“The Phylogenetic Tree Topples”

The following was taken from International Scientific Discoveries Since Kitzmiller Which Support ID (Part II)

- Leading biologist Lynn Margulis (who rejects ID) explained in the article “The Phylogenetic Tree Topples” 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: “‘No!’ I say.” Margulis notes that “[e]specially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don't study ancestors.” She explains that many Darwinian scientists are “[v]ictims of a Whiteheadian ‘fallacy of misplaced concreteness,’ they correlate computer code with names given by ‘authorities’ to organisms they never see! Our zealous research, ever faithful to the god who dwells in the details, openly challenges such dogmatic certainty. This is science.” Margulis also stated in a news article this year that, "Random mutation indisputably exists . . . But I claim that new mutations don't create new species; they create offspring that are impaired."


- Two biologists from Canada and the United Kingdom were brave enough to admit in Trends in Ecology and Evolution that the animal phylogeny has undergone “major reorganisations over the past few years” as genetic evidence is overturning previously held ideas about common ancestry. Their article recommends building the tree of life by comparing large numbers of genes because trees based upon one individual protein so commonly conflict with trees based upon other proteins. However, resorting to such techniques requires biologists to assume common descent is true, and not engage in robust testing of the theory.


- Similarly, three days after Kitzmiller was issued, biologists in Science acknowledged that “[t]he phylogenetic relationships among most metazoan phyla remain uncertain.” Again, the problem lies in the fact that trees based upon one gene or protein often conflict with trees based upon other genes. Their study employed the many-gene technique, and yet still found that "[a] 50-gene data matrix does not resolve relationships among most metazoan phyla." The en vogue ad hoc explanations for the discrepancies between trees are said to be "insufficient amounts of available sequence data, mutational saturation, the occurrence of unequal rates of evolution between lineages, or the rapidity with which metazoan phyla diversified."


-The most striking admissions of deficiencies in the tree of life (TOL) came from a paper entitled "Bushes in the Tree of Life" by Antonis Rokas and Sean B. Carroll, who also co-authored the above-mentioned Science paper. They acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that in one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.” What about the technique of simply adding more data? They suggest that "certain critical parts of the TOL may be difficult to resolve, regardless of the quantity of conventional data available." This means that the excuse that problems exist because of "insufficient amounts of available sequence data" is not panning out and more data is not fixing the discrepancies. The paper suggests that "[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics." Rokas and Carroll are Neo-Darwinists, and thus one assumption they unfortunately do not re-evaluate is common descent. They suggest the problems can be fixed by using less studied types of molecular characteristics--in short, they appeal to new untried techniques. Perhaps the inability to construct robust phylogenetic trees using molecular data is because common descent is not the answer. Consider what the article says:

"For example, in the case of metazoan superclades (Figure 2D) what has been reported in two different studies is not a lack of resolution but two apparently well supported but contradicting phylogenies."
"Although it may be heresy to say so, it could be argued that knowing that strikingly different groups form a clade and that the time spans between the branching of these groups must have been very short, makes the knowledge of the branching order among groups potentially a secondary concern."

(Antonis Rokas & Sean B. Carroll, "Bushes in the Tree of Life," PLOS Biology, Vol 4(11):1899-1904 (November, 2006) (internal citations and figures omitted))