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A Primer on the Tree of Life

By Casey Luskin

[Editor's Note: This was originally posted as a 5-part series titled "A Primer on the Tree of Life" on Evolution News & Views. Read Part 1 here, Part 2 here, Part 3 here, Part 4 here, and Part 5 here.]

Evolutionists often claim that universal common ancestry and the “tree of life” are established facts. One recent opinion article in argued, “The evidence that all life, plants and animals, humans and fruit flies, evolved from a common ancestor by mutation and natural selection is beyond theory. It is a fact. Anyone who takes the time to read the evidence with an open mind will join scientists and the well-educated.”1 The take-home message is that if you doubt Darwin’s tree of life, you’re ignorant. No one wants to be ridiculed, so it’s a lot easier to buy the rhetoric and “join scientists and the well-educated.”

But what is the evidence for their claim, and how much of it is based upon assumptions? The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.

Some of these ad hoc rationalizations may appear reasonable — horizontal gene transfer, convergent evolution, differing rates of evolution (rapid evolution is conveniently said to muddy any phylogenetic signal), fusion of genomes — but at the end of the day, we must call them what they are: ad hoc rationalizations designed to save a theory that has already been falsified. Because it is taken as an assumption, evolutionists effectively treat common ancestry in an unfalsifiable and unscientific fashion, where any data that contradicts the expectations of common descent is simply explained away via one of the above ad hoc rationalizations. But if we treat common descent as it ought to be treated — as a testable hypothesis — then it contradicts much data.

The Main Assumption
As noted, the first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor. That is, except for when it isn’t. (And then the similarity is purportedly said to be the result of convergent evolution, etc.) But even if we take this claim at face value — that similarity between different organisms is the result of inheritance from a common ancestor — let’s recognize it for what it is: a mere assumption. But are there other possibilities?

The Molecular Evidence
When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later 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 this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ 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.2Of course, these scientists are all committed evolutionists, which makes their admissions all the more weighty. 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.3Likewise, 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.”4 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 doesn’t hold 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.5Even among higher organisms, “[t]he problem was that different genes told contradictory evolutionary stories,” leading Syvanen to say, regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.” This directly contradicts Hillis’ claim that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence.”

Other scientists agree with the conclusions of the New Scientist article. 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.”6 Likewise, Carl Woese, a pioneer 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.7

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, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”8

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.”9 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.”10 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.”11

Unfortunately, one assumption that these evolutionary biologists aren’t willing to consider changing is the assumption that neo-Darwinism and universal common ancestry are correct.

Extreme Genetic Convergent Similarity: Common Design or Common Descent?
If common descent is leading to so many bad predictions, why not consider the possibility that biological similarity is instead the result of common design? After all, designers regularly re-use parts, programs, or components that work in different designs (such as using wheels on both cars and airplanes, or keyboards on both computers and cell-phones).

One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes. Because their eye-types are so different, it previously hadn’t been thought that these organisms even shared a common ancestor with an eye. Evolutionary biologist Ernst Mayr explains the havoc wreaked within the standard evolutionary phylogeny when it was discovered that the same gene controlled eye-development in many organisms with very different types of eyes:It had been shown that by morphological-phylogenetic research that photoreceptor organs (eyes) had developed at least 40 times independently during the evolution of animal diversity. A developmental geneticist, however, showed that all animals with eyes have the same regulator gene, Pax 6, which organizes the construction of the eye. It was therefore concluded at first concluded that all eyes were derived from a single ancestral eye with the Pax 6 gene. But then the geneticist also found Pax 6 in species without eyes, and proposed that they must have descended from ancestors with eyes. However, this scenario turned out to be quite improbable and the wide distribution of Pax 6 required a different explanation. It is now believed that Pax 6, even before the origin of eyes, had an unknown function in eyeless organisms, and was subsequently recruited for its role as an eye organizer.12Typically, extreme genetic similarity is thought to mandate inheritance from a common ancestor, because the odds of different species independently arriving at the same genetic solution are exceedingly small. But if we require a Darwinian evolutionary scheme, such an improbable event is exactly what must have occurred. The observed distribution of genes like pax-6 demand extreme “convergent evolution” at the genetic level. Mayr tries to argue that such improbable examples of extreme genetic convergent evolution are not not only acceptable, but common: That a structure like the eye could originate numerous times independently in very different kinds of organisms is not unique in the living world. After photoreceptors had evolved in animals, bioluminescence originated at least 30 times independently among various kinds of organisms. In most cases, essentially similar biochemical mechanisms were used. Virtually scores of similar cases have been discovered in recent years, and they often make use of hidden potentials of the genotype inherited from early ancestors.13Mayr tries to explain away this extreme genetic convergent similarity by appealing to “hidden potentials of the genotype.” Does this sound compatible with the kind of blind, unguided, and even random processes inherent in neo-Darwinian evolution? No. This sounds like a goal-directed process — intelligent design.

Homology in Crisis
As Mayr suggests, there are other examples where genetic similarity appears in unexpected places. Biologically functional similarity that is thought to be the result of inheritance from a common ancestor is called “homology.”

The concept of “homology” has been thrown into a crisis via observations, like those of Mayr, that the same genes control the growth of non-homologous body parts. Pax-6 is just one example. Another is the fact that the same gene controls the development of limbs in widely diverse types organisms that have wholly different types of limbs, where their common ancestor is not thought to have a common type of limb.14 The methodology used to infer homology was also challenged when it was discovered that different developmental pathways control the growth of body parts otherwise thought to be homologous. As the textbook Explore Evolution observes:In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery—that homologous structures can be produced by different developmental pathways—contradicts what we would expect to find if all vertebrates share a common ancestor. … To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations.15Perhaps this evidence is just the result of what Mayr called “hidden potentials of the genotype,” or perhaps it contradicts neo-Darwinian expectations because neo-Darwinism is wrong.

Molecules Contradict Morphology
A final way that evolutionists overstate the evidence for common descent is by claiming that molecular phylogenies have confirmed or buttressed phylogenies based upon morphology. For example, in his book Galileo’s Finger, Oxford University scientist Peter Atkins discusses evolution and boldly states, “The effective prediction is that the details of molecular evolution must be consistent with those of macroscopic evolution.”16 Likewise, when testifying before the Texas State Board of Education, David Hillis claimed 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 a variety of studies — typically unmentioned when evolutionists promote common descent to the public — 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).

One authoritative 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

For example, pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article in Trends in Ecology and Evolution stated: “the mitochondrial cytochrome b gene absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”19

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.”20 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.21Likewise, 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.”22 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.”23

Despite the inaccurate claims of some evolutionists and their cherry picking of data, the truth is that there is great incongruence between these two different types of phylogenies, and that this incongruence is a huge issue, problem, and debate within systematics.

The methodology for inferring common descent has broken down. Proponents of neo-Darwinian evolution are forced into reasoning that similarity implies common ancestry, except for when it doesn’t. And when it doesn’t, they appeal to all sorts of ad hoc rationalizations to save common ancestry. Tellingly, the one assumption and view that they are not willing to jettison is the overall assumption of common ancestry itself. This shows that evolutionists treat common descent in an unfalsifiable, and therefore unscientific and ideological, fashion.

Meanwhile, as far as the data is concerned, the New Scientist article admits, “Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth,” but because “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.” Perhaps the reason why different genes are telling “different evolutionary stories” is because the genes have wholly different stories to tell, namely stories that indicate that all organisms are not genetically related. For those open-minded enough to consider it, common design is a viable alternative to common descent.

References Cited:
[1.] Perry Mann, "The Dinky Insect That Helps Demonstrate Darwin's Theory," at (April 27, 2009).

[2.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009) (emphasis added).

[3.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[4.] W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science, Vol. 284:2124-2128 (June 25, 1999).

[5.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[6.] 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).

[7.] Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) (emphasis added).

[8.] Lynn Margulis, “The Phylogenetic Tree Topples,” American Scientist, Vol 94 (3) (May-June, 2006).

[9.] 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).

[10.] 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).

[11.] 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).

[12.] Ernst Mayr, What Evolution Is?, pg. 113 (Basic Books, 2001).

[13.] Id. at 205-207.

[14.] Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, John Angus Campbell and Stephen C. Meyer eds. (East Lansing: Michigan State University Press, 2003).

[15.] Stephen C. Meyer, Scott Minnich, Jonathan Moneymaker, Paul A. Nelson, and Ralph Seelke, Explore Evolution: The Arguments For and Against Neo-Darwinism, pgs. 44-45 (Hill House, 2007).”

[16.] Peter Atkins, Galileo's Finger: The Ten Great Ideas of Science, pg. 16 (Oxford University Press, 2003).

[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.] See Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14:177-178 (1999) (emphasis added).

[20.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000) (emphasis added).

[21.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).

[22.] 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).

[23.] W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pgs. 270-274 (July 7, 1998).