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 [http://commons.wikimedia.org/wiki/Image:Chirality_with_hands.jpg]Left-Right Chirality: Image from WikiCommons [http://commons.wikimedia.org/wiki/Image:Chirality_with_hands.jpg]

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]