The Tree of Life – Part 1 of 2

Imagine that you are trying to guess the relationship between Ross, Alan and Peter. When you look at their chins, it seems clear that Ross and Alan are brothers – they share the same chiselled chin, complete with dimple. Peter is left out. Is this enough, though, to conclude that Ross and Alan are brothers, and that Peter is distantly related, if at all? How would we feel if another anatomical feature were compared – the subjects’ eyes, say – and it was discovered that now it is Peter and Alan who have virtually-identical apertures, with Ross the odd man out?

One of the boldest icons of evolutionary biology is the provocatively-titled Tree of Life. It is a core belief of modern evolutionary theory that all life forms – from bacteria to bananas to blue whales to Barry Manilow – are related to one another. This is a corollary of the notion of universal common descent. Evolutionary biologists believe that all life-forms that inhabit Earth today evolved from simpler ancestors. The diagram that depicts the putative relationships between these ancestors and descendants is known as the Tree of Life. Countless students have been shown images of alleged relationships between organisms depicted as points on a tree. At its base is LUCA, the Last Universal Common Ancestor, a one-celled organism from which all of life supposedly evolved. The trunk, branches, boughs and twigs all represent hypothetical relationships between species, with the outermost twigs representing existing species, while extinct species lie lower. So the Tree of Life is no mere diagram; it captures the essence of Neo-Darwinism. It is telling that in Charles Darwin’s On the Origin of Species, there is but one illustration – that of the Tree of Life.

How do biologists decide where to place various organisms on a Tree of Life diagram? One method is to analyse anatomical similarities and differences among various animals. Chimpanzees are anatomically closer to humans than are, say, armadillos. Other methods, adopted since the biochemical revolution in the latter part of the twentieth century, involve the comparison of proteins and DNA. These large biological molecules are made up of numerous components – smaller molecules that join to make up the bigger ones. As a simplified illustration of the procedure used by biologists to determine similarities, let us imagine taking a specific protein from a human, a chimpanzee and an armadillo. When you look at the building blocks of this protein in all three organisms, you might end up with something like this:

Human          A    ^    π    ©    ¤    %    Ω    Я
Chimp            A   ^    B     ©    ¤    %    Ω    Я
Armadillo    A   #    C      *     ≈    ◊     ∫     >

Each entry in the table above designates a building-block of a protein, called an amino acid. The first two strings of letters are very similar; they only differ in the third position (π in humans and B in chimps). So these two proteins have near-identical components. But the third row is very different to the other two; in fact, it is only equal in the first position (A in all three cases). Evolutionary biologists would say that this is evidence that the first two organisms are closely related, but that the third protein comes from a distantly-related creature.

But there’s a catch, and it is related to the thought experiment we conducted at the beginning of this article. Protein or gene comparison is valid, if at all, only if it is consistent regardless of which genes or proteins were used in the comparison. Reverting to our simplified example above, imagine that we compare the three creatures (human, chimp and armadillo) using a different protein. What if the two strings of symbols for chimp and armadillo match perfectly, but the one for humans is different? This exercise would then indicate that the chimp and armadillo are cousins, with humans only distantly-related. Overall, such a clash between the analyses of two proteins would discredit the entire exercise of discovering relationships among organisms based on this methodology. Ellen Prager and Allan Wilson warned in 1976 that:

To test the reliability of the use of proteins for working out phylogenetic relationships, it is essential to determine whether the branching order of the evolutionary tree one obtains depends on the protein studied.[1]

If the analysis gives different trees when applied to different proteins, then something is amiss. A decade later, David Hillis was equally emphatic:

A primary objective of phylogenetic studies is to reconstruct the evolutionary history of a group of organisms. Because the organisms under study have a single history, systematic studies of any set of genetically determined characters should be congruent with other such studies based on different sets of characters in the same organisms. Congruence between studies is strong
evidence that the underlying historical pattern has been discovered; conflict
may indicate theoretical or procedural problems in one or both analyses, or it may indicate that additional data are needed to resolve the phylogenetic relationships in question.[2] [E,phasis added.]

Fast-forward two decades, and the consistent picture that everyone expected – all proteins and genes confirming the same pattern of species relationships – turns out to be illusory. What emerged instead is chaos, as James Degnan and Noah Rosenberg made clear in a paper published in 2009:

Many of the first studies to examine the conflicting signal of different genes have found considerable discordance across gene trees: studies of hominids, pines, cichlids, finches, grasshoppers and fruit flies have all detected genealogical discordance so widespread that no single tree topology predominates.[3]

Translation: the results of protein and DNA studies that purport to shed light on relationships in the living world are desultory to the point of being useless.

The latest research to upset the applecart concerns microRNAs. These are short molecules which regulate gene expression – they help control whether a particular gene will “shout” or “whisper”. MicroRNAs are poorly understood, but it is thought that they may have a major influence on the developmental course of organisms. Consider some statements from a recent Nature article, entitled Rewriting Evolution, about these molecules:

• “Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree.”
• “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree.”
• “What we know at this stage is that we do have a very serious incongruence.”
• “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.”[4]

The article in Nature – perhaps the world’s most prestigious science journal – focused on the work of Kevin Peterson. A molecular paleobiologist at Dartmouth College and a leading researcher in this field, Peterson has “sketched out a radically different diagram for mammals…” The Nature article continues:

When Peterson started his work on the placental [mammal] phylogeny, he had originally intended to validate the traditional mammal tree, not chop it down. As he was experimenting with his growing microRNA library, he applied it to mammals because their tree was so well established that they seemed an ideal test. Alas, the data didn’t cooperate… “The microRNAs are totally unambiguous,” he says, “but they give a totally different tree from what everyone else wants.”

For anybody who follows the research about genetic relationships among organisms, nothing quite captures the situation like the famous novel by the Scottish author Robert Louis Stevenson, The Strange Case of Dr. Jekyll and Mr. Hyde. Evolutionary biology suffers from a case of split personality. The dichotomy between announcements to the public on the one hand, and actual research as reported in professional journals on the other hand, is little short of psychotic. As the misanthropic Edward Hyde, evolutionary biologists insist that phylogenetic trees – pictures of relationships drawn on the basis of comparisons of genes or proteins – lead to the inescapable conclusion that all organisms are related and descend from common ancestors. And then they turn into Dr. Jekyll and confess, among themselves, that this is fantasy.

Meet Mr. Hyde. On 21st January 2009, University of Texas evolutionary biologist David Hillis testified before the Texas State Board of Education. He claimed to be one of the “world’s leading experts on the tree of life”. Hillis 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. Hillis was saying that such research has proceeded as smoothly as silk, confirming all predictions made by evolutionary biology, regardless of which organisms and structures were analysed.

Enter Dr. Jekyll. The technical literature is replete with scientific papers that have found contradictions, inconsistencies, and failures of the molecular data to provide a clear picture of universal common descent. In a delicious irony, the issue of New Scientist that was published on the very day that Dr. Hillis testified carried the cover story Darwin Was Wrong. The story was subtitled Cutting down the Tree of Life. (When reading this, one should keep in mind that New Scientist is a bastion of evolution diehards. This cover story was as surprising as reading a denunciation of Stalin in Pravda in 1937 would have been.) The cover story quoted Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France, Michael Rose, an evolutionary biologist at the University of California, Irvine and John Dupré, a philosopher of biology at the University of Exeter, UK.

The article begins with a review of the orthodoxy. “For a long time the holy grail was to build a tree of life,” says Bapteste. “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,” he continues. “The problem was that different genes told contradictory evolutionary stories.” “It’s part of a revolutionary change in biology,” says Dupré. “Our standard model of evolution is under enormous pressure.” Rose goes even further. “The tree of life is being politely buried, we all know that,” he says. “What’s less accepted is that our whole fundamental view of biology needs to change.” Biology is vastly more complex than we thought, he says, and facing up to this complexity will be as scary as the conceptual upheavals physicists had to take on board in the early 20th century.

The New Scientist article also cited research by Dr. Michael Syvanen, of the University of California at Davis. He 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 organisms. He failed. Once again, different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says. His conclusion: “We’ve just annihilated the tree of life.” [5]

Bapteste, Rose and Dupré by no means represent fringe opinions. One of the leaders in this field, W. Ford Doolittle, explains 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.” [6] Looking higher up the tree of life, a study published in Science tried to construct an evolutionary history of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.” [7] Likewise, Carl Woese, a pioneer in this field, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [read: contradictions in the relationships picture] can be seen everywhere in the universal tree, from its root to the major branching…”[8]

Lynn Margulis was, until she passed away in November 2011, a world-famous biologist. She was elected to the United States National Academy of Sciences in 1983 and inducted into the World Academy of Art and Science, the Russian Academy of Natural Sciences, and the American Academy of Arts and Sciences between 1995 and 1998. She was the recipient of the William Procter Prize for Scientific Achievement (1999) and was awarded the National Medal of Science by President Bill Clinton in that same year. She was also the first wife of the famous late astronomer Carl Sagan. Even though Margulis herself was certainly not religious, she had little patience for practitioners in this field. In an article entitled The Phylogenetic Tree Topples, she explained that “many biologists claim they know for sure that random mutation is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk… pattern!” But she dissented from that view and attacked 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.” [9]

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.” They observe that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” [10] 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.”

Glug, glug ,glug – swill some magic potion and here’s Mr. Hyde again. Biology textbooks often tout the tree-of-life constructed on the basis of the protein Cytochrome C as confirming the traditional relationships of many animal groups. This is presented as evidence for universal common descent. Over to Dr. Jekyll now. Said textbooks rarely talk about the Cytochrome B tree, which differs strikingly from the classical story. As an 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… Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.” [11]

References:

[1] http://www.springerlink.com/content/j7315x8081517q53/. Retrieved 15th July 2012.

[2] http://www.lifesci.utexas.edu/faculty/antisense/papers/Hillis1987ARES.pdf.
Retrieved 15th July 2012.

[3] http://www.stanford.edu/group/rosenberglab/papers/DegnanRosenberg2009-TREE.pdf.
Retrieved 15th July 2012.

[4] The article can be read here: http://www.nature.com/polopoly_fs/1.10885!/menu/main/topColumns/topLeftColumn/pdf/486460a.pdf.
Retrieved 11th July 2012.

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

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

[7] 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).

[8] Carl Woese “The Universal Ancestor,” Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998).

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

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

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