancestry – Casey Luskin February 13, 2015
    Excerpt: The researchers conclude that the evidence is “[c]ontrary to the evolutionary hourglass model” and “difficult to reconcile” with the existence of a pharyngula stage.135 Likewise, a paper in Proceedings of the Royal Society of London found the data was “counter to the predictions of the [phylotypic stage]: phenotypic variation between species was highest in the middle of the developmental sequence.” It concluded that a “surprising degree of developmental character independence argues against the existence of a phylotypic stage in vertebrates.”136
    http://www.evolutionnews.org/2.....91171.html

    Heads or Tales – How Evolutionary Theory “Predicts” What It Finds by Casey Luskin – Fall 2014
    Excerpt: PZ did make a few substantive points in response to the student and me. He conceded that early vertebrate embryos can “vary greatly” and that “there is wide variation in the status of the embryo.”9 But he wasn’t going to let those facts challenge his theory, as he countered: “I wish I could get that one thought into these guys’ heads: evolutionary theory predicts differences as well as similarities.”10
    That’s intriguing, I thought. Earlier we saw PZ cite the “substantial similarities” between vertebrate embryos in the pharyngula stage as “evidence of common descent.” But later, when forced to admit the “wide variation” among embryos, PZ tells us that “evolutionary theory predicts differences” too. Perhaps that’s true, but then how can he cite the “similarities” among embryos in the pharyngula stage as evidence for common ancestry?
    In reality, according to PZ, evolutionary theory predicts whatever it finds. Such logic might help save his theory from falsification in light of all the differences between vertebrate embryos across many stages of development, but it doesn’t help construct a robust theory that makes testable predictions. As the old adage says, “the theory that explains anything really explains nothing.”
    http://salvomag.com/new/articl.....-tails.php

    Vertebrate Gene Expression and Other Properties Don’t Support a “Phylotypic” Stage – Casey Luskin – June 14, 2013
    Excerpt: a new article in PLoS Genetics, “The Hourglass and the Early Conservation Models — Co-Existing Patterns of Developmental Constraints in Vertebrates,” shows that,, an analysis of the genome based on Darwinian assumptions fails to confirm many predictions of the “phylotypic” stage. ,,, (as they report),,,
    “During development, vertebrate embryos pass through a “phylotypic” stage, during which their morphology is most similar between different species. This gave rise to the hourglass model, which predicts the highest developmental constraints during mid-embryogenesis. In the last decade, a large effort has been made to uncover the relation between developmental constraints and the evolution of the genome. Several studies reported gene characteristics that change according to the hourglass model, e.g. sequence conservation, age, or expression. Here, we first show that some of the previous conclusions do not hold out under detailed analysis of the data.”
    (Barbara Piasecka, Pawe? Lichocki, Sebastien Moretti, Sven Bergmann, Marc Robinson-Rechavi, “The Hourglass and the Early Conservation Models — Co-Existing Patterns of Developmental Constraints in Vertebrates Barbara Piasecka,” PLoS Genetics, Vol. 9(4) (April, 2013).),,,
    http://www.evolutionnews.org/2.....73171.html

    Three Flawed Evolutionary Models of Embryological Development and One Correct One – Casey Luskin – 2011
    Excerpt: When biologists carefully compare embryological data, they find that there is considerable variability at the purported phylotypic stage, leading increasing numbers of biologists to question whether this pharyngular stage exists. As a paper in Nature said last year: “both the model and the concept of the phylotypic period remain controversial subjects in the literature.” PZ generally refuses to address this literature, but it nonetheless calls into question the very concept that defines this model and gives PZ’s Pharyngula blog its name.
    http://www.evolutionnews.org/2.....48541.html

  7. 7
    mk says:

    see also this article from the evolution news:

    http://www.evolutionnews.org/2.....91171.html

  8. 8
    gpuccio says:

    VJ:

    I suppose it is equally true that we are prokaryotes. You cannot escape your ancestry.

  9. 9
    Mung says:

    I suppose it is equally true that we are prokaryotes.

    And here I thought we were eukaryotes.

  10. 10
    gpuccio says:

    Mung:

    We are probably a case of multiple personality! 🙂

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