David Klinghoffer has recently posted some excellent (and entertaining) summaries of the highlights of Discovery Institute’s responses to the testimony of evolutionist experts David Hillis and Ronald Wetherington before the Texas State Board of Education (TSBOE) on January 21, 2009. (See also Ralph Seelke’s response to Hillis.) One part of the response to self-proclaimed tree of life “expert” David Hillis that should not be missed is Discovery’s response to his bluffs and misrepresentations regarding the congruence of molecular and morphological phylogenies within the tree of life. Specifically, Hillis told the board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But anyone accurately testifying about the state of molecular systematics would never make that claim, and there is much documentation in the mainstream scientific literature refuting it. What follows is this section of the rebuttal to Hillis that is of interest to those wondering about the viability of Hillis’ claims about congruence and correspondence within the “tree of life”:

B. Hillis Misled Board about Challenges to Darwin’s Tree of Life
Hillis cited himself as a “world’s leading exper[t] on the tree of life” and later told the TSBOE that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. Hillis’s self-proclaimed expertise makes it all the more egregious that he tried to mislead the TSBOE about the widespread prevalence of incongruencies between various molecular phylogenies within his field of systematics.
Indeed, the cover story of the journal New Scientist, published on the very day that Hillis testified before the TSBOE, was titled “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’s gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

“For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.⁷

To reiterate, the basic problem is that one gene or protein yields one version of the “tree of life,” while another gene or protein yields an entirely different tree. As the New Scientist article stated:

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.⁸

Likewise, leading evolutionary bioinformatics specialist W. Ford Doolittle explains, “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.”⁹ Hillis (and others) may claim that this problem is only encountered when one tries to reconstruct the evolutionary relationships of microorganisms, such as bacteria, which can swap genes through a process called “horizontal gene transfer,” thereby muddying any phylogenetic signal. But this objection holds no water, because the tree of life is challenged even among higher organisms where such gene-swapping does not take place. As the article explains:

Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts–also known as tunicates–are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren’t chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.¹⁰

To reiterate, even among higher organisms, the article explains that “The problem was that different genes told contradictory evolutionary stories,” therefore leading Syvanen to say regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” This directly contradicts the claims of Hillis.

Other scientists agree. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”¹¹ Likewise, Carl Woese, the father of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”¹²

Striking admissions of troubles in reconstructing the “tree of life” also came from a paper in the journal PLOS Biology, entitled “Bushes in the Tree of Life.” 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.”¹³ The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.”¹⁴ The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”¹⁵

Likewise, National Academy of Sciences biologist Lynn Margulis has had harsh words for the field of molecular systematics which Hillis studies. In her article, “The Phylogenetic Tree Topples” she explains that “many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting that “[e]specially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”¹⁶

Hillis may put up non-credible protests that none of this represents a “weakness” in neo-Darwinian evolution. He told the TSBOE that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence.” But should we believe him? As the New Scientist article admits, “Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth,” but since “different genes told contradictory evolutionary stories,” the notion of a tree of life is now quickly becoming a vision of the past–as the article stated, it’s being “annihilated.”

C. Hillis Misled the Board about the Congruence between Anatomical Phylogenies and Molecular Phylogenies
Despite the fact that he called himself a “tree of life expert,” David Hillis also made the grossly inaccurate claim that “there’s overwhelming correspondence between the basic structures we have about the tree of life from anatomical data, from biochemical data, molecular sequence data.” Yet many evolutionary scientists have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees).

For example, a review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.“¹⁷ Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.“¹⁸

The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led to a major article in Nature that reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.“¹⁹ The article’s revelation of the disparities between molecular and morphological phylogenies was striking:

When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history.

[…]

So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date.²⁰

Likewise, a review article in the journal Bioessays reported that despite a vast increase in the amount of data since Darwin’s time, “our ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years,” and that, “[d]espite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”²¹ Strikingly, an article in Trends in Ecology and Evolution concluded, “the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.”²²

Hillis claimed there is “overwhelming correspondence” between anatomical and molecular phylogenies, but he seems to be inaccurately stating the facts on this matter. The truth is that there is great incongruence between these two different types of phylogenies, and that this incongruence is a huge issue within own his field of systematics. Why did Hillis misrepresent this information to the TSBOE?

References Cited:
[7.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009) (emphasis added).
[8.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).
[9.] W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284:2124-2128 (June 25, 1999).
[10.] Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist (January 21, 2009).
[11.] Antonis Rokas, Dirk Krueger, Sean B. Carroll, “Animal Evolution and the Molecular Signature of Radiations Compressed in Time,” Science, Vol. 310:1933-1938 (Dec. 23, 2005).
[12.] Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) (emphasis added).
[13.] Antonis Rokas & Sean B. Carroll, “Bushes in the Tree of Life,” PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).
[14.] Antonis Rokas & Sean B. Carroll, “Bushes in the Tree of Life,” PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).
[15.] Antonis Rokas & Sean B. Carroll, “Bushes in the Tree of Life,” PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).
[16.] Lynn Margulis, “The Phylogenetic Tree Topples,” American Scientist, Vol 94 (3) (May-June, 2006).
[17.] Patterson et al., “Congruence between Molecular and Morphological Phylogenies,” Annual Review of Ecology and Systematics, Vol 24, pg. 179 (1993) (emphasis added).
[18.] Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution, Vol. 44, pgs. S117-S120 (Supplement 1, 1997) (emphasis added).
[19.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000) (emphasis added).
[20.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).
[21.] Matthew A. Wills, “The tree of life and the rock of ages: are we getting better at estimating phylogeny,” BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, “Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century,” Proceedings of the Royal Society of London B, Vol. 268: 2123-2130 (2001).
[22.] W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7):270-274 (July 7, 1998).