Series - "Icons of Evolution, Darwin's Tree of Life, Molecular Phylogeny"

A phylogeny is the evolutionary history of a group of organisms. All living organisms, from bacteria to humans, contain DNA.  A DNA molecule is a long chain consisting of various combinations of four subunits, abbreviated A, T, C and G; and the order of these subunits specifies the sequence of amino acids in an organism's proteins. During reproduction, the sequence of subunits is copied from one DNA molecule to another, but molecular accidents, or mutations, sometimes make the copy slightly different from the parent molecule. Therefore, organisms may have DNA molecules (and thus proteins) that differ somewhat from the DNA and proteins of their ancestors.
In 1962 biologists Emile Zuckerkandl and Linus Pauling suggested that comparisons of DNA sequences and their protein products could be used to determine how closely organisms are related. Organisms whose DNA or proteins differ by only a few subunits are presumably more closely related in evolutionary terms than those which differ by more. If mutations have accumulated steadily over time, the number of differences between organisms can serve as a "molecular clock" indicating how many years have passed since their DNA or protein was identical-that is, how long ago they shared a common ancestor.
Comparing DNA sequences is simple in theory, but complex in practice. Since an actual segment of DNA may contain thousands of subunits, lining them up to start a comparison is itself a tricky task, and different alignments can give very different results. Nevertheless, conclusions drawn from molecular comparisons have been brought to bear on the Cambrian explosion.

Molecular phylogeny and the Cambrian explosion
Did the animal phyla originate abruptly in the Cambrian, as the fossils seem to indicate, or did they slowly diverge from a common ancestor millions of years before, as Darwin's theory implies? It's not possible to analyze DNA from Cambrian fossils, but molecular biologists are able to compare protein and DNA sequences in living species. Assuming that sequence differences among the major animal phyla are due to mutations, and that mutations accumulate at the same rate in various organisms over long periods of time, biologists use sequence differences as a "molecular clock" to estimate how long ago the phyla shared a common ancestor.
 It turns out that the dates obtained by this method cover a wide range. Bruce Runnegar started the bidding in 1982 with an estimate of 900-1000 million years for the initial divergence of the animal phyla. In 1996 Russell Doolittle and his colleagues proposed a date of 670 million years, while Gregory Wray and his colleagues proposed 1200 million. In 1997 Richard Fortey and his colleagues endorsed the older date, and in 1998 Francisco Ayala and his colleagues endorsed the younger. But these two dates represent a spread of 530 million years, or as much time as has elapsed between the Cambrian explosion and the present. This "range of divergence estimates," in the opinion of American geneticist Kenneth Halanych, testifies "against the ability to date such ancient events" using molecular methods.
So the Cambrian explosion remains a paradox. The fossil evidence shows that the major animal phyla and classes appeared right at the start, contradicting a major tenet of Darwin's theory. Molecular phylogeny has not resolved the paradox, because the dates inferred from it vary over such a wide range.
The failure of molecular phylogeny to resolve the paradox now appears to be part of a larger problem. Since the early 1970s, evolutionary biologists have been hoping that sequence comparisons would overcome many of the difficulties arising from more traditional approaches, and would enable them to construct a "universal tree of life" based on molecules alone. Recent discoveries, however, have dashed that hope.

The growing problem in molecular phylogeny
Modern versions of the Darwinian tree of life are called "phylogenetic trees" In a typical phylogenetic tree, the "root" is the common ancestor of all the other organisms in the tree. The lower branches represent lineages that diverged relatively early, while the upper branches diverged later. The tips of the branches are actual species. Wherever two branches diverge, the branch-point indicates the hypothetical common ancestor of the two branching lineages. Many phylogenetic trees are drawn so that the lengths of the branches are proportional to sequence differences, which are often assumed to indicate how much time has elapsed since lineages diverged.
It is important to remember that the only actual data in a phylogenetic tree (with rare exceptions) come from living organisms, which are the tips of the branches. Everything else about a phylogenetic tree is hypothetical. Ideally, phylogenetic trees should be approximately the same regardless of which molecules are chosen for comparison. Indeed, there has been a general expectation among evolutionary biologists that the more molecules they include in a phylogenetic analysis, the more reliable their results are likely to be. But the expectation that more data would help matters "began to crumble a decade ago," wrote University of California molecular biologists James Lake, Ravi Jain, and Maria Rivera in 1999, "when scientists started analyzing a variety of genes from different organisms and found that their relationships to each other contradicted the evolutionary tree of life derived from rRNA analysis alone." According to French biologists Herve Philippe and Patrick Forterre: "With more and more sequences available, it turned out that most protein phylogenies contradict each other as well as the rRNA tree." In other words, different molecules lead to very different phylogenetic trees. According to University of Illinois biologist Carl Woese, an early pioneer in constructing rRNA-based phylogenetic trees: "No consistent organismal phylogeny has emerged from the many individual protein phylogenies so far produced. Phylogenetic incongruities can be seen everywhere in the universal tree, from its root to the major branching within and among the various [groups] to the makeup of the primary groupings themselves."

Inconsistencies among trees based on different molecules, and the bizarre trees that result from some molecular analyses, have now plunged molecular phylogeny into a crisis.

Jonathan Wells, author of the book we are busy studying, is a senior fellow at the discovery institute. Here is a link to an article from the discovery institute about the Cambrian Explosion. 

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