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.
Have an Intelligent Faith!!
-Nelis
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