July 23, 2009 | David F. Coppedge

Biological Big Bang: Another Explosion at the Dawn of Life

Eugene Koonin and two friends from the NIH went tree-hunting.  They examined almost 7,000 genomes of prokaryotes.  They found trees all right – a whole forest of them.  They even found 102 NUTs (nearly universal trees) in the forest.  Unfortunately, it’s not what they wanted to find: a single universal tree of life that Darwin’s theory requires.  They had to seriously consider the question: was there a biological big bang?
    Publishing in an open-access article in the Journal of Biology,1 they began with the founding father’s vision: “The tree of life is, probably, the single dominating metaphor that permeates the discourse of evolutionary biology, from the famous single illustration in Darwin’s On the Origin of Species to 21st-century textbooks.”  Alas, that 150-year-old icon must be dismantled.  In their conclusion, they said, “the original tree of life concept is obsolete: it would not even be a ‘tree of one percent’.
    What happened?  It appears that horizontal gene transfer (HGT) has scrambled the genes in prokaryotes so much that any trace of common ancestry has been lost.  This means that Darwin’s metaphor lacks empirical evidence.  A fair-minded scientist would have to consider the possibility of a biological big bang (BBB), in which all the diversity in prokaryotes arose explosively.  And that’s what they did.  They evaluated their evidence with the BBB model and a slower type of explosion, called compressed cladogenesis (CC).2  Whichever was better, it was not very tree-like.  The strong tree-of-life image is unsupportable in the data.  They asked, “However, is there any hope of salvaging the tree of life as a statistical central trend?”  Searching diligently, they thought they found some things that “suggest a positive answer to this crucial question.”

The message from this analysis is twofold.  On the one hand, we detected high levels of inconsistency among the trees comprising the forest of life, most probably due to extensive HGT, a conclusion that is supported by more direct observations of numerous probable transfers of genes between archaea and bacteria.  On the other hand, we detected a distinct signal of a consensus topology that was particularly strong in the NUTs.  Although the NUTs showed a substantial amount of apparent HGT, the transfer events seemed to be distributed randomly and did not obscure the vertical signal.  Moreover, the topology of the NUTs was quite similar to those of numerous other trees in the forest, so although the NUTs certainly cannot represent the forest completely, this set of largely consistent, nearly universal trees is a reasonable candidate for representing a central trend.  However, the opposite side of the coin is that the consistency between the trees in the forest is high at shallow depths of the trees and abruptly drops, almost down to the level of random trees, at greater phylogenetic depths that correspond to the radiation of archaeal and bacterial phyla.  This observation casts doubt on the existence of a central trend in the forest of life and suggests the possibility that the early phases of evolution might have been non-tree-like (a Biological Big Bang).  To address this problem directly, we simulated evolution under the CC model and under the BBB model, and found that the CC scenario better approximates the observed dependence between tree inconsistency and phylogenetic depth.  Thus, a consistent phylogenetic signal seems to be discernible throughout the evolution of archaea and bacteria but, under the CC model, the prospect of unequivocally resolving the relationships between the major archaeal and bacterial clades is bleak.

Keeping some hope alive in the bleakness, therefore, they thought they could discern a weak central phylogenetic (evolutionary) trend in their data.  But it was, at best, only a composite of “nearly universal” trees that was obscured by a thicket of cross branches.  The same data seem to fit just as well with the big bang or compressed cladogenesis models (see footnote 2 for explanation).  The short message is, “A central trend that most probably represents vertical inheritance is discernible throughout the evolution of archaea and bacteria, although compressed cladogenesis complicates unambiguous resolution of the relationships between the major archaeal and bacterial clades.”
    This paper is the latest in a series of “bleak” findings by Koonin about the missing tree of life (see “Mystery of Intron Evolution,” 09/03/2003; “Introns Stump Evolutionary Theorists,” 03/09/2006, “What Are Human Genes Doing in a Sea Anemone?”, 07/08/2007; “Will Darwinism End in a Big Bang?”, 10/08/2007).


1.  Puigbo, Wolf and Koonin, “Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest,” Journal of Biology, 2009, 8:59doi:10.1186/jbiol159.
2.  “More specifically, we considered two models of early evolution at the level of archaeal and bacterial phyla: a compressed cladogenesis (CC) model, whereby there is a tree structure even at the deepest levels but the internal branches are extremely short; and a Biological Big Bang (BBB) model under which the early phase of evolution involved horizontal gene exchange so intensive that there is no signal of vertical inheritance in principle.”  But even with CC, a tree without branches is not really an evolutionary tree; it is a lineage.

The Darwinists are in the throes of withdrawal.  The thought of not having a tree to comfort them is too much to endure.  Their tree at the Cambrian exploded, and now they are hearing a big bang at the origin of the most primitive forms of life.  Darwin hates those explosions.  They ruin his whole day.
    Get a load of this line from the paper.  It is almost unsurpassed as an example of euphemism covering up a crisis: “The results of this analysis do not rule out the BBB model as the generative mechanism underlying the divergence of archaea and bacteria….”  Did you catch that?  That is hilarious!  A big bang as a generative mechanism?  What are they saying?  Generative – Genesis – they’re talking about creation, folks!  The prokaryotes just burst onto the scene.  Explosions are generally not considered to be creative mechanisms, you realize.  They just hid their little “problem” inside a big bang, hoping the concussion would distract you from what they just admitted.  A big bang as a generative mechanism?  Ha!  However that happened, it was definitely NOT a Darwinian process.  It sounds like creation.  There is no possible, conceivable way that Darwin can account for the sudden appearance of prokaryotes and bacteria, with all their molecular machines, systems, networks, genetic codes and complexity.  Why don’t they just admit it?  Why don’t they follow the evidence where it leads?  Why this craving to smoke the Darwin dope and push it on the youth? (DOPE = Darwin-Only Public Education).  They said the DOPE is still in 21st century textbooks.  Come clean!  Break the habit.  Clean up your act.
    Darwinism’s only tenuous grasp on science is empirical evidence.  Admittedly, Darwin was a good storyteller.  He was a genteel guy with a lot of friends.  But who cares if his book makes a nice story or one long argument?  Science wants data.  The empirical evidence has been slipping from his disciples’ grasp since the Origin hit the bookshelves.  It sent his disciples on many a wild goose chase, looking for missing links that were trumpeted only to be falsified later (like Piltdown Man), Precambrian transitional forms that never appeared, pangenesis that was challenged by Mendelian discrete alleles, and promissory notes they kept delaying to pay.  They kept distracting us with little finch beaks and peppered moths to make us believe they had everything explained.  Their grip on empirical evidence was nearly lost when the genetic code was discovered.  Now this: no tree of life!  A biological big bang.  Face it, Darwinists: it’s over.  The tree was a myth.  It’s obsolete.  Stop trying to imagine a tree in the thicket.  It’s not even “a tree of one percent.”  Five percent is the usual scientific minimum threshold for statistical significance; this is way below that.  The data do not “suggest” an imaginary tree that might be used to “salvage” the icon.  If there’s anything “suggested” by the empirical evidence, it is a loud, clear call of design.
    Stop the doubletalk and the moonwalk.  “Compressed cladogenesis” (another euphemism for “hurry-up origin of groups”) is not going to save the theory now.  They tried that with the Cambrian explosion, too, remember?  They tried to stretch it out a few more million years, from 2 minutes on a 24-hour clock to 4 minutes.  It’s not going to work.  Give it up.  Let’s all pitch in, clean up the mess and move on.  There’s work to do.  Systems biology has some gold to mine (07/21/2009) and we can at least learn some things that might improve our living standards from the intelligent designs in biology (07/11/2009, 06/25/2005, 10/29/2005).

(Visited 25 times, 1 visits today)
Categories: Cell Biology, Genetics

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.