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A Primer on the Tree of Life (Part 5): Molecules Contradict Morphology

Note: This is Part 5 in a 5-part series titled “A Primer on the Tree of Life.” Read Part 1 here, Part 2 here, Part 3 here, and Part 4 here. The full article can be found, here.

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,” further claiming, “That is found to be the case: there is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms.”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 implied…an 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.21

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.”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 aforementioned 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 “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,” and as scientists quoted in the article said, “We have no evidence at all that the tree of life is a reality” or the tree is 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:
[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).


Casey Luskin

Associate Director and Senior Fellow, 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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