Fossil Succession


This chapter promotes the view that different lineages of living things have independent histories and do not share common ancestry. This idea attacks the core tenet of evolutionary theory--that all living things are genealogically related. The refusal to accept common ancestry is the sine qua non (indispensable idea) of creationism in all of its various guises.

To try to undermine confidence in common ancestry, this chapter trots out some hackneyed creationist claims:

  1. transitional fossils are rare.
  2. the major animal phyla appeared abruptly in the Cambrian explosion.

The chapter also misuses the work of scientists who study the tempo and mode of evolution by implying that criticisms of gradual change in evolution undercuts common ancestry.

This chapter also engages in a truly atrocious brand of pedagogy. Rather than teaching students what we do know about fossils, it focuses on what we do not currently know. The dangers of this approach can be seen when we examine the actual history of fossil discoveries, and the steadily shrinking lacunae (gaps) in the fossil record. A student who is made to learn about unfilled gaps in 9th grade is likely to carry a memory of that lesson for the rest of his or her life, long after paleontologists have found fossils which clarify the situation.

Scientific inquiry thrives by identifying gaps in our knowledge, proposing a hypothesis which explains the underlying situation, and then testing that hypothesis with experiments. Fossil hunters do the same, combining their knowledge of geology with evolutionary history to narrow down their search for particular fossils. This approach has revealed details of the evolution of humans, of whales, and of life itself which were unimagined when the authors of this critique were in high school. Had our teachers taught us that science could never fill in the gaps, we might be as incurious as the authors of Explore Evolution seem to be.

Transitional Fossils

Although creationists frequently claim that there are no transitional fossils, the paleontological record tells a very different story.

Transitional Fossils Are Not Rare

Are Transitional fossils are extremely rare?

Summary of problems with claim:

Fossils with transitional morphology are not rare. Fossils illustrating the gradual origin of humans, horses, rhinos, whales, seacows, mammals, birds, tetrapods, and various major Cambrian "phyla" have been discovered and are well-known to scientists. Explore Evolution's claims to the contrary are just a rehash of older creationist arguments on this point, relying on out-of-context quotes, confusion over terminology and classification, and ignoring inconvenient evidence.
"Though a possible whale-to-mammal transitional sequence has recently been unearthed, critics maintain that transitional sequences are rare, at best. For this reason, critics argue that Darwin's theory has failed an important test.
Explore Evolution, p. 27
Scientists have long thought that amphibians were a transitioinal form between aquatic and land-dwelling life forms. Why? Because amphibians can live in both the water and on land. Yet, the fossil record has revealed at least two problems with this idea... land-dwelling amphibians, themselves, appear suddenly in the fossil record.
Explore Evolution, p. 27
Darwin himself was well aware of the problems that the fossil record posed for his theory. … Where were the multitudes of transitional forms connecting different groups, as predicted (and expected) by his theory?
Explore Evolution, p. 30
Some critics say neo-Darwinism is not consistent with fossil data. Other critics say that punctuated equilibrium is consistent with fossil evidence, but lacks and adequate mechanism. Critics of both views argue that there are still far fewer transitional forms in the fossil record than we would expect, even if new forms of life did arise quickly.
Explore Evolution, p. 33

Full discussion:

First, a note on terminology. The phrase "neo-Darwinism" is not widely used by scientists, and may reflect a desire by creationists to dismiss Darwin's ideas merely as another "-ism," rather than a robust scientific theory. A PubMed search of over 18 million scientific articles found 131 variations on "neo-Darwinism," compared to 226,476 uses of "evolution."

Explore Evolution compounds many errors in attempting to claim that fossils representing evolutionary transitions are rare. The first error is its reliance on concepts like 'missing links' and 'transitional forms'. These terms are outdated and founded in incorrect and archaic ways of categorizing life. Until relatively recently, the classification system used to group living things did not aim to represent true evolutionary relationships, and some groups contained only some descendants of a common ancestor, excluding others. For example, birds were not traditionally placed within the reptiles while the 'Sarcopterygii' (lungfish, coelocanths, etc.) classically excludes tetrapods. When we try to connect these poorly defined groups with the grade school evolutionary view that, "fish gave rise to amphibians, which gave rise to reptiles, which gave rise to…," the problems with the underlying classification system confuse the matter. Some so-called 'fish' were more closely related to amphibians than to other so-called 'fish' – and some so-called 'reptiles' were more closely related to non-reptiles (e.g., birds) than they were to other 'reptiles'. Drawing upon discontinuities produced by our misclassification, people sought to find 'transitions' or 'links' between wrongly grouped 'fish' and 'amphibians' or 'reptiles' and 'birds' – historically, and quite literally creating the concept of 'missing link' or 'transitional form.'

Fortunately, evolutionary biologists have been doing away with such artificial groups for some time now. We no longer accept that birds evolved from reptiles and that birds are not reptiles themselves - since the term Reptilia now includes birds. Viewing life's history and classification in this more realistic (i.e., evolutionary) context – where we name groups based on a common ancestor plus all of it's descendants – we come to realize that quite literally, all critters have 'transitional' features. In other words, all living things possess a combination of ancestral and derived traits. The shared derived traits (discussed further in the response to chapter 4) inform us of close relationships, while ancestral traits include ancient features retained from an early evolutionary heritage. For example, salmon – which most people wouldn't have any trouble classifying – retain paired appendages and jaws – ancestral traits shared with species like sharks – but also have derived traits like bone that forms from a cartilaginous precursor – a trait which sharks do not have, but which tetrapods do. This sort of bone is a derived feature linking salmon as closer relatives of tetrapods than sharks are, even though salmon still have fins and other 'fishy' traits that sharks share.

Does this mean salmon are transitional forms or 'links' between sharks and tetrapods? Were salmon our ancestors? Of course not. The issue is that upon properly classifying life into groups sharing a common ancestor, we see that all of life is characterized by these ancestral and derived traits. Just as salmon did not give rise to tetrapods, frogs are not links between salmon and reptiles. These traits inform us of common ancestry among groups, not a sequential movement of an entire group into another group (e.g., amphibians to reptiles).

As to the actual rarity of fossils illustrating evolutionary transitions, Explore Evolution makes additional errors. First, fossils in general are rare, relative to the actual diversity of life which once existed. The chances of a given species fossilizing are slight. Thus, the fossils referred to as transitional are not necessarily the direct ancestors of modern taxa, but may represent failed branches off of the stem which led to modern forms. Depending where they branched off, they possess some, but not all, of the traits we associate with modern groups, which provides evidence of the form the transition took, even if we lack fossils of the directly ancestral species. Knowing the age of these fossils, we can have substantial certainty about the latest date at which various evolutionary novelties must have originated. Explore Evolution fails to explain what paleontologists actually use fossils to illustrate, sowing confusion among students where it ought to bring clarity.

Given the general rarity of fossils, fossils showing evolutionary transitions are not at all rare. This can be illustrated with a range of examples, of which the record of hominid fossils is especially striking. The skulls shown below display a clear, smooth transition from the early ancestors of modern humans to the modern form of the human skull. A wag might suggest that there is a gap between each of those fossils, and demand a transitional fossil to fill each such gap. Because this evolutionary sequence is relatively recent, there are enough fossils that we can only show the full transition with graphs like the one below. Fossil hominid skulls:  Labeled with specimen name, species, age, and cranial capacity in milliliters (cranial capacity is the volume of the space inside the skull, and correlates closely with brain size). Images © 2000  Smithsonian Institution, modified from: TalkOrigins Common Ancestry FAQFossil hominid skulls: Labeled with specimen name, species, age, and cranial capacity in milliliters (cranial capacity is the volume of the space inside the skull, and correlates closely with brain size). Images © 2000 Smithsonian Institution, modified from: TalkOrigins Common Ancestry FAQ

That graph illustrates one particular aspect of human evolution, the growth of the brain over the last 3.5 million years of human evolution. At no point could anyone credibly point to a discontinuity between our australopithecine ancestors and modern humans which is not filled by some ancestral fossil form.

Ages and cranial capacity data: C. De Miguel and M. Henneberg (2001). "Variation in hominid brain size: How much is due to method?"  Homo 52(1), pp. 3-58.    Cranial capacity of modern humans: McHenry et al. (1994). "Tempo and mode in human evolution." Proceedings of the National Academy of Sciences, 91:6780-6.  Graphic by Nick Matzke, National Center for Science Education.  May be freely reproduced for nonprofit educational purposes.Ages and cranial capacity data: C. De Miguel and M. Henneberg (2001). "Variation in hominid brain size: How much is due to method?" Homo 52(1), pp. 3-58. Cranial capacity of modern humans: McHenry et al. (1994). "Tempo and mode in human evolution." Proceedings of the National Academy of Sciences, 91:6780-6. Graphic by Nick Matzke, National Center for Science Education. May be freely reproduced for nonprofit educational purposes. As we look at events further back in time, the chances of a fossil surviving decrease, so forms of life from the more distant past tend to show larger gaps - greater morphological variation - between fossils. Nonetheless, new fossils are constantly being found which shrink the gaps between ancient species, such that cases once presented by creationists as insurmountable problems for evolution are now textbook examples of fossil transitions. Indeed, of the two sources Explore Evolution cites to support the claim that "Paleontologists have identified many gaps that remain to be filled in the fossil record" (p. 20), only one actually addresses the quality of the fossil record, and it is from 1981. Even that paper does not support the claim that such gaps reflect an absence of transitional forms. Everett C. Olson wrote:
The problem of the existence of linkages and phylogenies at the species and generic levels has been much reduced during the last one hundred and twenty years. How this reduction supports or denies Darwin's concepts of phyletic gradualism is still a matter of interpretation of the evidence. At familial and higher levels, the establishment of linkages between categories has been much less successful, and decreasingly so at each successive higher level. Under the very best circumstances, however, morphological and stratigraphically graded transitions between classes and subclasses have been found.
Everett C. Olson (1980) "The Problem of Missing Links: Today and Yesterday," The Quarterly Review of Biology 56(4):405-442.

Even twenty-seven years ago, the record of species-level transitions was considered quite good, and at higher taxonomic levels, the situation was improving and quite strong in situations where preservation of fossils had been favorable. Since that time, the state of transitional fossils has only improved. Explore Evolution uses a 1982 reference in an attempt to discredit these recent fossil discoveries (without actually mentioning what those discoveries are). Staying up to date with research in science is critical for students and for textbook authors, and Explore Evolution's reliance on an outdated, non-applicable, 25 year old reference is unacceptable.

Tiktaalik roseae: a transitional fossil. Image from WikiCommons.Tiktaalik roseae: a transitional fossil. Image from WikiCommons.

A recent example from the news is the discovery of the fossil species Tiktaalik roseae.

Tiktaalik is a transitional form in the evolution of vertebrates on four legs. Ahlberg and Clack (2006) describe the importance of the discovery:

It demonstrates the predictive capacity of palaeontology. The Nunavut field project had the express aim of finding an intermediate between Panderichthys and tetrapods, by searching in sediments from the most probable environment (rivers) and time (early Late Devonian). Second, Tiktaalik adds enormously to our understanding of the fish–tetrapod transition because of its position on the tree and the combination of characters it displays.
Per Erik Ahlberg and Jennifer A. Clack (2006) "Palaeontology: A firm step from water to land," Nature 440:747-749
Tiktaalik roseae was predicted before it was discovered. As Neil Shubin describes in his 2008 book Your Inner Fish:
Neil Shubin, 2008. Your Inner Fish. Pantheon Books, New York, 0375424472. P. 10.
Tiktaalik roseae: Its wrist configuration allowed it to "do a pushup." Image from WikiCommons.Tiktaalik roseae: Its wrist configuration allowed it to "do a pushup." Image from WikiCommons.    

And when Shubin started investigating sedimentary rocks laid down in shallow water about 375 million years old, he found Tiktaalik roseae.


Subsequent investigation confirmed that Tiktaalik roseae's transitional morphology.

[Tiktaalik roseae shows] a marked reorganization of the cranial endoskeleton ... [with] morphology intermediate between the condition observed in more primitive fish and that observed in tetrapods.
Downs, J.P., Daescher, E.B., Jenkins, F.A., and Shubin, N.H., 2008. "The cranial endoskeleton of Tiktaalik roseae." Nature, vol. 455, no. 16, 16 Oct 2008, pp. 925-929.

Image courtesy of Brian Swartz.

Based on known fossils, scientists could estimate what time period the transitional form had to have existed in. Based on the known locations of fossil beds, they could select a bed known to be from the right time and to have possessed the right environment 375 million years ago to contain a transitional form. They knew what sorts of fossils to look for at that site by considering the known fossils from before and after the era in question. And after selecting that site, they found exactly the fossils they sought, a transitional form which allowed a detailed examination of the evolution of critical structures in the transition from aquatic fish to terrestrial tetrapods.

This process is exactly how science works, and a textbook interested in encouraging students to explore the way evolutionary biology is practiced would do well to help students see how paleontologists actually deal with gaps in our knowledge of the fossil record.

The approach Explore Evolution takes does not present any such understanding of the inquiry-based process of science. Gaps in our current knowledge are treated as insurmountable barriers. If scientists truly took that approach, we would never have achieved the sorts of advances seen in paleontology over the last 20 years, let alone the last 150.

Some scientists say the absence of transitional forms should dramatically change the story we tell about life's history. They point out that when we study the fossil we have actually found, the evidence does not lead us to connect the major lines of descent through a single, branching tree.
Explore Evolution, p. 35

It would be very interesting to know who "some scientists" actually are. The "they" Explore Evolution discusses have not published in the peer-reviewed literature, because there is in fact substantial agreement that all the major phyla lines do indeed come from a single, branching tree.

Look through any college-level biology textbook (Campbell, p. 470-71; Raven, p. 654-55; Starr, p. 318-321), and you will see diagrams showing only the single, branching tree model. A multiple-tree view is not shown simply because the evidence for it is so weak, and the evidence for a single-tree so strong, that the multiple-tree model can be discarded in the same way a flat earth model can be discarded from a geography textbook.

This straw man logic—set up a false claim, knock it down easily, declare victory—is itself a lesson on how not to teach logic and rhetoric to children.

Some advocates of punctuated equilibrium do acknowledge that the absence of transitions between major groups of organisms is an unsolved problem for evolutionary theory as whole.
Explore Evolution, p. 35

These unnamed, uncited "advocates" strike again. While certainly paleontologists would enjoy having more "transitional" fossils—whatever that vague terms actually means—there are many examples of fossils that bridge the gap between species. Thus, the phrase "absence of transitions" is wrong to imply that there are no transitions.

Do animal forms change or stay the same?

The fossil record provides many examples of living organisms that have remained stable in their form and structure over many millions of years--sometimes over hundreds of millions of years.
Explore Evolution, p. 25

Summary of problems with claim: This is not evidence against evolution.

Full discussion: Explore Evolution brings this up to suggest:

  • Something is wrong with the model of evolution if organisms do not change.
  • Something may be wrong with the geologic timeline, if organisms show no change over such a long time period.
Coelacanth: a "living fossil." Image from WikiCommons. Coelacanth: a "living fossil." Image from WikiCommons.

The long-lived, unchanged existence of an organism in the fossil only poses a problem to evolution is one makes the (false) assumption that change occurs at a steady background pace. In fact, a better analogy is Newton's First Law: "Objects at rest stay at rest unless acted upon." If an organism lives in a stable environment and is able to reproduce in sufficient numbers to pass on its genes, then there is no impetus to change.

Other examples of long-lived, relatively unchanged species include sharks, the coelacanth, the oppossum, crocodiles, and the horseshoe crab.

Darwin on Transitional Fossils

Darwin himself was well aware of the problems that the fossil record posed for his theory...Where were the multitudes of transitional forms connecting different groups, as predicted (and expected) by his theory?
Explore Evolution, p. 30

What Darwin actually wrote:

Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and gravest objection which can be urged against my theory. The explanation lies, as I believe, in the extreme imperfection of the geological record. Charles Darwin (1859), The Origin of Species, p. 280.

Darwin's statement acknowledges an incomplete fossil record rather than a problem with his theory.

The Sequence of Transitional Fossils

Do transitional fossils appear in sequence as they should? problem

Summary of problems with claim:

Paleontologists employ methods to test whether their results are better than would be expected by chance. Evolutionary biologists draw data from multiple lines of evidence, and each of those lines of evidence reveals the same pattern — the same branching tree of life.

Full discussion:

Explore Evolution asserts:

Given the millions of different fossil forms in the fossil record, critics argue that we would expect to find, if only by pure chance, at least a few fossil forms that could be arranged in plausible evolutionary sequences. To understand what they mean, imagine that a representative of every organism that has ever lived on earth was randomly pasted to an enormous wall representing the geologic column. Most of the fossils would bear no relationship to the other fossils stuck closest to them on the wall. Nevertheless, by chance a few of them might end up next to forms that do have some resemblance. These forms might then appear to be related as ancestors and descendants, even if they were not. Is it possible that the mammal-like reptile sequence is a statistical anomaly rather than a legitimate sequence of ancestors and descendants.
Explore Evolution, p. 27
Paleontologist at Work: Image from WikiCommonsPaleontologist at Work: Image from WikiCommons

Paleontology doesn't work in a vacuum. In other words, paleontology is only one branch (or subset) of evolutionary biology. Paleontological contributions consist of morphology and stratigraphic sequence data, data that is then integrated with morphological data from living critters, their DNA (and other molecules), as well as developmental data that all work together to support common descent.

In other words, as DNA changes, that affects the proteins produced, the developmental trajectory, and the subsequent morphology of traits in individuals and lineages through time. All of these fields – molecular biology, developmental biology, and comparative anatomy – are intertwined at the heart of evolutionary theory. These fields each work from independent data sets, yet still return to converge on similar answers. For example, molecular sequence data tells us that humans and rats share more DNA in common than either do with a bird; that birds, humans, and rats are more genetically similar than any are to salamanders; and that salamanders, birds, rats, and humans share more DNA with each other than any do with salmon. In turn, developmental and morphological features are shared uniquely with this same pattern of similarity and dissimilarity. For example, humans and rats have placentas (as embryos) and hair as adults while birds do not. Birds, rats, and humans possess a chorion and allantois (extra-embryonic membranes – modified in mammals, though still present) during development, and a fully developed atlas/axis (vertebral arches) that allow up/down and side-to-side movement of the head – features which salamanders do not have. Finally, salamanders, birds, humans, and rats all share unique modes of digit development and adult hips that are fused to the vertebral column – features lacking in salmon. Thus, evolutionary biologists do not solely rely on fossils to understand evolutionary relationships; instead, fossils fall into a much larger picture of other data that returns to corroborate our understanding of history.

The statistical argument presented by Explore Evolution not only fails from a strict paleontological perspective – since paleontologists test for randomness in their data sets – but moreover, paleontologists work within the bracket of extant diversity, and data from living critters also contributes to our understanding of relationships and ancestral/derived traits.

A recent paper addressing this evidence explained:

It is clear that the fossil record cannot be read literally (Darwin 1859). There are many gaps, and many organisms, and indeed whole groups of poorly preservable organisms that have never been preserved and are doubtless lost for ever (Raup 1972). Some have even gone so far as to suggest that the fossil record is almost entirely an artifact of the rock record, with appearances and disappearances of fossil taxa controlled by the occurrence of suitable rock units for their preservation (Peters and Foote 2001, 2002), or the matching rock and fossil records controlled by a third common cause (Peters 2005). However, the widespread congruence between the order of fossils in the rocks and the order of nodes in cladograms (Norell and Novacek 1992; Benton et al. 2000) indicates that the order of appearance of lineages within the fossil record is not a random pattern.
Michael J. Benton and Philip C. J. Donoghue (2007) "Paleontological Evidence to Date the Tree of Life,"Molecular Biology and Evolution, 24(1): 26-53

The Norell and Novacek (1992) citation is the same source Explore Evolution cites to justify the claim that the fossil record is statistically problematic. How can this conflict exist? The problem comes from two sources. First, that the authors of Explore Evolution do not understand (and count on their audience not understanding) how fossils are actually used. As Benton and Donoghue observe, "Fossils can provide good 'minimum' age estimates for branches in the tree, but 'maximum' constraints on those ages are poorer." In order to find a fossil possessing a transitional feature, it is necessary for that feature to have evolved, for the population in which it evolved to diversify, and for some descendant of the first individual with that trait to have died, been fossilized, and that a paleontologist have discovered that fossil. More intense sampling will never move the oldest date of a feature closer to the present, but will move that earliest occurrence back further, approaching the time of its first occurrence.

A second error derives from the authors' fundamental misunderstanding of evolutionary processes. Lineages with traits characteristic of a transitional form may persist long after another lineage has evolved novel traits, and which lineage will have the oldest fossil will depend on where and how fossils from each group formed, and where paleontologists have looked for those fossils. Complaints that such fossils are not in sequence are equivalent to claiming that my grandmother could not be ancestor because she and I lived at the same time. The figure illustrating mammalian evolution in the section below demonstrates how the overlapping histories of different lineages could produce fossils which appear to be out of order if the branching evolutionary process were not clear.

This explains why Norrell and Novacek, after observing that the fossil record of primates is spotty because the sequence of the earliest representatives (as of 1992) of two groups is not as predicted (because the fossil record is limited or absent for those groups), nonetheless state, "Despite these discrepancies, there is a noteworthy correspondence between the fossil record and the independently constructed phylogeny for many vertebrate groups. Statistically significant correlations were found in 18 of 24 cases examined" (Mark A. Norrell and Michael J. Novacek (1992) "The fossil record and evolution: comparing cladistic and paleontological evidence for vertebrate history," Science 255(5052):1690-1693). It is worth noting that new fossil discoveries and improved phylogenetic reconstructions in the 15 years since they wrote that paper, have resulted in a much improved fit between hypothesis and the hominid fossil record. This illustrates the danger in basing an argument on what we don't know, the core of the argument of Explore Evolution.

Whale Evolution



Explore Evolution, p. 20




Duane Gish (1992)



Denton (1985) Evolution: A Theory in Crisis

Adler & Adler Publishers:Chevy Chase, MD. p. 174


The Sizes of Transitional Fossils

Explore Evolution claims that because transitional fossils come in different sizes, they aren't really transitional

Summary of problems with claim: The point of presenting fossils at the same size is to illustrate the appearance of novel anatomical structures. Size is a feature that changes with age, diet and changes relatively easily in response to evolutionary pressures. The shift from three bones on each side of the lower jaw to a single dentary bone is far rarer and more informative about evolutionary history.

Full discussion: Explore Evolution takes umbrage at a diagram from T.S. Kemp's 2005 book The Origin and Evolution of Mammals. Page 21 of Explore Evolution shows a series of skulls (Figure 1:6), each the same size, and then compares this on page 29 (Figure 1:8) to the same skulls at relative sizes, where some are much larger than others.

Scaling for Clarity: A shovel, a mole paw, a human hand, and a mole cricket forelimb. Scaling for Clarity: A shovel, a mole paw, a human hand, and a mole cricket forelimb. Altering the scale is done for clarity, not deception, as the authors well know. Explore Evolution does the very same scaling in its Figures 2:1 and 2:4, on pages 41 and 43, where the arm of a bat, a porpoise, a horse, and a human (2:1) and cricket and a mole (2:4) are all drawn at similar scales.

In Figure 1:8 the miniscule size of Thrinaxodon or Probainognathus makes it impossible to identify bones and structures. In Figure 1:6, critical features which distinguish mammals from their amniote ancestors (structures like the opening in the bones behind the eyes and the locations of bones in the lower jaw) can be seen quite clearly. Mammals range in size from a few grams (e.g., the Bumblebee Bat) to several tons (e.g., a Blue Whale), but nevertheless, all of them have a single bone (the dentary) that makes up their lower jaw, hair, mammary glands, and numerous other features that diagnoses them as "mammals." Indeed, the range of sizes seen in domestic dogs is greater than the range shown in figure 1:8 (see the discussion of dog size and morphology in the critique of chapter 7), and that size range does not interfere with our understanding of the "close genealogical relationship" (Explore Evolution, p. 29) between dogs. The illustration in figure 1:6 (from Kemp's The Origin and Evolution of Mammals) is meant to illustrate the transition of a particular set of structures, and not (as Explore Evolution suggests) to make a point about the size of the organisms. Explore Evolution’s point about size is ultimately a semantic and silly argument which misrepresents (or misunderstands) what scientists look for in assessing fossil transitions. Size is not regarded as a factor which signifies "close genealogical relationship," while the arrangement of post-orbital and jaw bones is significant.

Proper scaling in figures is a great pedagogical tool that helps students and researchers in their comparative anatomy - and at least in professional publications, scale bars are commonly included so viewers and critics can ascertain specimen size. Explore Evolution’s figure 1.8 hides information, obscuring evidence of the evolution of evolutionarily significant features like postdentary bones whose modification is coupled to the origin of the mammalian middle ear.

In evaluating the evolution of modern mammals from the amniote ancestors of reptiles and mammals, there are several important traits that scientists examine. Mammalogy, by Vaughan, et al. (2000) lists 25 major features, selected from a much longer list of traits distinguishing mammals. The traits that do not fossilize from that list include skin glands (mammary glands, sweat glands, sebaceous glands), hair, specialized muscles in the skin, the epiglottis, details of the soft anatomy of the lung and diaphragm, brain structures, facial muscles, red blood cells lacking nuclei, and the anatomy of the heart. We will discuss some of them in more detail in the critique of chapter 12.

Skeletal characteristics are easier to identify in fossils. These include a change in the bones of the jaw with a shift of three bones out of the structure of the jaw and their reuse in the ear, a trait paleontologists regard as the dividing line between mammals and their non-mammalian ancestors. Vaughan, et al. explain "By this definition, Mammalia does not include the extinct near-mammals, the Mammaliaformes" (p. 11). Paleontologists debate which fossils represent the earliest mammals because of differing criteria, and the increasingly fine differences between the fossils make it harder to draw a clear line. Vaughan, et al. explain:

…when mammals first appeared in the Triassic period, they represented no radical structural departure from the therapsid plan but had attained a level of development … that is interpreted by most vertebrate paleontologists as a key indication that the animals had crossed the non-mammalian-mammalian boundary. … Many of the mammalian characters discussed in this chapter resulted from evolutionary trends clearly characteristic of therapsids.
Terry A. Vaughan, James M. Ryan and Nicholas J. Czaplewski (2000) Mammalogy 4th ed., Saunders College Publishing: Orlando, FL. p. 10 of 565.

The "mammal-like reptiles" that Explore Evolution refers to are these therapsids, as well as other members of the Clade Synapsida. As mentioned above, scientists do not refer to the group as "mammal-like reptiles." The University of California Museum of Paleontology explains "This term is now discouraged because although many had characteristics in common with mammals, none of them were actually reptiles." Reptiles are a lineage which shares a common ancestor with mammals and other synapsids, not a group ancestral to mammals. Understanding that relationship can help clarify much of the confusion that laces the treatment of transitions in Explore Evolution.

The ancestors of modern reptiles, mammals and birds are known as amniotes. That name refers to a feature of the eggs of all those groups, one of several shared, derived characteristics which suggests that those groups share a common ancestor. A common challenge in talking about the transitional forms between mammals and reptiles is attempting to imagine a form intermediate to modern reptiles and modern mammals. In evolutionary terms, a transitional form is a common ancestor of two groups, one which shares traits with earlier forms and possesses a few of the traits which uniquely identify later lineages. We have such fossils illustrating the transition of early amniotes to the several lineages which led to modern mammals and to reptiles.

Early Amniotes: Despite their morphological similarities, critical differences show that these fossils represent the first branches between the lineages that would go on to produce diverse modern groups.  From fig. 10.11 of Robert L. Carroll (1988) Vertebrate Paleontology and Evolution W. H. Freeman and Co.: New York. 698 p.Early Amniotes: Despite their morphological similarities, critical differences show that these fossils represent the first branches between the lineages that would go on to produce diverse modern groups. From fig. 10.11 of Robert L. Carroll (1988) Vertebrate Paleontology and Evolution W. H. Freeman and Co.: New York. 698 p. The first skull in the figure at the right shows the basic anatomy of the ancestral condition of the amniote lineage. Of particular importance, there is no hole in the skull behind the eye socket. The lower jaw in all of these fossil species consists of three bones, one of which is on the inside of the jaw, not visible in the illustration.

That first skull dates to roughly 315 million years ago, and represents one of the earliest known amniotes. Fossils of this and other early amniotes are found in the fossilized stumps of a species of tree which grew in floodplains. These early amniotes took refuge in the hollow stumps of those trees, and without the discovery of those stumps, our knowledge of the base of the amniote tree of life would be much poorer. Those sorts of historical contingencies are common in paleontology, and help explain the unevenness of the fossil record.

The next skull dates from around 300 million years ago, and belongs to an ancestor of mammals. The main difference between it and the first species is that there is a gap between two bones behind the eye socket. This gap may have allowed greater freedom for jaw muscles, or may have carried neither adaptive benefit nor harm. The size of that gap varies between fossils, as does the size of that gap, but its existence marks descendants of a common ancestor. Complaints about the size of the skull miss a critical point about the shared derived characters that united that lineage, named the synapsids (to which all mammals belong). Another major branch of the amniotes evolved two holes in the skull, as shown in the third part of the figure. This group, the diapsids, includes birds and most reptiles. The fourth skull represents a derived lineage of diapsids, in which one of the gaps expanded, secondarily producing a skull with a single hole but which shares other traits with diapsids that demonstrate its common ancestry.

By examining the traits that these skulls share, it is possible to trace the origin of several separate lineages as they originated. The many similarities between these skulls demonstrate their close relatedness, and suggest that they all would have looked more similar to a large iguana or salamander than to any living mammal or bird. Nonetheless, certain novel traits in the skulls indicate that they represent very different lineages, the ancestors of modern groups that differ widely.

The evolution of early mammals, mentioned briefly, then criticized trivially in Explore Evolution helps demonstrate other important aspects of the scientific evaluation of fossils. As mentioned previously, the major feature that distinguishes the earliest mammals from their ancestors is the presence of a single bone in the lower jaw, rather than the four bones seen in amniotes and in amniotes other than mammals. PICTURE 2 Mammal Jaw Evolution: The transition from a four-boned lower jaw to the mammalian jaw with a single element.  Skull illustrations from Kardong (2002), as reproduced by Theobald (2004).  The jawbones on the left illustrate the the inside of the mouth; the illustrations on the right show the outside of the jaw. The quadrate (the incus or anvil of the mammalian ear) is in turquoise, the articular (malleus or hammer in the mammalian ear) is in yellow, and the angular (tympanic annulus in the mammalian ear) is in pink. Teeth are not shown, and skulls are scaled to constant size for clarity. Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary.     Skull figures reproduced from Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. 3 ed. New York: McGraw Hill, fig. 1.4.3.  The bubble plot of mammalian evolution is based on figure 17.1 in Carroll (1988), and shows the diversification of major groups and the separation of distinct lineages through time.Mammal Jaw Evolution: The transition from a four-boned lower jaw to the mammalian jaw with a single element. Skull illustrations from Kardong (2002), as reproduced by Theobald (2004). The jawbones on the left illustrate the the inside of the mouth; the illustrations on the right show the outside of the jaw. The quadrate (the incus or anvil of the mammalian ear) is in turquoise, the articular (malleus or hammer in the mammalian ear) is in yellow, and the angular (tympanic annulus in the mammalian ear) is in pink. Teeth are not shown, and skulls are scaled to constant size for clarity. Q = quadrate, Ar = articular, An = angular, I = incus (anvil), Ma = malleus (hammer), Ty = tympanic annulus, D = dentary. Skull figures reproduced from Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. 3 ed. New York: McGraw Hill, fig. 1.4.3. The bubble plot of mammalian evolution is based on figure 17.1 in Carroll (1988), and shows the diversification of major groups and the separation of distinct lineages through time. As the figure above shows, the transition in the jaw bones can be traced through fossils. Figure 1:6 in Explore Evolution shows additional transitional fossils, and there are even more species which fill in the gaps between those species. The figure above highlights the bones that transitioned into the ear in different colors, making it easier to see how the relative sizes and locations of those bones changed over a hundred million years, allowing them to serve a greater role in transmitting sound, while the jaw hinge shifted from one of those bones (the articulate) to the dentary. In pelycosaurs, the first major lineage of synapsids, the four bones of the lower jaw are firmly joined together. One bone, the articulate, has structures which may have helped transmit sound, but it is unclear how effectively that would have worked.

The pelycosaurs differentiated into several major lineages, and a branch from one of those lineages further diversified into the therapsids. In therapsids, the sutures joining the post-dentary bones became looser, allowing the bones to vibrate in response to sound, and making them less useful as structural components of the jaw. While the major hinge in the jaw remained on the articulate in the therapsids, members of a group of therapsids known as cynodonts developed a second hinge on the dentary bone. This transition was probably driven partly by the increasing strength of jaw musculature, and the growing role of the postdentary bones in the ears. The formation of the second joint can be found in later cynodonts, and the older joint is much reduced in early mammals like Morganucodon, disappearing entirely in modern mammals. The jaws of embryonic marsupials go through similar transitions, indicating that the ancestral developmental processes are still at work in the formation of the jaw.

The shift in the jaw hinge and the change in size, shape, and location of earbones/jawbones is powerful evidence linking modern mammals with therapsids, pelycosaurs and the ancestors of all amniotes. Other transitions in the shape of the teeth and other details of the skeleton confirm this pattern, revealing the nested hierarchy of traits that is predicted by evolution and common descent.

Explore Evolution invites to consider this and other transitions, but without actually presenting any actual evidence for them to consider. Indeed, it is not clear whether the authors of Explore Evolution themselves understand this transition, since their main objection to calling these fossils "transitional" seems to be that the fossils are of different sizes. They ignore the actual morphological transitions that scientists study, instead focusing on size differences which carry little evolutionary significance. Far from establishing any problem with the fossil record of the transition from amniotes to mammals (not, as Explore Evolution puts it, from reptiles to mammals), the discussion in Explore Evolution yet again demonstrates the authors' own problems.

The Cambrian Radiation



Sudden Appearance?

Did animal phyla suddenly appear in the Cambrian Explosion?

Explore Evolution, p. 22

Explore Evolution, p. 22











Explore Evolution, p. 30


Explore Evolution, p. 22

We need better math in creationist textbooks:
American football field = 100 yards
1 yard = 3 feet
football field = 300 feet
1 foot = 12 inches
football field = 3600 inches
4 inches/3600 inches = 0.0011 = 0.11%

age of the Earth = 4.54 billion years = 4,540 million years
length of Cambrian Explosion according to
Explore Evolution = ~10 million years
10 million / 4540 million = 0.0022 = 0.22%

0.11% does not equal 0.22%. Q.E.D.

The Cambrian Radiation in the Geologic Record










Creationist Statistics

Explore Evolution, p. 31



There's an old joke that goes like this:


The businessman says, "Sheep are black."



Soft-bodied fossils




Explore Evolution, p. 31


The USF webpage lists Chien's research interests thusly













Cal Academy of Sciences display


Explore Evolution, p. 34


Full discussion:



1. Explore Evolution Misunderstands the Definition of Phyla


2. Phyla Remain Distinct



Polyphyletic vs. Monophyletic

One major issue for creationists is whether organisms are best described by polyphyletism or monophyletism. While science views organisms as having a common ancestor, creationism posits multiple creations into biblical "kinds," which are also termed "baramins."

Do scientists support polyphyletism?

Do many scientists think that the fossil record supports a polyphyletic view of the history of life?

Summary of problems with claim: There is no evidence to support this assertion; moreover, Explore Evolution misunderstands the terminology.

Full discussion:

Diagram 1:12 shows three models of evolution.

In the first, we see a diagram labeled "the neo-Darwinist picture." This diagram shows smooth transitions between branches.

In the second, this diagram is labeled "punctuated equilibrium," and shows a similar structure to the first diagram, with the exception of the branches being sharp and angular. The idea with this diagram is that transitions occur more rapidly than in the first diagram.

The third diagram is labeled "a polyphyletic view," and shows five separate trees all beginning at the same time. Curiously, the transitions between branches seem to be a mixture of the first and second diagrams.

A Orchard?: Explore Evolution's inaccurate diagram of polyphyletic relationshipsA Orchard?: Explore Evolution's inaccurate diagram of polyphyletic relationships

The writers of Explore Evolution do not understand the term polyphyletic.

In the sense that they mean it, a polyphyletic model involves several different trees of life, each starting separately (Explore Evolution, p. 10). This is not what scientists mean when they use the term polyphyletic.

From Campbell (p. 471):

A taxon is said to be monophyletic is a single ancestor gave rise to all species in that taxon and to no species placed in any other taxon. A taxon is polyphyletic if its members are derived from two or more ancestral forms not common to all members. A paraphyletic taxon excludes species that share a common ancestor that gave rise to the species included in the taxon.
Campbell, Biology, 4th edition, 1996

Therefore, in this diagram, A = monophyletic, B = paraphyletic , and C = polyphyletic

Trees of Life:: Monophyletic (A), paraphyletic (B), and polyphyletic (C) relationshipsTrees of Life:: Monophyletic (A), paraphyletic (B), and polyphyletic (C) relationships

This is a completely different sense than the way Explore Evolution uses these terms. Note that in the case of C, polyphyletic, the splitting branches still originate from a single common ancestor.

On page 19 of Explore Evolution, three cartoons show Charles Darwin drawing a "Tree of Life."

Explore Evolution asks:

His famous tree analogy was Darwin’s way of interpreting (or making sense of) the fossil data. But what sense did he make of it?
Explore Evolution, p. 19

Explore Evolution answers its own question, saying that Darwin thought "younger fossil forms arose from older ones," and

Every creature on Earth must ultimately be linked to a single common ancestor in the distant past: the root or trunk of the Tree Life.
Explore Evolution, p. 19
Haeckel's Tree of Life: Image from WikiCommons Haeckel's Tree of Life: Image from WikiCommons

Although he discussed the concept, Darwin did not actually make any Tree of Life diagram in Origin of Species. Showing Darwin, even in cartoon form, drawing such a tree is a distortion of Darwin's writings.

Ernst Haeckel drew the earliest phylogenetic trees. The modern term for phylogenetic trees is cladograms. Cladograms are a very useful way to represent the phylogenetic tree of life and to show the common descent of animals.

Explore Evolution asserts:

In the overwhelming majority of cases, Common Descent does not match the evidence of the fossil record.
Explore Evolution, p. 27

This is an absurd claim, completely at odds with the scholarship of 150 years of paleontological research. Explore Evolution does not have a citation to back up this claim because no such reference exists outside creationist works.

Evidence for Single Origin of Life

Sidebar: Evidence for a single origin of life

There is significant scientific evidence that life originated from a single source. Two major lines of evidence involve RNA and the shape of amino acids.

Left-Right Chirality:  Image from WikiCommons []Left-Right Chirality: Image from WikiCommons []

1. RNA Evidence

All cells use ribosomes and transfer RNA (tRNA) to synthesize proteins from chains of amino acids. This process is very similar in all living organisms. This strongly argues for a single origin.

Ribosomal RNA (rRNA) is one of the most conserved genes, meaning that it changes very little between organisms. Because rRNA is so similar among organisms, this strongly suggests a single origin.

2. Amino Acid Evidence

Amino acids are the building blocks of proteins. The three-dimensional structure of proteins is vital to their function. However, amino acids exist in two structures that can be described as left or right “handed.”

chirality = orientation of molecules into left or right “handedness” A left hand is identical to a right hand except for its chirality. Likewise, an L-amino acid (left orientation) is identical to a D-amino acid (dextral, or right orientation) except for its chirality.

Both L and D-amino acids are found on Earth and in organic materials from meteorites. Theoretically, either form should work equally well to build proteins. However, biochemical processes only use L-amino acids. This strongly suggests that life arose once, and by happenstance employed the L-amino acid configuration.

Another hypothesis is that if the earliest forms of life used both L and D-amino acids, then this binary system would have greatly complicated nutrition. Imagine that your cell needs R-amino acids, but what you eat is a combination of R and L; only half of your food can be used to make proteins--a very inefficient system. It would be much more efficient if everything you ate or recycled already had the orientation you needed. If an early organism evolved to utilize just one form (L), this would have conferred a great benefit, allowing the L species to drive its binary rivals into extinction.

[Rare bacteria employ D-amino acids in a kind of chemical warfare to defeat antibiotics. This works because antibiotics are specific for L-amino acids. However, these D-amino acids are added outside the normal protein manufacturing process by specialized enzymes.]

Nature of Scientific Disagreement

Sidebar: The nature of scientific disagreement

Explore Evolution makes a big deal of their single tree/orchard analogy:

Some see evidence of an orchard of separate trees; others see a single, continuous, branching tree.
Explore Evolution, p. 34

Scientists see evolution as a continuous, branching tree, not as separate trees. This statement is simply a misrepresentation and does not cite any sources for its claim.

We have seen that scientists disagree over how to interpret the fossil evidence.
Explore Evolution, p. 34

While there can certainly be disagreement over interpretation, Explore Evolution has not cited any specific argument among legitimate scientists. Who are these mysterious dissenting "scientists"?

But how can there be disagreements? Facts are facts, right? How can qualified scientists disagree over evidence?
Explore Evolution, p. 34

This statement is one of the most egregious of in this chapter. This is wrong in so many ways it is hard to know where to begin to parse this, but first let us examine some assumptions here:

1. The Nature of Evidence

Explore Evolution seems to think that the word evidence means something clear and unchallengeable. However, in the scientific sense, new evidence is often fiercely challenged. Evidence is rarely 100% clear.

By way of analogy, think of this question in Hamlet: Is Hamlet insane, or merely pretending to be insane? The answer, of course, is yes. And no. One can cite passages of Hamlet where the prince talks about pretending to fake insanity. One can also cite passages where Hamlet sees things no one else sees (the ghost of his father in his mother's bedroom, for example). The "evidence" found in the play isn't clear, and a bald statement--Hamlet is not insane--will certainly be challenged. This analogy is a better way to think of the nature of scientific evidence than Explore Evolution's false assumption.

2. Scientists Shouldn't Disagree.

Anyone who has ever attended a scientific conference knows that speakers rarely get far into their prepared talks before some member of the audience challenges them. As soon as one makes any claim in a scientific conference or scientific paper, other scientists pounce with questions that are substantive and challenging. Such criticism isn't necessarily personal, but rather is part of the process of science. Explore Evolution incorrectly assumes that if good evidence exists, scientists will not disagree. Explore Evolution misunderstands science.

Malcolm Gordon

Does Biologist Malcolm Gordon thinks that tetrapods arose multiple times and are therefore "polyphyletic"?

Summary of problems with claim:

Gordon and Olson's point is far narrower than Explore Evolution presents it, and is marred by the authors' inexperience with the field. Even if the problems raised were valid when the paper was written, substantial new material has been found which clarifies many of the issues, and which has spawned new research.

Full discussion:

Explore Evolution introduces this sidebar with a blatant error:

Scientists have long thought that amphibians were a transitional form between aquatic and land-dwelling life forms. Why? Because amphibians can live in both the water and on land. Yet, the fossil record has revealed at least two problems with this idea.
Explore Evolution, p. 28

Tetrapod crown groups:  with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups.  Fossil stem groups are very problematic for Linnaean ranks such as "class."  Graphic by Nick Matzke.  May be reproduced freely for nonprofit educational purposes.Tetrapod crown groups: with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups. Fossil stem groups are very problematic for Linnaean ranks such as "class." Graphic by Nick Matzke. May be reproduced freely for nonprofit educational purposes.

Tetrapod crown groups with some fossil stem groups added, with an attempt made to map the Linnaean classes onto the stem groups. Fossil stem groups are very problematic for Linnaean ranks such as "class." The use of the term "transitional form" here is so vague as to be meaningless. As discussed above, this use of the term is hopelessly mired in a way of categorizing life that does not incorporate evolutionary thinking, and has been rejected by biologists precisely because of its ambiguity. For more on this shift in the way groups are named, see Appendix 2 and the figure at right. A traditional Linnaean classification would treat all the species in the area shaded pink as amphibians, while a modern classifications regard the amphibians as the major lineage branching off at the base of the phylogeny in the figure, and the species below that branch are regarded as "stem tetrapods," neither amphibians, reptiles, nor mammals. Similarly, the species before the split between reptiles and mammals are neither mammals nor reptiles, and are no longer referred to as "mammal-like reptiles," despite the use of that term in Explore Evolution.

This shift in terminology invalidates the first sentence of the sidebar (since the transitional form would not have been an amphibian, but a stem tetrapod from before the main split shown in the figure above). This also helps clarify the first supposed problem raised by Explore Evolution. The authors cite a paper by Gordon and Olsen authors who are not phylogeneticists and used terminology vaguely. When they make comments like, "no fossils are known that relate directly to the vertebrate transitions to land. No amphibious rhipidistian crossopterygians have been identified," they’re speaking in the context of direct ancestors, a single fossil which has the properties of a certain group of fish ("rhipidistian crossopterygians") and the tetrapods. The tetrapods, however, share many traits with those fish, and treating these groups as totally separate is an inaccurate holdover from non-evolutionary classification schemes. Tetrapods are members of the same lineage as those fish, making the distinction Gordon and Olsen draw very ambiguous.

The book with the paper by Gordon and Olsen was published in 1995, with Everett Olson dying in 1993, meaning these chapters were written well over 15 years ago. Paleontologists these days do not speak in terms of direct ancestors – i.e., that taxon ‘x’ is the common ancestor of all tetrapods. There are 2 problems with such a claim: it is very difficult to demonstrate direct ancestry; and the fossils we have almost always have features uniquely derived within that group, telling us they were their own lineage. We are more likely to find something like an 'aunt' or 'cousin' as opposed to a 'parent,' 'child' or 'grandparent'. In other words, paleontologists do not claim to find direct ancestors, but instead find what are referred to as collateral ancestors or sister groups. Gordon and Olson working in an old and outdated methodology of viewing fossils as direct ancestors and their claim that no direct ancestor have been named in the vertebrate transition to land is meaningless — no one claims there has been! The authors of Explore Evolution obscure these methodological revisions (either intentionally or through their own outdated understanding) and use Gordon and Olsen's claims to discredit recent research of the numerous sister groups that document this transition quite nicely. These sister groups are identified because they possess traits predicted to be present in the stem groups between modern forms and other known fossils. The sequence of changes in the anatomy of the skull, the legs and the shoulders match the sequence of hierarchal changes predicted by common descent.

There are thus two major problems with Explore Evolution’s representation of tetrapod origins: (1) Gordon and Olson is long outdated, and Explore Evolution is using old quotes to discredit recent research they only vaguely mention – "More recently, paleontologists have found fossils that seemed to show a connection between fish and tetrapods"; and (2) Gordon and Olson were operating in a scheme of classification which was not rooted in evolutionary relationships, and viewed the world in terms of direct ancestors, a view long abandoned by paleontologists. Explore Evolution's description of Gordon and Olsen's claims show exactly why it's important to stay up to date with recent research — if you do not, you run the risk of misrepresenting a field and confounding long-outdated remarks with well established data. If the job of science education is to expose students to scientific methodology and hypotheses that explain the best and most recent data available, Explore Evolution certainly falls short of achieving such goals.

The second point Explore Evolution raises is that the earliest fossil tetrapods are too widely scattered, in Greenland, South America, Russia and Australia. Again, the evidence they cite is long outdated. In the words of Jenny Clack from a 1997 paper describing the evidence of South American tetrapods,

A single, isolated print from the Ponta Grossa Formation of Brazil was interpreted by Leonard (1983) as the left manus… and its date was given as probably the base of the Upper Devonian. As an isolated block, there is room for doubt about this print's provenance and thus its date. As a natural cast, there is doubt about the circumstances in which the print was formed. Further doubt has been cast recently on its identity as a footprint. Rocek and Rage (1994) have commented on the description of this specimen working from a cast and photographs, and suggest that it is more plausibly interpreted as the resting trace of a starfish. … until further material from the same locality comes to light, it should be treated with extreme caution as a record of a Devonian tetrapod. Furthermore, the specimen derives from an apparently marine environment which contains brachiopods (Rotek and Rage, 1994). Thus it would normally be considered as subaqueous in origin. This specimen provides no convincing evidence of terrestriality among Devonian tetrapods.
Jennifer Clack (1997)

There is indeed good tetrapod evidence from the other locations. The current hypothesis is that tetrapods originated in the northern continents, explaining the fossil occurrences in Greenland and Russia areas which were, at the time, equatorial. But what about Australia? The Australian evidence consists of a lower jaw and trackways — evidence that seems to be clearly of tetrapod origin. However, we don’t exactly know where Australia was back 360 Ma. We have a good approximation, but of course in science, details matter! Thus, we’re still working on establishing this question — but that’s how science works. New data opens new questions and gets people thinking. Far from being the unsolvable problem Explore Evolution presents, requiring the evolution of tetrapods multiple time in multiple places, this is an area where ongoing research in geology, and new paleontological digs, are allowing scientists to test hypotheses and refine our understanding. Explore Evolution presents a vision of science trapped by unanswered questions, the exact opposite of an inquiry-based approach, and the opposite of the way scientists work. [say more]

Phylogeny & the Nature of the Fossil Record

Explore Evolution misunderstands and misrepresents the nature of phylogeny and the fossil record.

Stability of Phyla

Does the stability of phyla means phyla do not evolve?

Summary of problems with claim: Explore Evolution misunderstands the definition of phyla.

Full discussion:

But stability also characterizes the body designs of the organisms representing the higher categories of life--the orders, classes and phyla.(13)
Explore Evolution, p. 26

and in footnote #13 continues:

Technically, to say that phyla remain stable is almost redundant. After all, scientists define phyla by referring to an unchanging set of anatomical characteristics. In another sense, however, the stability of phyla is remarkable.

Think of the different phyla as though they were arranged like bars on a bar chart. Each bar represents a unique body plan. The farther apart two individual bars are from one another, the more different the anatomical characteristics are.

In nature, an animal body plan could theoretically fall anywhere along this continuum, even in the gaps between bars. Individual animals either falls [sic] within one of the existing phyla, or in some instances new animals are found that represent radically new body plans altogether.
Explore Evolution, p. 26

This is problematic in many respects. By giving this analogy to phyla arranged horizontally as bars in a bar chart, and arguing that one can "fall within" these bars, really misses the whole point of what phyla are.

Phyla are "body plans." They are the most fundamental ways that bodies can be put together. Phyla are based upon the internal, rather than external, arrangement of organisms. Because of this, many seemingly-similar animals (a number of phyla are "worms") are grouped into separate phyla, while many seemingly-different animals (jellies, anemones, corals are all Phylum Cnidaria) are grouped together.

An analogy for phyla can be made for cars. Think of all the different types of cars you see. They all have four wheels, an engine, a windshield, and so on. But beyond this, imagine that you were to classify cars into different automobile phyla. You could make a phylum for convertibles. Another for SUVs. Sedans get their own, as do coupes. Are two-door sedans different enough from four-door sedans that they deserve their own phylum? These kinds of questions, when applied to animal bodies, help scientists classify animals.

In recent years, advances in molecular biology have shed even more light on phylogeny. DNA-DNA hybridization, for example, takes single-strand DNA from two different organisms and measures how well the single strands bond together; the better the bonding, the more closely the DNA pairs match. The advent of PCR (polymerase chain reaction) allow DNA sequencing from living and some extinct organisms. DNA sequencing directly compares DNA at the base-pair level, yielding even more information. Some proteins--for example, cytochrome c--can be used as a "molecular clock" to judge phylogenetic relationships.

Depending on the exact definition of phylum used, the animal world can be divided into about 38 phyla. These are

# Phylum Features Example
1. Chordates spine or notochord fish, humans
2. Mollusca calcareous shell, muscular foot clams, octopi, nautiloids
3. Arthropods jointed, segmented exoskeleton crabs, spiders, insects
4. Echinoderms calcareous exoskeleton sea stars, sea urchins, sand dollars
5. Acanthocephala parasitic worm thorny-headed worm
6. Acoelomorpha no disgestive tract flatworms
7. Annelida complete digestive tract segmented worms
8. Brachiopoda similar to bivalves lamp shells
9. Chaetognatha long, streamlined body arrow worms
10. Cnidaria stinging cells (nematocysts) jellies, anemones, corals
11. Ctenophora no head, central nervous system comb jellies
12. Cycliophora lives in lobster mouths discovered 1995
13. Echuira unsegmented spoon worm
14. Entoprocta sessile goblet worm
15. Gastrotricha microscopic Meiofauna
16. Gnathostomulida hermaphroditic, 0.5-1.0 mm jaw worms
17. Hemichordata similar to worms acorn worms
18. Kinorhyncha <1 mm mud dragons
19. Loricifera sediment-dwelling, marine brush heads
20. Micrognathozoa <0.1mm, one of smallest animals known similar to Rotifera
21. Monoblastozoa "primitive" multicellular
22. Nematoda molting cuticle, 6 lips round worms
23. Nematophora parasites in arthopods horsehair worms
24. Nemertea unsegmented worms ribbon worms
25. Onycophora relatively large brain velvet worm
26. Orthonectida marine invertebrate parasite
27. Phoronida similar to worms
28. Placozoa pressure-filled body cavity tablet animal
29. Platyhgelminthes unsegmented worms flatworms
30. Porifera sessile suspension feeders sponges
31. Priapula marine worm "penis worm"
32. Rhombozoa cephalopod parasite
33. Rotifera microscopic
34. Siboglinidae no digestive system deep-sea vent worms, beard worms
35. Sipuncula mouth of tentacles peanut worms
36. Tardigrada four pairs clawed legs water bears, recently demonstrated to be able to survive in the vacuum of space
37. Xenoturbellida no brain, no digestive tract similar to flatworm

These represent the full diversity of animal body plans. But perhaps the most important thing about these is that they are all found very early in the Cambrian (542-488) fossil record (Gould, 2002, p. 1155). Only Phylum Bryozoa developed after Cambrian times, during the Ordovician (488-443 Ma).

Paleontologist Mike Foote points out that, although we continue to find new fossils, those we find belong to phyla and other major groups that we already know about.
Explore Evolution, p. 30

Trilobite: Elrathia (sp.) from the Burgess Shale. Photo by Steven Newton.Trilobite: Elrathia (sp.) from the Burgess Shale. Photo by Steven Newton.

This statement implies that the fact that we only find organisms that fit within our definitions of phyla is a circular reasoning problem. This misunderstands the fundamental tenet of common descent--that an animal has to evolve from something rather than spontaneously popping into existence.

According to Gould (1989), the fact that only 1 new phylum has originated since the Cambrian means that animal diversity has actually decreased since Cambrian times, since in early fauna such as the Burgess Shale all of today's major phyla exist plus many other phyla that are now extinct. There is considerable disagreement over Gould's argument.

One implication of this is that the majority of phyla came into being in a relatively short period of time, the ten million years between 535-525 Ma, followed by a dearth of new phyla. If a new body plan did not get in at the very beginning, at the "ground floor," then there would be little chance of its development at a later time.

Molecular phylogeny suggest a rather different story for the origin of the major phyla, in which:

1. echinoderms and chordates split ~ 670Ma (Ayala, 1998)

2. protosomes (arthopods, mollusks) and deuterostomes (chordates, echinoderms) split ~ 1.0-1.2 Ga (billion years ago) (Wray, 1996; Bromham, 1998)

A problem with these estimates, based primarily on protein-coding genes, is that rocks from the period of 1.2 Ga-0.67 Ga show little signs of active life at all. Bioturbation, the mixing of sediment layers by burrowing organisms, and trace fossils are not well expressed in the fossil record until early Cambrian times.

Sudden taxonomic levels

Do taxonomic levels appear too suddenly?

Explore Evolution, p. 24

Explore Evolution, p. 24
A bat: from WikicommonsA bat: from Wikicommons







Explore Evolution, p. 24



Fossil Preservation

The nature of fossil preservation

Sometimes the fossilized organism was buried in sediment.
Explore Evolution, p. 16

Fossils do not occur in igneous rock or metamorphic rock. So by default, then, fossilized organisms always--not "sometimes"--occur in sediment. Explore Evolution seems to misunderstand a basic tenet of taphonomy (the study of how organisms decay and become fossilized). Explore Evolution fundamentally misunderstands geologic processes.

Most paleontologists would argue that we have plenty of fossils
Explore Evolution, p. 30

No paleontologist would argue that we have enough fossils; no paleontologist would say that the fossil record is so complete that we should stop looking for new discoveries. Explore Evolution has no citation for this claim and is simply making it up.

Could it be that the intermediates weren't fossilized because they didn't have hard body parts like teeth or exoskeletons? Some defenders of Common Descent say yes, and point out that small structures and soft tissues are more susceptible to decay and destruction, and are, therefore, harder to preserve. This would explain why they are absent from the fossil record.
Explore Evolution, p. 31

Critics agree that soft, small structures are more difficult to preserve. However, they point out that Cambrian strata around the world have yielded fossils of entirely soft-bodied animals representing several phyla.
Explore Evolution, p. 31

Trilobite: Olenoides serratus from the Burgess Shale. Note the dark lines extending from the shell; these are rarely-preserved soft tissues, an indication of the unique preservation conditions of the Burgess Shale. Photo by Steven Newton.Trilobite: Olenoides serratus from the Burgess Shale. Note the dark lines extending from the shell; these are rarely-preserved soft tissues, an indication of the unique preservation conditions of the Burgess Shale. Photo by Steven Newton.

It is true that the mid-Cambrian Burgess Shale (~515 Ma) and the Chengjiang fauna (525-520 Ma) preserve soft body parts. But the conditions which allowed this preservation were unique.

In the Burgess Shale, a combination of submarine topography and anoxic oceans combined to preserve soft tissues. Approximately 86% of the animals in the Burgess Shale did not have a biomineralized skeleton (Briggs, 1994, p. 33). Walcott's Quarry, where the animals of the Burgess Shale are found, is a ~150 meter long pocket of thin shale between the Cathedral Formation dolomites and the Stephen Formation shales (Briggs, 1994, p. 21). It is located between Mt. Wapta and Mt. Burgess, near Field, Canada. Rocks just a few meters away on either side do not show the same quality of preservation, suggesting that this was a very small pocket of unusual conditions.

The Burgess Shale formed at the bottom of an undersea cliff (Briggs, 1994, p. 25). The steep escarpment allowed Burgess animals to be transported quickly from higher, more productive marine conditions into deeper water. Normally, this is not enough to preserve soft tissues; animals decaying on the bottom of the current ocean floor are usually completely scavenged in a matter of hours or days. However, the water at the base of this undersea escarpment was highly anoxic--meaning, it did not have enough oxygen to sustain scavengers. So Burgess animals that fell very close to the cliff were well preserved, while those slightly further away were not preserved at all. Sediment also accumulated rapidly at the base of the escarpment, effectively sealing the undecayed Burgess animals in mud.

Explore Evolution, p. 31

This presents false logic. If-->Can does not equal If-->Must. The rarity of rocks from this period, combined with the rarity of soft-bodied organisms being turned into fossils at all, means that in only a few places in the world can paleontologists even look for the ancestors to Cambrian animals.

If lots of soft-bodied animals existed before the Cambrian, then we should find lots of trace fossils. But we don't. Precambrian sedimentary rock records very little activity.
Explore Evolution, p. 31

Trace fossils:: Planolites trace fossils from the Middle Member of the Deep Springs Formation, just above the Cambrian-Precambrian boundary, White-Inyo Mountains, California. Photo by Steven Newton.Trace fossils:: Planolites trace fossils from the Middle Member of the Deep Springs Formation, just above the Cambrian-Precambrian boundary, White-Inyo Mountains, California. Photo by Steven Newton.

This makes the false assumption that if any animals existed, then those animals should have left trace fossils. Precambrian soft-bodied organisms such as Ediacarans did not leave copious trace fossils because they were most likely sessile; they simply did not move or burrow into sediment, as later forms of life would.

If you go to a place such as the White Mountains of California, you can walk a sequence of rocks that takes you from Precambrian sediment completely devoid of trace fossils (Wyman Formation), through carbonate assemblages (Reed Dolomite) into the early Cambrian and into shales in which you see increasing numbers and complexity of trace fossils. On top of these, you find trilobites and archaeocyathids.

Paleontologists define the boundary of the Precambrian from the Cambrian by the first appearance of the trace fossil Treptichnus pedum.

According to Jensen (2003), we find the earliest, and simplest, trace fossils at 560 Ma. By 550 Ma, we start to see more complex three-dimensional burrowing. At 542 Ma, we find Treptichnus pedum burrowing three-dimensionally in a complex pattern that suggests an active hunt for food. This behavior is radically different from the passive Ediacarans.

Possibly the earliest trace fossils are short unbranched forms, probably younger than about 560 Ma. Typical Neoproterozoic trace fossils are unbranched and essentially horizontal forms found associated with diverse assemblages of Ediacaran organisms. In sections younger than about 550 Ma a modest increase in trace fossil diversity occurs, including the appearance of rare three-dimensional burrow systems (treptichnids), and traces with a three-lobed lower surfaces.

Absence of Fossil Evidence

Does an absence of fossil evidence shows that ancestral species did not exist?

Summary of problems with claim:

The fact that a particular species at a given place and time didn't fossilize doesn't mean that the species didn't exist.

Full discussion:

Explore Evolution states:

…critics argue that Darwin's theory has failed an important test. Just as students are tested by exams, theories are tested by how well they match the evidence. In the overwhelming majority of cases, Common Descent does not match the evidence of the fossil record. A student who gets a correct answer only once in a while does not deserve a passing grade. In the same way, critics say that a scientific theory that only rarely matches the evidence fails the test of experience.
Explore Evolution, p. 27

Firstly, taphonomy and earth processes also help us understand why, where, and under what conditions fossils form – and explain low abundance (or absence) of fossils in certain situations. Just because paleontologists do not find fossils in certain rocks (or certain preservational environments) does not mean nothing ever lived there. There are many contingencies that explain fossilization, and any 'absence' of fossils is not – by default – positive evidence against evolutionary theory. There are two different hypotheses/processes at work, taphonomy and evolution, and fossil absence is also very well explained/understood by taphonomic data. Secondly, when fossils are preserved, there is a lot of evidence for common descent. See section on 'transitional fossils' above.

Punctuated Equilibrium

Is there a problem with Punctuated equilibrium?

Summary of problems with claim:

Full discussion:

Explore Evolution claims punctuated equilibrium is a more accurate description of the fossil record, but species selection doesn't work as a mechanism so punctuated equilibrium can't explain the origin of new body plans or new structures. So punctuated equilibrium confirms that there are few transitional forms, but leaves no mechanism for explaining transitions.


Explore Evolution says:

In the traditional view, the fossil record was always to blame for the missing pieces of the evolutionary puzzle… Eldredge and Gould decided to take a different approach. Instead of blaming the fossil record, they accepted the fossil data at face value. They agreed that the fossil record really does show many groups of organisms appearing abruptly, continuing unchanged for millions of years, then going extinct.
Explore Evolution, p. 32

Explore Evolution's tone in this quote is one of gloating: Here Darwin has been corrected by real scientists. If Darwin was wrong on one point, Explore Evolution suggests, Darwin might have been wrong on every point. This is, of course, false logic. Moreover, Explore Evolution fails to understand that science is replete with corrections and clarifications of existing theories; ongoing research and critical testing, far from being a sign of the weakness of the theory of evolution, is a sign of its strength.

This is one of the ways in which science is fundamentally different from other human endeavors. In science, no idea is unquestionable, no expert beyond criticism, no theory safe from new evidence. There are no authorities, no equivalent of a clergy to whom one can turn for infallible answers.

In a sidebar, Explore Evolution says:

The Vendian Fossils: Was the 'Cambrian Explosion' Really Explosive? … Some scientists have suggested that those odd creatures may well be the fossilized intermediates that neo-Darwinists have been looking for.
Explore Evolution, p. 32

The exact relationship of the Ediacarans to modern animals is very unclear. Some of the Ediacarans do not even appear to be animals, as they lack features such as mouths and anuses and digestive tracts. But if there is any phylogenetic relationship between the Ediacarans and modern phyla, then this means they probably weren't "intermediate," but rather first.

Explore Evolution says:

Many critics of the theory pointed out that punctuated equilibrium has never explained how the major changes recorded in the fossil record could have taken place in such a short time.
Explore Evolution, p. 33

Eldredge & Gould's punctuated equilibrium concept is based on observations of the fossil record. The "how" or "why" of changes is not required to understand the "what" of the observations.

In fact, arguing that a concept must be wrong if it does not contain a ready explanation of how it occurs is an exercise in teleology. Teleology is concerned with design of things and their inherent purpose. This presupposes, however, that there is a design, that there is a purpose, and such an assumption is not part of science.

As an analogy, imagine that a teleologist argued against a quantum physicist about the structure of the proton. Sure, the teleologist might say, you can prove with your fancy machines that a proton is composed of two up-spinning quarks and one down-spinning quark, but if you cannot say why, then this invalids your observation. Such an argument would, of course, be absurd--yet this is precisely the argument Explore Evolution makes about punctuated equilibrium.

[Punctuated equilibrium] does not explain the origin of higher taxonomic groups (like phyla or classes). To describe how one species of trilobite evolved into another is not the same as explaining how trilobites arose in the first place.
Explore Evolution, p. 33

Eldredge and Gould never claimed that punctuated equilibrium explained the origin of the phyla. It does, however, do a darn good job of explaining the changes in trilobites.

If the theory of Punctuated Equilibrium is right about the rate of evolutionary change… then it has no mechanism that can produce new structures as rapidly as the fossil record shows.
Explore Evolution, p. 33

Eldredge and Gould never claimed that punctuated equilibrium could explain the rate of new body structures. Punctuated equilibrium focuses on what we can see in the fossil record, leaving broader explanations for subsequent research.

Recent discoveries involving the Hox and Pax genes have, in fact, shown how major body plan changes can be made from relatively minor genetic variation. The Pax-6 gene, for example, is common to both invertebrates and vertebrates, and small changes determine whether and organism develops a compound eye (like a fly) or a eye with a cornea and lens (like a human eye) (Zuker, 1994).

It is hard to refute unnamed, anonymous "critics." This is like being accused of a crime, but being unable to question witness against you. If Explore Evolution were serious about this, each one of these three statements would have several examples from the peer-reviewed literature to back up each claim. A search of the peer-reviewed literature turns up, however, zero peer-reviewed papers showing "critics of both views" agreeing that there are fewer than "expected" transitional fossils.

Other Errors in Chapter 3

Four miscellaneous problems found in Chapter 3.

Time Represented in Outcrops

Time Represented in Rock Outcrops

The strata in Figure 1:1 show a relatively small segment of rock. Figure 1:1 also shows four fossils--a one-toed horse, a frog, a trilobite, and a coral.

While the one-toed horse (genus Equus) dates from less than 5 million years ago (Ma), the coral could be Cambrian (>500 Ma). This makes a several meter outcrop of rock appear to show a half-billion years of rock deposition. While there are certainly gaps (unconformities) of this much time, what one would tend to see would be the old corals set right below the younger horse, without trilobites and frogs in between.

Figure 1:1, therefore, is misleading in that it suggests a very long span of geologic time can be shown in a few layers on the side of a cliff. This might be a tenet of Young Earth Creationism, but geologists would tend not to find such a range of fossils in such a short succession of strata.

Explore Evolution claims:

Another problem is that fossils don't always appear in the order they're predicted to.
Explore Evolution, p. 27

This is blatantly false. In fact, fossils show a great uniformity in terms of their stratigraphic position in rock outcrops. In every case where, for example, an older fossils is set stratigraphically above a younger fossils, this can be explained by features such as reverse faulting.

The fossil record seemed to show a trend from simple to complex.
Explore Evolution, p. 17

Complexity in organisms can be subjective. In many ways, fossils from the middle Cambrian show features as complicated as modern animals: eyes, teeth, claws, digestive tracts, articulated limbs, exoskeletons. While we can discern an increase in brain size and complex behaviors in our own species as it evolved from earlier hominids, complexity in body design is more problematic.

Geologic "Closeness"

How much time is shown in a rock outcrop?

Explore Evolution says:

Textbooks also frequently fail to mention that the different skeletons shown in transitional sequences (including the mammal-like reptiles) were not found close together geologically.
Explore Evolution, p. 27

The problem with this idea is the definition of "close." To a Young Earth creationist, close might mean hundreds or perhaps thousands of years. To a geologist or paleontologist, gaps of tens of millions of years are commonplace.

To give you an idea of the scale gaps involved, let's examine the layers (stratigraphy) of the Grand Canyon. The oldest rocks of the Grand Canyon, called the Vishnu Schist, began forming about 2 Ga (billion years ago) as marine sediment that was then metamorphosed and intruded by the younger Zoroaster Granite. All this completed by about 1.7 Ga.

The next sequence of rocks in the Grand Canyon, the Grand Canyon Supergroup, is a set of highly-tilted sediments deposited between 1.2 and 0.8 Ga.

The third sequence involves the relatively younger, flat-lying rocks that make up the majority of what one sees in the Grand Canyon's cliffs. These were deposited between ~500 Ma to ~250 Ma.

To summarize:

Sequence Age Range Time Gap
Upper Sequence 500-250 Ma 250 Ma missing above, 300 Ma missing below
Grand Canyon Supergroup 1.2 - 0.8 Ga 300 Ma missing above, 500 Ma missing below
Vishnu Schist 2.0-1.7 Ga 500 Ma missing above

These kinds of sequences--where more time is missing than is shown--are common in the rocks of the world. Geologists call these gaps "unconformities"; unconformities are so common that it is rare to find a continuous, uninterrupted sequence of rock. Therefore, to argue that fossil finds not being "close together geologically" is evidence against them is to misunderstand the nature of how rock layers are actually deposited.

Explore Evolution goes on to quote Henry Gee:

As zoologist Henry Gee writes, referring to fossil vertebrates in general, "The intervals of time that separate the fossils are so huge that we cannot say anything definite about their possible connection through ancestry and descent."
Explore Evolution, p. 29

Gee's full quote is:

It is impossible to know, for certain, that the fossil I hold in my hand [found at LO5] is my lineal ancestor. Even if it really was my ancestor, I could never know this unless every generation between the fossil and me had preserved some record of its existence and its pedigree…It might have been, but we can never know this for certain… We cannot know if the fossil found at LO5 was the lineal ancestor of the specimens found at Olduvai Gorge or Koobi Fora. It might have been, but we can never know this for certain. The intervals of time that separate the fossils are so huge that we cannot say anything definite about their possible connection through ancestry and descent.
Henry Gee, 1999, In Search of Deep Time 068485421x, p. 22-23

Gee was therefore not, as Explore Evolution claims, talking about fossils in general, but about a specific hominid tooth, which he recognized to have some relationship to his own species. The real doubt in his mind was exactly how direct the connection was. Moreover, Gee explains that the only way he could know for sure would be to have some preserved record of the entire family sequence, and he recognizes that this would be an unreasonable standard of evidence.

Gee makes a broader point, which he summarizes as:

The disconnection and isolation of events worsens further as centuries turn into millennia, tens of millennia, and finally into millions of years: intervals so vast that they dwarf the events within them… This is geological time, far beyond everyday human experience.
Henry Gee, 1999, In Search of Deep Time, 068485421x, p. 26

Gee is correct to point out that the fossil record does not contain an exact, year-by-year sequence of evidence, which is how most people think of time. By acknowledging his personal connection to the hominid tooth he is discussing, Gee posits that despite the gaps in time, we may still understand relationships between fossils, even if "we cannot say anything definite."

The Three Domains


The 3 Domains

Page 23 is a sidebar showing "Biological Classification." The page correctly points out that the most fundamental taxonomic split of organisms is into the three domains: Bacteria, Archaea, Eukaryota. Of these domains, Explore Evolution says, "Each of these has a fundamentally different cell structure."

While true, this is only half the story--the most important differences are genetic, not morphological. In fact, bacteria and archaea have such a close superficial resemblance that for a long time they were not distinguished into different domains.

The 3 Domains model is relatively new; it was proposed by Carl Woese in 1990. (Woese C, Kandler O, Wheelis M (1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.". Proc Natl Acad Sci USA 87 (12): 4576–9.)

Weasel Words

"Weasel Words"




A few examples from Explore Evolution, with weasel words italicized:









p. 26: "No, say the critics…"





p. 27: "Some critics are unpersuaded…"



p. 30: "Many paleontologists would argue…"

p. 31: "Critics agree that…"


p. 34: "Critics of both argue…"



