In my previous article, I presented a critique of the first of Wikipedia’s eight lines of evidence for common descent: the evidence from comparative physiology and biochemistry. In this article, I will discuss the second of those lines of argument, namely, the evidence from comparative anatomy.

Atavisms

Wikipedia’s first subheading regarding the evidence from comparative anatomy is “Atavisms.” What is an atavism? Wikipedia explains:

An atavism is an evolutionary throwback, such as traits reappearing which had disappeared generations ago.²⁹ Atavisms occur because genes for previously existing phenotypical features are often preserved in DNA, even though the genes are not expressed in some or most of the organisms possessing them.³⁰ Some examples of this are hind-legged snakes³¹ or whales (see specific example below);³² the extra toes of ungulates that do not even reach the ground,³³ chicken’s teeth,³⁴ reemergence of sexual reproduction in Hieracium pilosella and Crotoniidae;³⁵ and humans with tails,²⁹ extra nipples,³¹ and large canine teeth.³¹

Let’s consider a couple of these examples.

In the case of chicken teeth, I would offer three main observations:

1. At best, all it would demonstrate is that the ancestors of certain birds had teeth. It wouldn’t necessarily tell us that these genes for making teeth were inherited from a common ancestor with reptiles. Actually, as I have noted before, there is a positive selective-pressure against the retention of dormant genes (because of the energy required in transcribing them), and these dormant or inactive genes are unlikely to be retained seemingly virtually intact (Mitsiadis et al. 2003) for 70-80 million years.

2. The genes which are involved are not even specific to teeth formation, and serve a wide variety of embryological roles.

3. In the Mitsiadis et al. paper, cited above, the researchers essentially transplanted part of a mouse embryo that ordinarily produces teeth into the chick embryo, and the result was the partial formation of teeth. But the chick develops an “egg tooth” anyway, which it uses to break open the egg shell. So it’s not hugely impressive because chicks already have the genes involved in specifying the formation of tooth-like appendages.

In the case of humans with tails, I would make two points:

1. The human coccyx (tail bone) is functional inasmuch as it provides essential anchorage points for muscles.

2. The rare congenital deformities where a human is born with a tail-like appendage bear little resemblance to the tail of a monkey, but are usually the product a type of fatty tumor.

Evolutionary developmental biology and embryonic development

Wikipedia proceeds into a discussion of evolutionary developmental biology and embryonic development, observing,

Evolutionary developmental biology is the biological field that compares the developmental process of different organisms to determine ancestral relationships between species. A large variety of organisms’ genomes contain a small fraction of genes that control the organisms’ development. Hox genes are an example of these types of nearly universal genes in organisms pointing to an origin of common ancestry. Embryological evidence comes from the development of organisms at the embryological level with the comparison of different organisms embryos similarity. Remains of ancestral traits often appear and disappear in different stages of the embryological development process. Examples include such as hair growth and loss (lanugo) during human development;³⁶ the appearance of transitions from fish to amphibians to reptiles and then to mammals in all mammal embryos; development and degeneration of a yolk sac; terrestrial frogs and salamanders passing through the larval stage within the egg — with features of typically aquatic larvae — but hatch ready for life on land;³⁷ and the appearance of gill-like structures (pharyngeal arch) in vertebrate embryo development. Note that in fish the arches become gills while in humans, for example, they become the pharynx.

One can sympathize somewhat with this argument. Indeed, this is probably one of the stronger arguments for common descent. But I’m not convinced. Several comments are warranted.

First, it is important that one consider all the evidence relevant to embryology, and not merely the seemingly confirming evidence. Indeed, one of the biggest conundrums facing modern evolutionary embryology is the fact that early embryonic development is widely divergent, and phylotypic stages are generally attained by non-homologous developmental routes. This is especially striking since large-scale screens in organisms such as Zebrafish and Drosophila reveal that one thing which is uniformly NOT evolutionarily hereditable are modifications to early development (e.g., see Haffter et al., 1996; or Driever et al., 1996). See my previous articles (here and here) for more on this fascinating subject.

Second, many of these structures are not functionally redundant, and serve important roles in the developing embryo. For example, the human so-called “yolk sac” is essential inasmuch as it is responsible for supplying the embryo with its first blood cells. To take another example, the pharyngeal pouches and ridges (the “gill slit” region) in humans does not develop even partly into gills. In fish, these structures are slits that allow water to enter in and out of the gills that remove oxygen from the water. In human embryos, however, the pharyngeal pouches develop into structures such as the thymus, thyroid and parathyroid glands. If this is the case, then whence the mandate for supposing that these systems are vestigial gill slits?

Indeed, the embryonic hair (lanugo) mentioned by Wikipedia also serves an important function. A substance called the “vernix caseosa” (a waxy coating, secreted from the sebaceous glands, composed of dead skin cells and oil) protects the skin of the fetus from constant exposure to the surrounding amniotic fluid. In addition, its slippery nature aids in the birth process. The “vernix caseosa” could easily be pulled off the skin, as a result of the constant motion in the womb, in its initial stage of formation. The function of the lanugo is to anchor it to the skin, holding it in place. If the lanugo has an important embryonic function, there is no obvious reason why it could not have been designed with the specific intention of fulfilling that purpose. If this is the case, why must it be understood as evolutionarily derived from primate hair?

Homologous Structures and Divergent (Adaptive) Evolution

According to Wikipedia,

If widely separated groups of organisms are originated from a common ancestry, they are expected to have certain basic features in common. The degree of resemblance between two organisms should indicate how closely related they are in evolution:

• Groups with little in common are assumed to have diverged from a common ancestor much earlier in geological history than groups which have a lot in common;
• In deciding how closely related two animals are, a comparative anatomist looks for structures that are fundamentally similar, even though they may serve different functions in the adult. Such structures are described as homologous and suggest a common origin.
• In cases where the similar structures serve different functions in adults, it may be necessary to trace their origin and embryonic development. A similar developmental origin suggests they are the same structure, and thus likely to be derived from a common ancestor.

When a group of organisms share a homologous structure which is specialized to perform a variety of functions in order to adapt different environmental conditions and modes of life are called adaptive radiation. The gradual spreading of organisms with adaptive radiation is known as divergent evolution.

This raises the old specter of the “similarity = common descent” argument. For reasons that I have discussed before, the argument is circular. The discipline of cladistics presumes phylogeny, no matter what the evidence says. For example, no matter how similar or different birds and reptiles are, it is possible to identify some group of reptiles that are closest to birds, despite the lack of evidence that they are in fact related at all. If there is a range of possible ancestors to birds, then the discipline of cladistics is able to identify the most probable candidate. But the initial assumption of common ancestry is never tested.

And there are many cases (as I noted previously) where shared features cannot be explained as the result of inheritance from a common ancestor.

Examples of such instances of convergent evolution include:

1. The multiple appearances of eyes;
2. Echolocation in bats and whales;
3. Pigmentation modifications in vertebrates;
4. The large canines of the saber-toothed cats and the marsupial thylacosmilids;
5. Antifreeze glycoproteins in Antarctic nototheniod Fish and Arctic Cod;
6. Mimicry in butterflies.

Wikipedia has another page that lists dozens of other examples of convergent evolution.

But the case for common ancestry based on shared features becomes even more dubious when one looks at their respective developmental pathways. Tellingly, Wikipedia states that “In cases where the similar structures serve different functions in adults, it may be necessary to trace their origin and embryonic development. A similar developmental origin suggests they are the same structure, and thus likely to be derived from a common ancestor.”

This is a curious statement, especially since many structures that are widely thought to be of a common evolutionary origin exhibit widely divergent developmental pathways. One classic example is the developmental origin of the neural tube, and the vertebrae, in chordates.

Consider the embryological development of the neural tube, one of the defining features of vertebrates. The neural tube always develops from the neural plate, but it does so in different ways. In the majority of vertebrates, it forms by the neural plate invaginating to form a deep furrow. The edges of this subsequently seal over to enclose a long, thin, hollow tube. In lamphreys and teleost fish, however, the neural plate thickens to form a neural keel. The neural tube then forms by the emergence of a cavity within the thickening.

But it gets even more interesting when we consider that among different classes of vertebrate, the vertebrae form embryologically in significantly different manners, and even use different source materials!

The neural tube of vertebrate embryos extends along the back of the embryo. A notochord runs alongside and beneath it. During the very early stages of development, temporary structures (called “somites”) are formed, in pairs, along the neural tube. These somites develop into the vertebrae.
In most tetrapods, the somite cells differentiate into three discrete layers:

1. The dermatome: This is located on the outside, and develops into connective tissue.
2. The myotome: This is the middle layer, which will develop into muscle.
3. The sclerotome: This is the innermost layer, which grows in the direction of the notocord and surrounds it, to form the so-called perichordal tube. It is this that will subsequently develop into vertebrae.

In birds, the vertebrae don’t develop from somite pairs on a one-for-one basis. Rather, each of the vertebrae is formed from the rear halves of one somite pair and the forward halves of the next. This process is called “resegmentation,” a phenomenon that, curiously, does not occur in mammals.

In some amphibians (e.g., the toad Xenopus), the somites don’t differentiate into the three types of cell. Rather, they consist exclusively of — and the vertebrae develop from — the myotomal cells.
In cartilaginous fish (e.g., sharks and bony fish), the sclerotome only partially grows in the direction of the notochord, and molds into so-called “arcualia” (i.e., blocks of cartilaginous tissue). Each pair of somites will typically produce four pairs of arcualia. One of each pair will be placed on either side of the neural cord / notochord. These arcualia are then morphed into the vertebrae.

In teleost fish, this process is even more different still! It involves three steps:

1.The sheath of the notocord (which, in this case, isn’t composed of somites) differentiates into so-called “chordal centers,” cartilaginous elements which become the main body of the vertebrae.
2. Cells near these chordal centers become the vertebrae dorsal and ventral arches.
3. Some sclerotome cells move in the direction of, and fuse with, the chordal centers. They thus contribute to components of the vertebrae.

So, not only do the vertebrae form from fundamentally different developmental routes between different vertebrate classes, but major components of the vertebrae are substantially derived from different source materials!

Similar surprises await us when we examine vertebrate ribs. Tetrapods, for example, have only one pair of ribs associated with each vertebra. Many fish, in contrast, have two sets of ribs: ventral and dorsal. While the ventral ribs, much like our own, surround the body cavity, the dorsal ribs are situated between the ventral and dorsal muscles (which are found along the back and sides of the fish). Amphibians also have ribs that surround the body cavity, in a manner similar to that of the ventral ribs to which I just alluded. But here’s the thing: Their embryological source is equivalent to dorsal, and not ventral, ribs!

These types of anomalies are very difficult to square with the paradigm of common descent.

Nested Hierarchies and Classification

Wikipedia states,

Taxonomy is based on the fact that all organisms are related to each other in nested hierarchies based on shared characteristics. Most existing species can be organized rather easily in a nested hierarchical classification. This is evident from the Linnaean classification scheme. Based on shared derived characters, closely related organisms can be placed in one group (such as a genus), several genera can be grouped together into one family, several families can be grouped together into an order, etc.³⁸ The existence of these nested hierarchies was recognized by many biologists before Darwin, but he showed that his theory of evolution with its branching pattern of common descent could explain them.³⁸³⁹ Darwin described how common descent could provide a logical basis for classification:⁴⁰

This has the potential to be a compelling argument for common descent; that is, if the nested hierarchies yielded by gene phylogenies were consistent.

Indeed, with a limited amount of data, it is possible to produce well-defined trees that link characteristics in a nested hierarchical pattern. The problem arises when more data is available. The more data, the less clear and consistent the trees tend to be. As one 2009 article in New Scientist put it,

[Biologist Michael Syvanen of the University of California, Davis] recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts — also known as tunicates — are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.

See Casey Luskin’s article here for a thorough discussion on this topic.

Vestigial Structures

On the topic of vestigial structures, Wikipedia observes,

A strong and direct evidence for common descent comes from vestigial structures.⁴¹ Rudimentary body parts, those that are smaller and simpler in structure than corresponding parts in the ancestral species, are called vestigial organs. They are usually degenerated or underdeveloped. The existence of vestigial organs can be explained in terms of changes in the environment or modes of life of the species. Those organs are typically functional in the ancestral species but are now either nonfunctional or re-purposed. Examples are the pelvic girdles of whales, halteres (hind wings) of flies and mosquitos, wings of flightless birds such as ostriches, and the leaves of some xerophytes (e.g., cactus) and parasitic plants (e.g., dodder). However, vestigial structures may have their original function replaced with another. For example, the halteres in dipterists help balance the insect while in flight and the wings of ostriches are used in mating rituals.

In general, the argument from vestigial structures is among the weaker arguments for common descent. For one thing, vestigial structures, at best, only point to the loss of function, perhaps through lack of use. This is perfectly consistent with what one might expect given a paradigm of design. For example, the wings of flightless birds may well suggest that those birds were once capable of flight. There is nothing that would surprise me about that. But the existence of wings on many flightless birds seems to be for purposes of mating behavior.

The same may be said for the hind wings of flies and mosquitos. At best, the evidence would only suggest that these organisms once possessed functional hind wings. But these halteres are known to serve as balancers that stabilize the insect during flight. There is no reason to think that this was not the originally designed purpose of those structures.

In the case of whale hind limbs, these structures serve important functions associated with the reproductive tract necessary for reproduction and live birth in the water. Indeed, the bones are associated with the genital apparatus and are found within the muscalature of the body wall.

Circuitous Routes?

The final part of this section reports on several “specific examples.” Among these are the apparently circuitous routes taken by the vas deferens from the testis, looping over the ureter and back down to the urethra; and the recurrent laryngeal nerve. Let’s take a brief look at those.

In the case of the vas deferens, the testes develop from the same structure as the ovaries in females, which is called the genital ridge and which is near where the kidneys will develop. There is a cord called the gubernaculum testis that connects the testis to the scrotum. As the fetus grows, the gubernaculum testis does not, so the testis is pulled downward, eventually through the body wall and into the scrotum. The lengthening vas deferens merely follows. So it’s not a circuitous route. Besides, before the vas deferens joins the urethra there needs to be a place where the seminal vesicle adds its contents.

In the case of the recurrent laryngeal nerve, ENV’s Casey Luskin notes several potential design reasons for the chosen route:

(1) There is evidence that supposed fundamental evolutionary constraints which would prevent loss of the circuitous route of the RLN do not exist. This implies that there is some beneficial function for the circuitous route.

(2) The path of the RLN allows it to give off filaments to the heart, to the mucous membranes and to the muscles of the trachea along the way to the larynx.

(3) There is dual-innervation of the larynx from the SLN and RLN, and in fact the SLN innervates the larynx directly from the brain. The direct innervation of the larynx via the superior laryngeal SLN shows the laryngeal innervations in fact follows the very design demanded by ID critics like Jerry Coyne and Richard Dawkins. Various medical conditions encountered when either the SLN or RLN are damaged point to special functions for each nerve, indicating that the RLN has a specific laryngeal function when everything is functioning properly. This segregation may be necessary to achieve this function, and the redundancy seems to preserve some level of functionality if one nerve gets damaged. This dual-innervation seems like rational design principle.

Casey Luskin also quotes Michael Egnor, who lists some other interesting advantages to the route taken by the RLN:

There is actually a design advantage to the course of the recurrent nerves, if one wishes to pursue this line of argumentation. The course of the nerves brings them through the mediastinum, where the heart and lungs meet. There are many lymph nodes there, and enlargement of these lymph nodes from processes such as cancer or infection (e.g., tuberculosis) often irritates these nerves and causes hoarseness or coughing. The course of the nerves reveals disease in an otherwise hidden part of the body (deep in the chest) by interfering with a process (speech) that is readily evident. It serves as an early warning to get medical care (or, with infectious diseases, as a warning to others that this person is ill), and this early warning has saved many more lives than the redundant course of the nerves has cost lives. The risk/benefit ratio needs to be examined comprehensively before one claims that the course of the nerves is biologically disadvantageous.

Egnor further notes,

Of course ID advocates have never claimed perfect design. But the argument that the anatomy of the recurrent laryngeal nerve is evidence for “bad design” fails on many levels. The descent of the recurrent nerves below the aortic arch and subclavian artery is the result of patterns of coalescence and movements of components of the aortic arch during embryogenesis. It appears that proximity of various layers and structures in the embryo serve to guide embryogenesis (it’s called induction). The details of this process are only beginning to be understood, and the Darwinist argument that the relationship between the recurrent nerves and the aortic arch is evidence of bad design fails to take into account the enormous complexities of embryonic development. It’s analogous to a 3 year old taking apart a computer and asserting that it was designed badly because some of the circuit board patterns were “curvy” instead of straight. The design wisdom of the anatomy of the recurrent nerves can only be judged by someone who knows all of the design specifications necessary for that region of the human body. Even the best embryologists are preschoolers when it comes to that.

In the next entry in this series, I shall discuss Wikipedia’s arguments for common descent based upon paleontology.