A Primer on the Tree of Life (Part 2): Conflicts in the Molecular Evidence - Evolution News & Views

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A Primer on the Tree of Life (Part 2): Conflicts in the Molecular Evidence

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

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 Many biologists now argue that the tree concept is obsolete and needs to be discarded.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.2
Of 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.3
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."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.5
Even 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.

References Cited
[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).