Is DNA Providing a Coherent View of Evolution?

Darwin's Proposed 'Tree of Life'

Darwin believed that all forms of life existing on this planet arose from “a few…or one”1 form(s) of life. While mulling over this idea, he sketched in one of his notebooks something that has been an icon of evolution ever since: the tree of life. His idea was that if you could properly trace the evolutionary relationships of all organisms, you would find that they would form a “giant tree,” with all the “branches” eventually tracing back to the one or few life forms that started all of evolution. Since that time, evolutionists have been trying to construct such a “tree of life,” but they have met with limited success. The problem is that different methods for constructing the “tree of life” give rather different results. For example, if you look at the morphology (form and structure) of organisms, you construct one “tree.” However, if you look at common molecules, such as the RNA found in a cell’s ribosomes, you get a different “tree.” As Masami Hasegawa and colleagues 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.2

Once scientists got to the point where they could sequence many, many genes and compare the genes in one organism directly to the genes in another organism, it was thought that a “definitive tree of life” would be produced. After all, since evolution is supposed to occur via mutations in the genome being acted on by natural selection, genetics should provide a clear map of how evolution progressed.

The problem is that DNA has simply muddied the waters even more when it comes to evolutionary relationships. Indeed, it has caused some biologists to say that evolution cannot even be represented by a tree.

The first problem is that concentrating on different genes produces different evolutionary “trees.” For example, Karen Nelson and her colleagues identified 33 genes that are common to two bacteria that are thought by evolutionists to be quite ancient, Thermotoga and Aquifex. They wanted to use those genes to construct evolutionary relationships between these two bacteria as well as several other single-celled organisms. Specifically, they wanted to compare their evolutionary “trees” to the ones that had already been constructed by comparing the RNA found in the ribosomes of the organisms. As a review article in Science puts it:

They found, she says, that “there’s no consistent picture [of] where these two organisms fall.” As she described at the meeting, Nelson first identified 33 genes that are found in both Thermotoga and Aquifex, as well as in an additional 10 bacterial species, four Archaea, and the eukaryote yeast. She then used the base changes in the genes of the various organisms to construct separate trees reflecting the evolutionary history of each gene. “We could find only three situations that supported the branching order [derived] from the ribosomal subunit,” she said. “It was impossible to say whether Aquifex or Thermotoga was more ancient.”3

So the “trees” produced by genetic analysis differed depending on the gene. In only three of the 33 genes could they reproduce the RNA “trees” that had already been established, and they couldn’t even decide which of the two bacteria came first!

Now, of course, bacterial genetics can be hard to understand because bacteria “swap” genes all of the time. Bacteria can even “pick up” genes from a dead bacterium of another species through a process called transformation. Thus, it might not be all that surprising to find that it is difficult to “tease out” the evolutionary relationships of bacteria, as all that gene-swapping would blur any genetic relationships.

Surely, however, that problem goes away once you consider the animals. After all, we aren’t familiar with any cases in which animals swap genes among species. Thus, genetic analyses of animals should produce clear evolutionary “trees,” right? Wrong! Biologist Michael Syvanen (University of California Davis) compared 2,000 genes that are common in a diverse set of animals like frogs, fruit flies, tunicates, nematodes, and sea urchins. He also included people in the analysis. This should have allowed him to determine the evolutionary relationships among the people and the animals. The problem is that he couldn’t. As the New Scientist article that reported on his research says:

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.4

The second problem, which I consider to be even more serious, is that very similar genes show up in animals that no evolutionist wants to believe are closely related to one another. For example, two studies published in Current Biology, 5,6 show that the hearing gene (Prestin) is very similar in bats and bottlenose dolphins. No evolutionist would suggest that there is a common echolocating ancestor between these two organisms, yet if that gene were used to construct an evolutionary “tree,” it would most certainly show that they have a recent common ancestor.

To give an even more dramatic example of this problem, consider the Pax-6 gene, which was originally discovered because of its role in the development of eyes. When you compare Pax-6 genes from different organisms with eyes, you find amazing similarity. For example, the Pax-6 gene in humans and Murine rats produce identical proteins. The protein produced by the zebrafish Pax-6 gene is 97% similar to the protein in humans. Fruit flies, sea urchins, cephalopods, and nematodes all have Pax-6 genes that produce proteins that are more than 90% similar to the protein produced by the human Pax-6 gene.7 As Ernst Mayr says:

It was therefore 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.8

So despite the fact that the Pax-6 gene is incredibly similar among many animals with eyes, we cannot assume these animals all had a common ancestor with eyes. Indeed, Mayr suggests in the same discussion that evolutionists believe eyes have developed in 40 independent evolutionary lines. Furthermore, we have to assume that the Pax-6 gene had some “unknown” function in organisms without eyes, but it was then “recruited” for eye development in organisms that developed eyes.

Does this look like a coherent view of evolution? Of course not! No wonder many biologists are arguing that the concept of a “tree of life” must be scrapped altogether. As the New Scientist article in reference (4) reports, evolutionary biologist Eric Bapteste says:

We have no evidence at all that the tree of life is a reality.

Or, as W. Ford Doolittle says in Science:

Molecular phylogeneticists 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


1. Charles Darwin, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, London: John Murray, 1859, p. 490 available online
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2. Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” J. Mol. Ev., 44:S117-S120, 1997
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3. Elizabeth Pennisi, “Microbes, Immunity, and Disease: Is It Time to Uproot the Tree of Life?” Science 284:1305-1307, 1999 available online with subscription
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4. Graham Lawton, “Why Darwin was wrong about the tree of life,” New Scientist Magazine, issue 2692, 2009, available online with subscription
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5. Yiang Liu, et al., “Convergent sequence evolution between echolocating bats and dolphins,” Current Biology 20:R53 – 4, 2010
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6. Ying Li, et al., “The hearing gene Prestin unites echolocating bats and whales,” Current Biology 20:R55 – 6, 2010
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7. Colin Berry, “An unexpected light,” QJM: An International Journal of Medicine 95:61–2, 2002 available online
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8. Ernst Mayr, What Evolution Is,Basic Books, 2001, p. 113.
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9. W. Ford Doolittle, “Phylogenetic Classification and the Universal Tree ,” Science 264:2124-2128, 1999 available online with subscription
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  1. On a taxonomic streak are you? Well, you’re right. Yup, there is plenty of disagreement on the “tree” of life, and even scientists who have used a “bush” as a much more apt metaphor for a long time have seriously different ideas about what the big picture really is. Even the entire fields of cladistics and systematics have significant disagreements both between and among each other. There are even different definitions of “species”! That’s quite a lot of disagreement. Doesn’t sound like a High Priesthood at all, does it?

    But none of that makes evolution by natural selection any less true.

    Btw, how do you argue on one hand that evolutionists follow their dogma like a religious order and thus are not practicing science AND on the other hand, criticize evolutionists for revising previous information and disagreeing? Which one is it?

    1. jlwile says:

      Actually, it sounds JUST like a high priesthood. You see, rather than following the data, the high priests of evolution decide on certain dogma. If you don’t question that dogma, you are free to argue about the fine points. However, if you question the dogma you are excommunicated. So you are free to argue about the MECHANISMS of evolution – you are just not allowed to doubt the DOGMA that evolution happened.

      Of course disagreement amongst evolutionists doesn’t make evolution any less true. What makes it clear that evolution is not true is the fact that the DATA disagree with the predictions of evolution – especially the data that come from DNA!

      As explained above, evolutionists act like any other high priesthood. You are allowed to disagree on certain details (like groups within ANY church do). You just can’t disagree with the dogma.

  2. How do you tell the difference between dogma and settle science?

    1. jlwile says:

      It’s very simple – the proponents of settled science aren’t afraid of debating what they consider settled science. Given that many evolutionists are terrified of debating the reality of evolution, it is clear that evolution is more dogma than science.