November 15, 2006 | David F. Coppedge

Darwin Can’t Find His Tree of Life

The “tree of life,” a branching pattern of evolutionary diversification, was the only illustration in Darwin’s Origin of Species.  In 1859, it only existed in his imagination as he speculated, with only circumstantial evidence based on similarities, that all living things descended from a common ancestor.  The fossil record did not show such a tree.  Darwin expected the record would be filled in by subsequent discoveries (but cf. 04/23/2006).  He could not have anticipated the revolution in genomics of the 20th century.  Neo-Darwinists met these discoveries with great anticipation that Darwin’s tree of life would now become visible in the genetic codes impressed in the cell of every organism.  Richard Dawkins predicted in A Devil’s Chaplain (2003, p. 272),

…there is, after all, one true tree of life, the unique pattern of evolutionary branchings that actually happened.  It exists.  It is in principle knowable.  We don’t know it all yet.  By 2050 we should – or if we do not, we shall have been defeated only at the terminal twigs, by the sheer number of species.

We are now at a stage where enough data have been published, including complete genomes of dozens of plants and animals, such that an assessment is now possible to see if a tree is coming into focus.  In addition, we have decades of comparative studies of proteins from different organisms.  A status report of sorts was published this week by Antonis Rokas and Sean B. Carroll in PLoS Biology.1  Though they began with Dawkins’ optimistic prophecy, the news is not good.  They see multiple bushes, not a tree.  These two evolutionary biologists admit that not only is a tree pattern indecipherable, it may never become visible, even as more data are added:

Genome analyses are delivering unprecedented amounts of data from an abundance of organisms, raising expectations that in the near future, resolving the tree of life (TOL) will simply be a matter of data collection.  However, recent analyses of some key clades in life’s history have produced bushes and not resolved trees.  The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.  Here we examine how the combination of the spacing of cladogenetic events and the high frequency of independently evolved characters (homoplasy) limit the resolution of ancient divergences.  Because some histories may not be resolvable by even vast increases in amounts of conventional data, the identification of new molecular characters will be crucial to future progress.

This frank admission by two believers in common ancestry demonstrates that molecular genetics has not delivered the hoped-for pattern: “Obtaining an accurate depiction of the evolutionary history of all living organisms has been and remains one of biology’s great challenges.”
    In addition to the problem of homoplasy (convergent evolution, or the independent origin of similar traits), the authors point to unexpected groupings that came out of molecular studies.  One study resulted in a grouping of “strikingly different mammals including elephants, aardvarks, manatees, and golden moles” in the same clade.  The pace of change presents another problem: some molecular events were explosively rapid, while others remained undisturbed (conserved) for hundreds of millions of years.  Opposite conclusions are sometimes reached depending on the method used.  Rokas and Carroll give an example of two papers within the same issue of Molecular Biology and Evolution that confirmed and falsified the existence of a certain group.  It’s not simply a matter that some methods are more accurate than others.  “The observed conflicts are not dependent on the optimality criterion used,” they said.  The problem is real, and it’s pervasive.
    It’s hard to tell if this paper is an admission of failure and hopelessness, or a call for a brief time out before an optimistic new charge:

Here we discuss how and why certain critical parts of the TOL [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.  We do not mean this essay to be a comprehensive review of molecular systematics.  Rather, we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation—which imply that the assembly of all branches of the TOL will simply be a matter of data collection.  We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge.  The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.  Now, as the field is transformed from a data-limited to an analysis-limited discipline, it is an opportune time to do so.

Most of the paper is taken up with examples.  For instance, despite what the media have often claimed, there is conflicting evidence linking humans to chimpanzees: “Specifically, analyses of almost 100 genes (under two different optimality criteria) show that ~55% of genes support a human-chimpanzee clade, 40% are evenly split among the two alternative topologies, with the remaining genes being uninformative” – and this is for two species considered so closely related, some political activists are advocating granting human rights to chimpanzees.
    To exhibit the scale of the problems, they list four notable “bushes” in the tree of life.  Notice how these are spread all over the evolutionary time scale:
(A) The human/chimpanzee/gorilla tree (5-8 million years ago).
(B) The elephant/sirenian/hyrax bush (57-65 million years ago).
(C) The tetrapod/coelacanth/lungfish bush (370-390 million years ago).
(D) The metazoan superbush (>550 million years ago).

They did not select these to be isolated examples.  These cases, despite getting the most detailed analysis by molecular phylogenists, are representative of the problems pervading the entire record.  Notice their use of words like “majority” and “large fraction” to indicate the scale of the challenge to Darwinian expectations:

Three observations generally hold true across metazoan datasets that indicate the pervasive influence of homoplasy at these evolutionary depths.  First, a large fraction of single genes produce phylogenies of poor quality.  For example, Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom (Figure 2D).  Second, in all studies, a large fraction of characters—genes, PICs or RGCs2disagree with the optimal phylogeny, indicating the existence of serious conflict in the DNA record.  For example, the majority of PICs conflict with the optimal topology in the Dopazo and Dopazo study.  Third, the conflict among these and other studies in metazoan phylogenetics is occurring at very “high” taxonomic levelsabove or at the phylum level.

If the best techniques applied to the most detailed data sets show these conflicts, it cannot be expected that poorer methods on smaller data sets will do any better.  Clearly, this is not a crisis that is going to go away with more data.
    So are molecular phylogenists “barking up the wrong trees,” they ask?  Is there “systematic bias” in tree-building efforts to date, that can “positively mislead phylogenetic inference”?  (see 06/08/2006).  Some sources of bias, like long-branch attraction, are understood.  If not careful, researchers can create trees out of wishful thinking: “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes.”  Researchers might just be engaged in self-fulfilling prophecy.  If this were the only source of bias, it might be possible to account for it, but Rokas and Carroll have shown that no method is consistently resolving one tree out of the bushes.
    Now for the recommendations.  Is there any hope?  If so, it is not in more data:

“Can we realistically hope to resolve diversification events spanning a few or even tens of millions of years that occurred in deep time?  It is widely accepted that nucleotide data are of limited use for resolving deep divergences because of mutational saturation and homoplasy.  Until the recent expansion in available data, it has not been possible to fully explore what the limits of the protein record might be.  Like others in the field, we also had expectations that scaling up dataset size would be sufficient to resolve interesting groups.  The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.  Just as it would be futile to use radioisotopes with modest half lives to date ancient rocks, it appears unrealistic to expect conventional linear, homoplasy-sensitive sequences to reliably resolve series of events that transpired in a small fraction of deep time.  Although we have known this from theory, we are now confronted with the actual pattern of molecular evolution.

The recommendations are: (1) the “prevalence and causes of homoplasy need to be better understood” and (2) “molecular systematics must now move beyond conventional characters and mine genomic data for new, less-homoplastic characters such as RGCs” [rare genomic changes].  This second plan, though is subject to confusion because of the widespread incidence of horizontal gene transfer and lineage sorting.  Earlier in the paper, Rokas and Carroll expressed frustration that the very stems in the tree of most interest to evolutionists are the very ones with the most problems:

Thus, absolutely or relatively short stems present distinct challenges that could be described as the bane of the molecular systematist.  Yet, it is precisely these stems—associated with some of the most interesting episodes in life’s history—that most intrigue the evolutionist.  Analyses of large molecular datasets from clades at different time depths of the TOL illustrate how short stems, whether placed just 6 million or 600 million years in the past, can confound phylogenetic resolution.

What to do?  When the tree of life is a lemon tree, make lemonade.  The authors ended by asking, “What’s wrong with bushes?”  Nothing, if you are willing to be called a heretic:

A bush in which series of cladogenetic events lie crammed and unresolved within a small section of a larger tree does harbour historical information.  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.
    For example, the lack of phylogenetic resolution at the base of the tetrapod/lungfish/coelacanth clade has not hampered in the least evolutionary research on the anatomical changes that occurred early on in the evolution of the tetrapod lineage.  Similarly, if the origin of most bilaterian phyla was compressed in time, more than 550 million years later it may matter little to know the exact relationships between most phyla to understand the evolution of the molecular tool kit that enabled the evolution of the body plans of the 35 or so animal phyla.
    We submit that if the current efforts to assemble the TOL have, by 2050 (if not much sooner), assembled an arborescent bush of life, Dawkins’ prediction will have come to fruition.

Translated, this may either mean that evolutionary thinking can proceed without evidence for a tree of life, or that there is still hope that somewhere hidden in the foliage there is a single trunk waiting to be found: the disparate bushes will become a single “arborescent bush of life.”  For now, it’s an article of faith foundering on confusing and contradictory evidence.

1 Antonis Rokas, Sean B. Carroll, “Bushes in the Tree of Life,” Public Library of Science Biology, 4(11): e352. DOI: 10.1371/journal.pbio.0040352.
2Abbreviations: TOL, tree of life; PIC, parsimony-informative character; RGC, rare genomic change.

Folks, do you have any idea how damaging this paper is?  Darwinism has been falsified.  It’s over.  We may as well dance on the grave of Charlie D, because both of the greatest hopes for confirming his tall tale have falsified it: the fossil record and the genetic record.  For Rokas and Carroll to have any hope now is as pathetic as watching a Las Vegas gambler continue on after being told the slot machine is broken and there is no money in it.
    Incredibly, these evolutionists do continue on in spite of the lack of evidence.  They do exactly what Charlie himself did: trust their imaginations.  Dawkins believes that the magical tree exists.  He accepts this myth, and the other evolutionists have so devoted their lies, their distortions, and their sacrilegious dishonor so much to it, that no amount of falsification will stop them.  The search must go on, till 2050 or beyond (after they are long dead), so that Charlie’s Myth can inspire a new generation of dreamers.  And Dawkins has the audacity to claim that creationists are the ones believing in fairy tales.
    You realize that a series of bushes does not look like evolution; it looks like creation.  The universality of the genetic code ensures that the phyla did not evolve independently.  Since they cannot connect the dots from a universal common ancestor to the plethora of organisms alive today, the dots are imaginary – no better than a Kipling tale.  The evidence is very consistent, by contrast, with a single Creator who made separate groupings of plants and animals that reproduce after their kind (with variability), while still exhibiting a common underlying plan.
    The only claim to authority and public trust that the evolutionary biologist can appeal to is empirical evidence.  This is what the Darwinists think makes their beliefs superior to religion.  For example, if you go to a new BBC Education site for kids, it will continue to propound the idea that religious truth is based on faith, while scientific truth is based on empirical evidence.

This same site also has a section on Evolution that blatantly presents known falsehoods about evolutionary evidence, including peppered moths, finch beaks and the horse series, while claiming that the fossil record proves evolution.  Each of these icons has been refuted in scientific journals and scholarly books, often written by believers in evolution.  Are the webmasters of Bite-Size Science merely uninformed about this, or are they deliberately deceiving students to promote an agenda?

The assumption of empirical support has been the main thing the Darwin Party has preached gives them superiority in truth claims and the right to rule the schools.  Only their myth gets exclusivity in “science” class.  Everyone else’s view must be consigned to the funny farm known as “religious studies.”
    That was then.  This is now.  Their assumed empirical evidence has vanished, leaving them with nothing but vivid imaginations to keep their creation myth intact.  Read what Rokas and Carroll have said, and then re-read what Marshall said about the fossil record in the 04/23/2006 entry (ignoring the spin, just examining the evidence).  We no longer need to claim Darwinian evolution has been falsified; they did it for us.  Q.E.D.  Mission accomplished.  Fait accompli.  Done deal.  Way to go.  High five.  Glory to God.  Now, let’s get back on the road to the real Tree of Life.  But this time, let’s follow the Manufacturer’s directions.
Boy, was that a bad detour, or what? (11/30/2005).

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