February 1, 2007 | David F. Coppedge

Darwinists Topple Darwin’s Tree of Life

Darwin’s “Tree of Life” is a myth.  It’s based on circular reasoning.  It is a pattern imposed on the data, not a fact emerging from the evidence.  We should give up the search for a single tree of life (TOL) as a record of the history of life on earth, because it is a “quixotic pursuit” unlikely to succeed – and the evidence is against it.  Who said this?  Not creationists, but a new member of the National Academy of Sciences in his inaugural paper for the academy’s Proceedings.1
    W. Ford Doolittle and Eric Bapteste decided to celebrate this inauguration with fireworks.  What they wrote is less a scientific paper than a reprimand.  They let Darwin-lovers have it between the eyes:

Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation.  However, there is no independent evidence that the natural order is an inclusive hierarchy, and incorporation of prokaryotes into the TOL is especially problematic.  The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree.  Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true.  This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation.  Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.

The last sentences from the abstract (above) and other quotations from the paper (below) show that they are not abandoning evolution.  They are simply claiming that this icon of a single branching tree is unsupportable, and indeed, is a figment of human imagination.  “We will argue that inclusive hierarchical classifications do not emerge naturally and consistently from the relevant prokaryotic data considered in general (in their entirety),” they state.  “Instead, they have been imposed on them by selective analyses that are based on the assumption that a tree must be the real natural pattern, even if only certain of the data can be trusted to reveal it.”  Later, they said, “Importantly, Darwin did not and could not test the reality of the tree pattern.  Indeed, one is hard pressed to find some theory-free body of evidence that such a single universal pattern relating all life forms exists independently of our habit of thinking that it should.”  Homologies, for instance, do not comprise independent evidence for a tree of life: “homologies are more often deduced from trees than trees are from homologies,” they explain.  “Thus, explanans melds with explanandum, and neither is tested.”  The reasoning is circular.  The fossil record and biogeography cannot be used to infer a universal tree except by extrapolation of limited evidence from “specific groups, areas, or times.”  No evidence, in short, produces a tree pattern necessarily; biologists should be open to other patterns, like networks.
    Growing realizations that lateral gene transfer (LGT) is rampant in biology, at least among the prokaryotes, render the discernment of a tree pattern impossible.  One cannot draw a tree out of a scrambled egg.  Is it justifiable to infer a tree when only 5% or less of the data conform to the expected pattern?  Some evolutionists have tried to dispute the extent of LGT, but commit another circular argument in doing so.  Doolittle and Bapteste explain: “to make ‘vertical descent’ the null hypothesis against which claims for LGT must be tested is to assume that which is to be proved: that an inclusive hierarchy exists independently of our beliefs.”  In addition, the authors complain that a “phylogenetic signal” in the genetic data is often weak at best.  Despite what students have been led to believe, “there is no strong expectation that a universal hierarchy that embraces all life should be produced with molecular markers.”
    They spent some time analyzing the TOL hypothesis from Darwin’s own words.  This next excerpt argues that Darwin committed a circular argument by confusing pattern with process.  Doolittle and Bapteste reveal that generations of scientists have grown up with this confusion.  They claim the TOL concept is unnecessary, given other strong evidence for evolution (which they did not specify):

Problematically, Darwin depended on the notion that the true pattern of natural relationships is a tree in the construction of his theory of the responsible process and, as Panchen (17) notes, his explanandum [the thing to be explained] was subsequently considered by him as a part of the proof that his theory (explanans [the explanation]) was right.  That classifications should be constructed as hierarchies because evolution is a branching process and that hierarchical classification is a proof of branching evolution is the mixed message many of us took from our early education as biologists.  But we now have ample other evidence supporting the reality of evolution.  We could thus dispense with the tree (and such semicircular reasoning), should this particular historical premise about branching fall short, without weakening the solid edifice of evolutionary biology.

Why Darwin’s argument was called semicircular instead of circular reasoning was not explained.  Also the “ample other evidence” and “solid edifice” was assumed, if by evolution they were implying a universal, mechanistic, unguided natural process that gave rise to all of life without a Designer or Creator.  Nevertheless, this paper clearly argued that there was no reason inherent from the data that the pattern of relationships we observe must look like a branching tree.  It could look like a web, or a network, or something else.2  In fact, some evolutionists have argued for a ring instead of a tree (09/09/2004).  The possibility of “pattern pluralism” arising from multiple mechanisms requires that evolutionary biologists rid themselves of the predilection for “tree-thinking.”
    Elsewhere, the authors chide critics of evolution.  They clearly do not want their statements to fuel the controversy.  Darwin’s Tree of Life may be false, but it was a useful lie that got many biologists fired up about a new path of inquiry.  That being accomplished, they no longer need the metaphor.  The metaphor of a tree is getting in the way of further understanding.  To argue this, they invoke a metaphor of their own: a ladder –

Darwin’s TOL hypothesis, like most biological theories, is a claim about the process that underlies a pattern.  It is important for modern phylogeneticists to remember that reconstructing the TOL was not the goal of Darwin’s theory, but rather it was an integral element of his developing model of the evolutionary process.  Importantly, this simile prompted generations of scientists to take Darwin’s claim that evolution had occurred seriously, for all his lack of a coherent theory of inheritance.  The TOL was thus the ladder that helped the community to climb the wall of acceptance and understanding of evolutionary process.  But now that we have climbed it, we do not need this ladder anymore.  In 2006, our understanding of evolution at the molecular, population genetic, and ecological levels is rich and pluralistic in character and does not require (or justify) a monistic view of the phylogenetic pattern.
    Holding onto this ladder of pattern is an unnecessary hindrance in the understanding of process (which is prior to pattern) both ontologically and in our more down-to-earth conceptualization of how evolution has occurred.  And it should not be an essential element in our struggle against those who doubt the validity of evolutionary theory, who can take comfort from this challenge to the TOL only by a willful misunderstanding of its import.  The patterns of similarity and difference seen among living things are historical in origin, the product of evolutionary mechanisms that, although various and complex, are not beyond comprehension and can sometimes be reconstructed.

Again, however, they did not provide examples of evidence supporting their emphatic assertion that life has evolved.  They just claim that it did: that the evidence is “rich” within the broad categories of molecular studies, population genetics and ecology.  They also did not explain why it was necessary to “struggle” against those who doubt this, if in fact, as they argued, pattern and process cannot be used as supports for each other.3
    Their final paragraph argues that evolutionary biology is like history.  Discerning the history of life on earth should invoke a variety of tools:

In this regard, our task is not different from that of contemporary cultural or social historians.  We know much about what can happen and have a variety of tools by which we might unravel what has happened.  We should use them all, but without seeking some elusive unifying “metanarrative,” either tree or web.  Phylogenetics could become again the rich and realistic science of the genesis of phyla and address within a multifaceted pluralistic framework not only new questions about the past [identification of networks, hubs and highways of gene exchange and vertical descent] but also the present (in particular, through integration of metagenomic data with evolutionary and ecological theory).

Yet this statement begs the question of why a pluralistic approach is better.  A pluralistic approach involving mutually contradictory presuppositions would seem fruitless.  And why one correct approach should be discounted merely in favor of pluralism seems equally pointless.  One thing is clear from their argument, though: Darwin’s Tree of Life has fallen.
    Radical as this paper seems, others have echoed similar ideas.  Carl Woese, the one who reorganized taxonomy into three kingdoms (archaea, bacteria, and eukarya), wrote an article with Nigel Goldenfield in Nature last week that is even more radical.4  They even call it revolutionary.  “The emerging picture of microbes as gene-swapping collectives demands a revision of such concepts as organism, species and evolution itself” they said in a Connections article called, “Biology’s next revolution.”  In a hail of verbal gunfire, they talked about an “extraordinary time for biology” in which multidisciplinary approaches and new definitions and concepts are about to overturn much of what we thought we knew about evolution.  Such new concepts might even include cybernetics and information theory.  Old Darwin himself may have to step back, and share the limelight with none other than his despised rival, Lamarck:

Nowhere are the implications of collective phenomena, mediated by HGT [horizontal gene transfer, same as LGT], so pervasive and important as in evolution.  A computer scientist might term the cell’s translational apparatus (used to convert genetic information to proteins) an ‘operating system’, by which all innovation is communicated and realized.  The fundamental role of translation, represented in particular by the genetic code, is shown by the clearly documented optimization of the code.  Its special role in any form of life leads to the striking prediction that early life evolved in a lamarckian way, with vertical descent marginalized by the more powerful early forms of HGT.
    Refinement through the horizontal sharing of genetic innovations would have triggered an explosion of genetic novelty, until the level of complexity required a transition to the current era of vertical evolution.  Thus, we regard as regrettable the conventional concatenation of Darwin’s name with evolution, because other modalities must also be considered.

They welcome new players into biology: statistical mechanics, dynamical systems theory, and other disciplines more capable in dealing with the concepts of generic energy, information and gene flow.  The old habits of post-hoc modelling will give way to the methods of quantitative prediction and experimental test more characteristic of the physical sciences.
    Progress in biology will require something else, they argue: a new language. 

Sometimes, language expresses ignorance rather than knowledge, as in the case of the word ‘prokaryote’, now superseded by the terms archaea and bacteria.  We foresee that in biology, new concepts will require a new language, grounded in mathematics and the discoveries emerging from the data we have highlighted.  During an earlier revolution, Antoine Lavoisier observed that scientific progress, like evolution, must overcome a challenge of communication: “We cannot improve the language of any science without at the same time improving the science itself; neither can we, on the other hand, improve a science without improving the language or nomenclature which belongs to it.”  Biology is about to meet this challenge.5

1W. Ford Doolittle and Eric Bapteste, “Inaugural Article: Evolution: Pattern Pluralism and the Tree of Life Hypothesis,” Proceedings of the National Academy of Sciences USA, 10.1073/pnas.0610699104, published online before print January 29, 2007.
2“So firm is the grip of tree-thinking” on biologists that they illustrated the fallacy with a spoof.  They gave two examples of tree-like patterns imposed on non-biological data sets that clearly could not represent an ancestral sequence.  One was a pattern of evolutionary authors with similar surnames that are not related.  Another showed a branching pattern of departments in France based on counts of similar surnames.  This “misapplication of tree-thinking” is a fallacy, they argued, that traps evolutionists intent on finding Darwin’s branching pattern when the pattern is not real.  The authors gave real-world examples of how, in some molecular studies, less than 5% of the data is in agreement with a TOL pattern.  In the case of the “tree of cells,” the phylogenetic signal is as low as 1%.  They decry “the continued enthusiasm for universal tree building and its broad application on the basis of very few and often contradictory data.”  The reader can decide whether this situation constitutes a Half Truth or a Big Lie.
3Here is another example of their defense of evolution: “To be sure, much of evolution has been tree-like and is captured in hierarchical classifications.  Although plant speciation is often effected by reticulation and radical primary and secondary symbioses lie at the base of the eukaryotes and several groups within them, it would be perverse to claim that Darwin’s TOL hypothesis has been falsified for animals (the taxon to which he primarily addressed himself) or that it is not an appropriate model for many taxa at many levels of analysis.  Birds are not bees, and animals are not plants.”  Yet these claims depend on generalities, dogmatic assertions, and arguments that are self-refuting from other arguments in the paper, such as the propensity of biologists to follow an “elusive unifying metanarrative” to explain the data when other metanarratives or patterns might explain it just as well.  At the risk of being perverse, we refer the reader to the 01/10/2007 discussion of animal phylogeny.
4Nigel Goldenfield and Carl Woese, “Connections: Biology’s next revolution,” Nature 445, 369 (25 January 2007) | doi:10.1038/445369a.
5Embedded within this paragraph are a couple of presuppositions: (1) that science is progressive, and (2) that a new language brings improvement.  If, as Woese has illustrated, language can express ignorance instead of knowledge, who would be able to judge that a new language for expressing evolution would not represent a regression into a new kind of ignorance?  Biology may be about to “meet this challenge,” but who is the judge who will be able to declare the outcome a victory?

Once in awhile, among the hundreds of tedious titles in scientific journals about the effect of gamma rays on marigolds or whatever, a paper announces its presence like a trumpet.  Without news sources like CEH to bring these papers to the attention of the lay public, this blast by Doolittle and Bapteste might have been muted.  The intellectual elite readership in academia, already deafened by Darwin, might fail to heed its warning.  They might explain it away as a false alarm, or hush it up.  No longer: the trumpet has sounded!  Darwin’s Tree of Life is fallen!  The sound has reached the Visigoth camp (05/06/2006) and elicited shouts of triumph.  Echoing through the valleys round about Darwin’s castle is heard the taunt, “We told you so!”
    First, it’s necessary to dispense with Doolittle and Bapteste’s protestations that the castle is still safe.  They bluffed that the walls are solid, buttressed with mounds of evidence from molecular biology, genetics and ecology.  They mocked the doubters who, by “willful misunderstanding,” would use their arguments to question evolutionary theory itself.  Don’t fall for this trick.  Their own arguments refute evolution without our help.  They have cut the branch Darwin was sitting on.  Worse, they cut down the whole tree!  They have replaced the tree with a web, Charlie’s Web, that spells out “SOME PIG” in a feeble attempt to bolster his self-esteem while doing nothing to change his circumstances.  Then Woese adds insult to injury by inviting Lamarck back into the leadership.  This is sure to bring on another of Charlie’s worst vomiting attacks, right when he was already gagging over intelligent design, to the point where he can’t stop gagging even when there’s nothing more down below to up Chuck.
    How could PNAS let this trade secret get out?  We know nothing of the motives or beliefs of the authors except what they stated in this paper, and by all appearances, they are loyal members of the Darwin Party.  They did, of course, pay the obligate incense to Charlie and curse the doubters.  You can’t publish in the Darwiniac-controlled Big Science journals without it.  But the damage is done.  Do you realize how big this admission is?  The Tree of Life is arguably the central icon of evolution.  From the single illustration in Charlie’s book till now, the image of a branching tree from a single root emerging from a primordial soup has been the symbol of evolution.  Papers are regularly published with phylogenetic trees.  There are whole journals devoted to tree-building.  Phylogenists employ elaborate software programs that take genomes and try to decipher the hidden tree within.  Is this all for naught?  Is it nothing more than playing games, tilting at windmills that don’t fight back and aren’t even aware of you?
    These authors basically said that tree-thinking evolutionists are dreaming.  Data don’t build trees, people do!  The software programs only succeed in finding a “consensus tree” or “maximum likelihood tree” or “maximum parsimony tree” because that is what biased programmers told them to find (see 07/25/2002).  If the program’s job is to find a tree, then find a tree it will.  It may have to throw out long-branch attraction (04/30/2005), massage the data to account for molecular clock heterogeneity (05/02/2006), and select between a dozen equally-valid results or whatever, but out pops a tree – whoop-de-doo!  The scientist gets a nice graphic to publish in his paper, and everyone is happy except Mother Nature.  If you doubt this, look at what they do with evidence in the 06/13/2003 and 04/30/2005 entries.
    The wishful-tree fallacy perpetuates itself because evolutionists approach the data with tree-thinking lenses on.  (Blinders help, too.)  Their tree may only be supported by 5% of the data, after tossing out the other 95% as irrelevant, but they feel justified in believing in it because they know in their hearts from the get-go that Darwin was The True Prophet.  Look how giddy some of the disciples get (see this Darwin Day advertisement with the “World’s Largest Edible Tree of Life”).
    Can you imagine how grating it must be to be told that Darwin confused pattern with process, that the trees exist only in their imaginations, and that the evidence contradicts this 146-year-old myth Darwin sketched on paper, the only place it exists in the world?  What does this paper do to the $150 million NSF project “Assembling the Tree of Life”? (09/08/2006, 10/30/2002, 03/14/2003).  It pulls the rug out from under it!  No amount of rationalizing about potential applications or better storytelling can justify spending $12 million a year of public money on a quixotic pursuit by a few dogmatic disciples of a tree-worshipping cult.
    Despite their pledges of allegiance to evolution, you will look in vain in these two papers for actual evidence that life emerged and diversified by a blind, materialistic, aimless process from molecules to man.  Yes, scientists observe mutations in genes.  They find variations within the clades, evidence of duplicated genes, and various homologies.  So what?  Other non-Darwinian, non-materialistic explanations are available.  The Darwinist may counter that all life uses the same genetic code, and that this proves a universal common ancestor.  But think outside the Darwin box: does this not fit the creation model?  A network of highly adapted kinds, each springing from a common Hand – what else would you expect?

For instance, Walter ReMine made it a theme of his book The Biotic Message that life was designed to indicate that it did not evolve, and that it came from a single Creator.  The universal genetic code proves the latter, and the intransigence of life’s nested hierarchies to fit a tree pattern proves the former.  If each group had completely separate codes, one might be justified in believing polytheism.  If all life had a clearly-traceable ancestry, then one might be justified in believing in evolution.  According to ReMine, the Creator guaranteed that the “biotic message” would rule out those alternatives and validate a single, intelligent origin.

While we’re outside the box, consider further that the evidence fits just what a Bible-believing Jew or Christian would expect.  The world was created perfect, but has degenerated since Creation and the Flood.  Limited diversification from the original created kinds has occurred because of variability built into the genomes of each created kind for robustness and adaptability to change – features perfectly consonant with good design.  Diseases represent degenerative process and a curse on the original creation.  Natural selection works on horizontal scales but does not add new genetic information or functional novelty.  If Carl Woese is justified in looking at the genetic code as an operating system, why should not these patterns based on a Biblical metanarrative, which fit the evidence to a T, be allowed in the Garden of science?  If everybody starts with a metanarrative, why should Charlie’s mythical Tree of Life be protected by angles with flaming words? (puns intended).6

6The pun density in our commentaries is proportional to p(u)n, where n is the number of stinking evolutionary ideas in paper p, a function of its underlying assumptions u.

    A sinister side of this comical tale is embedded in Doolittle and Bapteste’s fable of the ladder.  What does a ladder do?  It is not an end in itself, but a means to an end.  The ladder helped the Charlietans climb into the castle of Science and pretend to belong: “The TOL was thus the ladder that helped the [atheistic storytelling] community to climb the wall of acceptance and understanding of evolutionary process,” they admitted.  “But now that we have climbed it, we do not need this ladder anymore.”  Having invaded the stronghold, the cultists were in position to enter the inner sanctuary of Science.  They desecrated it by removing its Commandments of observability, testability and repeatability.  They built in its place a Temple of Charlie with a mystical Tree hidden behind a material veil, promising golden apples of enlightenment.
    The Darwin Party conspirators carried out their plot, working tirelessly till their cult became the State Religion.  They hypnotized the peasants with just-so stories to keep them from revolting.  They changed the language into a dialect of materialism and made it illegal to speak the old language of teleos.  Critics were shouted down by mob rule and kicked out of the city.  Former heads of state, despite their eminence and experience, were labeled barbarians and forced to build their own camps outside the walls.  Children were taught that the barbarians were ignorant, insane and wicked.  They had to be kept at bay lest they chop down the sacred Tree.  Children gasped at the prospect of never receiving the promised golden apples.
    Unopposed, the conspirators consolidated their power.  All groups in the castle were required to obtain and display the Darwin Party imprimatur.  They had achieved Utopia.
    For over a century, the Darwinian conspirators have maintained a totalitarian rule over Science.  Indulging their lusts at banquets amply supplied with tantalizing speculations (12/22/2003), they have become fat, lazy and corrupt.  They send their lackeys to enlist cult prostitutes (e.g., 12/11/2006), plan the Tree Festivals and Darwin Days, perform ritual child sacrifice (i.e., the Darwin-only rule in the schools), persecute infidels, brainwash reporters and supervise the cult propaganda in the media.  The noble barbarians, denied access to the institutions, communication channels, funding sources and positions of influence, have suffered long and done the best they can.
    But hark!  A messenger.  He brings word that the people inside are suspecting the Tree was a fake all along.  A trumpet blast from within the wall hints that officials inside are scrambling to maintain order.  Panicking, they issue public service announcements to explain away the embarrassing revelation, claiming that the Tree symbol was necessary to establish the Utopia they all need and enjoy.  They command the people to continue the Darwin Day celebrations, Tree or no Tree.  Edible icons of Darwin’s Tree of Life (example) are distributed to placate the crowds.  Yet murmurs of doubt and discontent remain.  The shrillness of the Party propaganda rises as the enthusiasm of the peasants wanes.  OK, Visigoths and Ostra(cized)goths, now you know why it’s time for Biology’s Next Revolution.

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