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?

Not only do new mammalian orders appear suddenly, but when they appear, they are already separated into their distinctive forms. For example, during the Eocene epoch (just after the Paleocene), the first fossil bat appears suddenly in the fossil record. When it does, it is unquestionably a bat, capable of true flight. Yet, we find nothing resembling a bat in the earlier rocks.
Explore Evolution, p. 24

Flowering plants appear suddenly in the early Cretaceous period, 145-125 million years ago.
Explore Evolution, p. 24
A bat: from WikicommonsA bat: from Wikicommons

Summary of problems with claim: Even if true, this claim does not undermine evolution. This is simply the way evolution proceeds.

Full discussion: Explore Evolution wants to make it seem as if the sudden appearance of new, well-formed organisms is problematic. In fact, this is exactly what punctuated equilibrium predicts.

Onychonycteris finneyi: a transitional bat described by Simmons et al. (2008). Modified image used with permission. Scale bar = 1 cm.Onychonycteris finneyi: a transitional bat described by Simmons et al. (2008). Modified image used with permission. Scale bar = 1 cm. Explore Evolution is inaccurate, however, in its claim that there are no transitional bat fossils. Simmons et al. (2008) describe a transitional bat, Onychonycteris finneyi, from the Eocene of Wyoming (52.5 Ma) that has clawed digits and lacks ears suitable for echolocation. O. finneyi has short wings and long legs.

The existence of O. finneyi shows two things: 1) bats evolved with intermediate, transitional forms, and 2) continued creationist usage of bats to bolster their claims of "sudden appearances" reflects more on creationist unfamiliarity with the subject material than the actual fossil record.

Flowering plants are called angiosperms. The oldest angiosperm fossil--an aquatic plant named Archaefructus liaoningensis--dates not from 145 Ma, but from 125 Ma. This discovery was described in 2002.

Explore Evolution, quoting a 2005 paper in Trends in Ecology and Evolution, goes on to say:

Angiosperms appear rather suddenly in the fossil record…" This contradiction was so perplexing that Darwin himself referred to it as "an abominable mystery.
Explore Evolution, p. 24

The sudden appearance of a new group in the fossil does not constitute a "contradiction." Rather, this is simply the way in which many organisms--either by rapid evolution or a sparse fossil record--show up in the fossil record.

Simmons, N.B., Seymour, K.L., Habersetzr, J., and Gunnell, G.F., 2008. "Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation." Nature 451, 818-821 (14 February 2008).

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.

If the Precambrian rocks can preserve microscopic soft-bodied organisms, why don't they contain the ancestors to the Cambrian animals?
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.

On this page, Explore Evolution finally tackled punctuated equilibrium, a major evolutionary idea first proposed by Niles Eldredge and Stephen Jay Gould in 1972.

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.