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The (Texas) Tree of Life: “Every Scientific Test To-Date” Supports “Darwin’s Basic Ideas”

Casey Luskin

.biologycover09_155.jpgAs I said earlier, in 2009 Texas adopted science standards that require students to “analyze, evaluate, and critique scientific explanations by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of scientific evidence of those scientific explanations, so as to encourage critical thinking by the student.” Enter biologist Ken Miller, who in 2013 submitted for adoption in Texas his textbook Biology, which promotes the opposite of critical thinking on evolution. Instead, we see statements in the book like this: “Astonishingly, every scientific test has supported Darwin’s basic ideas about evolution.” (p. 465)

Also astonishingly, when the reviewer pressed Pearson to change this sentence, the publisher agreed — the only instance out of all the alleged errors where Pearson agreed to do so. But most astonishing of all is the language that Pearson proposed in its place:

Although it is clear that a great deal about evolution remains to be learned, every scientific test to-date has supported Darwin’s basic ideas.

The new wording is equally dogmatic — and equally false. In fact, the fossil record shows a pattern of abrupt appearance that is the opposite of Darwin’s ideas. In embryology we now know that Darwin’s ideas about similarities in early vertebrate embryos were wrong.1 We know that the tree of life concept is flawed, challenging a core tenet of neo-Darwinian theory. Indeed, neo-Darwinian theory2 itself is thought to be highly flawed.

An article in Trends in Ecology and Evolution from 2008 acknowledges that there is a “healthy debate concerning the sufficiency of neo-Darwinian theory to explain macroevolution.”3 Also in 2008, William Provine, a Cornell University historian of science and evolutionary biologist, gave a talk before the History of Science Society arguing that “[e]very assertion of the evolutionary synthesis below is false”:

1. Natural selection was the primary mechanism at every level of the evolutionary process. Natural selection caused genetic adaptation . . . . 4. Evolution of phenotypic characters such as eyes and ears, etc, was a good guide to protein evolution: or, protein evolution was expected to mimic phenotypic evolution. 5. Protein evolution was a good guide to DNA sequence evolution. Even Lewontin and Hubby thought, at first, that understanding protein evolution was the key to understanding DNA evolution. 6. Recombination was far more important than mutation in evolution. 7. Macroevolution was a simple extension of microevolution. 8. Definition of “species” was clear[–]the biological species concept of Dobzhansky and Mayr. 9. Speciation was understood in principle. 10. Evolution is a process of sharing common ancestors back to the origin of life, or in other words, evolution produces a tree of life. 11. Inheritance of acquired characters was impossible in biological organisms. 12. Random genetic drift was a clear concept and invoked constantly whenever population sizes were small, including fossil organisms. 13. The evolutionary synthesis was actually a synthesis.4

Just for the record, many of these claims that Provine calls “false” (e.g., “Natural selection was the primary mechanism at every level of the evolutionary process” or “evolution produces a tree of life”) are Darwin’s basic ideas.

But let’s continue.

A 2011 paper in the journal Biological Theory stated, “Darwinism in its current scientific incarnation has pretty much reached the end of its rope.”5 In 2009, Eugene Koonin of the National Center for Biotechnology Information stated in Trends in Genetics that there are major problems in core neo-Darwinian tenets, such as the “traditional concept of the tree of life” and the view that “natural selection is the main driving force of evolution.” Said Koonin, “the modern synthesis has crumbled, apparently, beyond repair” and “all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution.”6 Koonin concludes, “not to mince words, the modern synthesis is gone.”7

Yet Pearson has the chutzpah to claim that its error is fixed by stating that “every scientific test to-date has supported Darwin’s basic ideas.” There are many scientists who would dispute this claim, which disregards both the letter and the spirit of TEKS.

Pearson never even offered to change its equally false and dogmatic language, such as a statement on page 447 that says: “Darwin’s theory of evolution by natural selection is often called ‘the most important scientific idea that anyone has ever had.’ Evolutionary theory provides the best scientific explanation for the unity and diversity of life. It unites all living things in a single tree of life and reminds us that humans are part of nature.” Since Miller mentions it, let’s look briefly at the “tree of life.”

Pearson’s textbook asserts as a general truth that “use of DNA characters … has helped to make evolutionary trees more accurate.” (p. 521) In reality, controversies are rampant in the technical literature about the extent to which DNA data accurately show evolutionary relationships. At heart, the problem is that “evolutionary trees” based upon some “DNA characters” commonly conflict — quite sharply in fact — with “evolutionary trees” based upon other “DNA characters.” This problem is pervasive in molecular phylogenetics, yet it is completely omitted from Ken Miller’s textbook. Student readers are led to think DNA characters universally provide accurate, “tree”-like information about evolutionary relationships. But they don’t.

In its rebuttal to the reviewer, Pearson notes that the text describes “a specific situation in which DNA characters were used to produce a more accurate taxonomy of American and African vultures.” I doubt anyone would dispute the relatedness of American and African vultures. The notion that DNA can be used to construct an accurate tree in that case is uncontroversial. But the text fails to discuss the numerous instances where the DNA evidence could not be resolved into a tree, or where the data provided strong non-treelike signals that led to conflicting trees.

For example, a 2012 study in Biological Reviews of the Cambridge Philosophical Society discussed how DNA evidence has made it difficult to resolve relationships: “Incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”8 The paper observed that “phylogenetic conflict is common, and frequently the norm rather than the exception.”9

Many other papers have made similar observations:

  • A paper in Genome Research observed “different proteins generate different phylogenetic tree[s].”10
  • A 2009 paper in Trends in Ecology and Evolution acknowledged “evolutionary trees from different genes often have conflicting branching patterns.”11
  • A 2006 study in PLoS Biology, “Bushes in the Tree of Life,” offered striking conclusions. The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.”12
  • A June, 2012 article in Nature reported that short strands of RNA called microRNAs “are tearing apart traditional ideas about the animal family tree.” Dartmouth biologist Kevin Peterson who studies microRNAs lamented, “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree.” According to the article, microRNAs yielded “a radically different diagram for mammals: one that aligns humans more closely with elephants than with rodents.” Peterson put it bluntly: “The microRNAs are totally unambiguous … they give a totally different tree from what everyone else wants.”13
  • A 2011 paper in Genome Biology and Evolution noted, “[A]s the sequences from genome projects accumulate, molecular data sets become massive and messy, with the majority of gene alignments presenting odd (patchy) taxonomic distributions and conflicting evolutionary histories.”14
  • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”15

In 2009, the journal New Scientist published a cover story titled, “Why Darwin was wrong about the tree of life.” The article explained:

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.16

Such data led biochemist W. Ford Doolittle to explain that “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”17 New Scientist put it this way: “For a long time the holy grail was to build a tree of life … But today the project lies in tatters, torn to pieces by an onslaught of negative evidence.”18 The article explains what happened when microbiologist Michael Syvanen tried to create a tree showing evolutionary relationships using 2000 genes from a diverse group of animals:

He failed. The problem was that different genes told contradictory evolutionary stories. … the genes were sending mixed signals. … Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another.19

The data were so difficult to resolve into a tree that Syvanen lamented, “We’ve just annihilated the tree of life.”20 That’s right: DNA data have “annihilated the tree of life.” This is certainly in direct conflict with the language in the Pearson textbook — that DNA “has helped to make evolutionary trees more accurate.’

Indeed, a major review article in Nature reported on how “disparities between molecular and morphological trees” lead to “evolution wars” because “[e]volutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”21

Difficulties encountered in using DNA data to reconstruct evolutionary relationships are well documented. Pearson paints a rosy picture about the ease with which DNA can help us reconstruct phylogenetic trees, but this picture is false. Now that they’ve refused to correct the textbook, students will be badly misled.

References Cited:
[1.] See Alex T. Kalinka et al., “Gene expression divergence recapitulates the developmental hourglass model,” Nature, Vol. 468: 811-814 (December 9, 2010); Brian K. Hall, “Phylotypic stage or phantom: is there a highly conserved embryonic stage in vertebrates?,” Trends in Ecology and Evolution, Vol. 12: 461-463 (December, 1997); Andres Collazo, “Developmental Variation, Homology, and the Pharyngula Stage,” Systematic Biology, Vol. 49:3 (2000).
[2.] Oddly, Pearson protests that the “Neo-Darwinian Synthesis” is an “older understanding of the evolutionary process,” and thus “not relevant” to discuss. This is a highly unorthodox position. University of Chicago evolutionary biologist Jerry Coyne notes that, “The modern theory of evolution, called neo-Darwinism in light of 150 years of post-Darwin research, has four parts…” Jerry Coyne, “Intelligent Design: The Faith That Dare Not Speak Its Name,” in John Brockman, ed., Intelligent Thought: Science Versus the Intelligent Design Movement (New York: Random House, 2007), p. 6. Coyne is far from an isolated example, as the usage of these terms is also commonplace in textbooks on evolution. Douglas Futuyma’s 2005 textbook Evolution defines “neo-Darwinism” as “[t]he modern belief that natural selection, acting on randomly generated genetic variation, is a major, but not the sole, cause of evolution.” Douglas J. Futuyma, Evolution (Sinaeur, 2005), p. 550. Strickberger’s textbook Evolution defines “neo-Darwinism” as the “modern synthesis,” which is “a change in the frequencies of genes introduced by mutation, with natural selection considered as the most important, although not the only, cause for such changes.” Monroe, W. Strickberger, Evolution (Jones & Bartlett, 3d ed., 2000), p. 649. It’s disturbing that Pearson is apparently not aware that neo-Darwinism remains the standard, leading paradigm of evolution today.
[3.] Michael A. Bell, “Gould’s Most Cherished Concept,” Trends in Ecology and Evolution, Vol. 23: 121-122 (2008) (reviewing Stephen Jay Gould, Punctuated Equilibrium (2007)).
[4.] William Provine, Random Drift and the Evolutionary Synthesis, History of Science Society HSS Abstracts.
[5.] David J. Depew and Bruce H. Weber, “The Fate of Darwinism: Evolution After the Modern Synthesis,” Biological Theory, Vol. 6: 89-102 (December, 2011).
[6.] Eugene V. Koonin, “The Origin at 150: Is a New Evolutionary Synthesis in Sight?,” Trends in Genetics, Vol. 25: 473 (2009) (internal citations omitted).
[7.] Ibid.
[8.] Liliana M. Dávalos, Andrea L. Cirranello, Jonathan H. Geisler, and Nancy B. Simmons, “Understanding phylogenetic incongruence: lessons from phyllostomid bats,” Biological Reviews of the Cambridge Philosophical Society, Vol. 87: 991-1024 (2012).
[9.] Ibid.
[10.] Mushegian et al., “Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes,” Genome Research, Vol. 8: 590-98 (1998).
[11.] Degnan and Rosenberg, “Gene tree discordance, phylogenetic inference and the multispecies coalescent,” Trends in Ecology and Evolution, Vol. 24:332-40 (2009).
[12.] Antonis Rokas and Sean B. Carroll, “Bushes in the Tree of Life,” PLoS Biology, Vol. 4(11): 1899-1904 (November, 2006) (internal citations and figures omitted).
[13.] Elie Dolgin, “Rewriting Evolution,” Nature, Vol. 486: 460-462 (June 28, 2012).
[14.] Leigh et al., “Evaluating Phylogenetic Congruence in the Post-Genomic Era,” Genome Biology and Evolution, Vol. 3: 571-587 (2011).
[15.] Bapteste et al., “Networks: expanding evolutionary thinking,” Trends in Genetics, Vol. 29: 439-41 (2013).
[16.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).
[17.] W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284: 2124-2128 (June 25, 1999).
[18.] Partly quoting Eric Bapteste, in Lawton, “Why Darwin was wrong about the tree of life,” (internal quotations omitted).
[19.] Partly quoting Michael Syvanen, in Lawton, “Why Darwin was wrong about the tree of life,” (internal quotations omitted).
[20.] Michael Syvanen, quoted in Lawton, “Why Darwin was wrong about the tree of life.”
[21.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406: 230-233 (July 20, 2000).

Casey Luskin

Associate Director, Center for Science and Culture
Casey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.



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