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Who stole Darwin’s Tree of Life?

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Hey, don’t look at us, we saw the Firewood Supply, Inc. truck in the vicinity, but we didn’t call them.

You’ll be surprised to learn who did …

The latest Salvo is out and features a piece by Casey Luskin on the fate of the Ol’ Deadwood:

The Best Proof of Macroevolution?

The project was first conceived in the 1960s, soon after the genetic code was uncovered. Two pioneering scientists, Linus Pauling and Emile Zuckerkandl, boldly predicted that phylogenetic trees based upon molecular data would confirm expectations of common descent already held by evolutionary biologists who studied morphology (i.e., the physical traits of organisms). They declared, “If the two phylogenic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished.”

Note, this was the task they set themselves.

Hoping to validate Pauling and Zuckerkandl’s prediction, biologists set themselves to the task of sequencing genes from all manner of living organisms. Technologies were refined, genomes were sequenced, and new discoveries were made. One revolutionary discovery was made in the 1990s, when it was realized that the “five kingdoms” view of life, taught to many previous generations of students, was incomplete. Examination of the gene sequences of living organisms revealed instead that they fell into three basic domains: Archaea, Bacteria, and Eukarya.

Not a big deal that, but

About the same time, another discovery was made that confounded evolutionary biologists who studied genes: they found that the three domains of life could not be resolved into a tree-like pattern. This led the prominent biochemist W. Ford Doolittle to famously lament: “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.” He later acknowledged, “It is as if we have failed at the task that Darwin set for us: delineating the unique structure of the tree of life.”

Note, he said it, we didn’t, and then it just got buried, perhaps reappearing in publicly funded textbooks as if nothing whatever has happened. More.

Be advised, the deadfall Tree of Life may not prompt  serious thought among the tenured. If you think otherwise, you might wish to revisit the “junk DNA” controversy.

See the serious lengths to which people will go to deny that major voices for Darwin ever thought that masses of junk DNA in our genomes was evidence for their theory (544 comments to date, on a post that merely referenced a UD post).

But we can meanwhile benefit from still more deadwood clearance, to get a look at the live stuff.

13 Replies to “Who stole Darwin’s Tree of Life?

  1. 1
    Mapou says:

    There is a tree of life. It is not Darwin’s purely nested tree but a non-nested tree. A non-nested hierarchy, which uses lateral inheritance across distant branches of the tree, is what one would expect from intelligent design over time.

    A non-nested tree of life clearly falsifies Darwinian evolution and common descent.

  2. 2
    News says:

    Some of us think, in that case Mapou, that “tree” is no longer the right metaphor. Anyone think of a better one?

  3. 3
    niwrad says:


    Mapou is right. A better metaphor? A forest of trees, where each tree represents a family/kind.

  4. 4
    Mapou says:

    News @2,

    You may be right. But “tree” is a general metaphor for a hierarchical structure and terrestrial lifeforms can be organized hierarchically. I think it is a good metaphor and I think we should keep it. When we use the term, we should be careful to specify whether or not we are referring to a Darwinian tree of life or an intelligent design tree of life.

    PS. As a Christian who believes that the Garden of Eden story is purely metaphorical, I think it is appropriate to continue to use the tree of life metaphor because it’s the exact same metaphor used in the book Genesis. So the Darwinists did not invent it. They stole it. It’s time for them to return it and ask for forgiveness. 🙂

  5. 5
    JLAfan2001 says:

    You guys should take a look at the three comments made under the article at Salvo. Luskin gets schooled real good. Maybe he should stick to lawyer things and not biology things. It seems the certificate that he has isn’t doing him any good.

  6. 6
    Mapou says:

    JLAfan2001 @5,

    Man, go pass wind somewhere else. Just because some ID-hating fool named Kevin has a bone to pick against creationists and Casey Luskin in particular does not mean that he refuted what Luskin wrote that article. Luskin is 100% correct and the fully nested tree of life based on common descent that the Darwinists predicted is fully falsified. I read Kevin’s comments and it’s obvious he is passing wind, just like you.

    In conclusion, Kevin’s tantrums simply means that the rest of us sensible people will need to stay upwind from the smelly folk. Cheers.

  7. 7
    JLAfan2001 says:


    Is arguments were scientific and he provided evidence for it. What do you do? Insult, distract from the issue and use propaganda to validate your claims. You cite not a single paper to show your claims. Show me where it’s been falsified. I expect that you will give me the same answer as other theists – I don’t have to, if I don’t want to. I’ve read some of your posts here and some of the stuff you believe is some really wacked out shit even for a christian. I guess I shouldn’t feel too bad about your reply knowing that.

  8. 8
    bornagain77 says:

    JLAfan2001, funny you are offended at insults but took no exception whatsoever to the many insults hurled towards Luskin in your and Kevin’s post.,,, Are you familiar with the concept of ‘first take the plank out of your own eye, and then you will see clearly to remove the speck from your brother’s eye.’?


    Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! – video
    Quote from video…
    “I think the tree of life is an artifact of some early scientific studies that aren’t really holding up.”
    – Dr. Craig Venter, American Biologist

    Darwin’s Tree of Life is a Tangled Bramble Bush – May 15, 2013
    Excerpt: ,,, One whole subsection in the paper is titled, “All gene trees differ from species phylogeny.” Another is titled, “Standard practices do not reduce incongruence.” A third, “Standard practices can mislead.” One of their major findings was “extensive conflict in certain internodes.”
    The authors not only advised throwing out some standard practices of tree-building, but (amazingly) proposed evolutionists throw out the “uninformative” conflicting data and only use data that seems to support the Darwinian tree: “the subset of genes with strong phylogenetic signal is more informative than the full set of genes, suggesting that phylogenomic analyses using conditional combination approaches, rather than approaches based on total evidence, may be more powerful.”,,,
    ,,,tossing out “uninformative” data sets and only using data that appear to support their foreordained conclusion. Were you told this in biology class? Did your textbook mention this?

    That Yeast Study is a Good Example of How Evolutionary Theory Works – Cornelius Hunter – June 2013
    Excerpt:,,, The evolutionists tried to fix the problem with all kinds of strategies. They removed parts of genes from the analysis, they removed a few genes that might have been outliers, they removed a few of the yeast species, they restricted the analysis to certain genes that agreed on parts of the evolutionary tree, they restricted the analysis to only those genes thought to be slowly evolving, and they tried restricting the gene comparisons to only certain parts of the gene.
    These various strategies each have their own rationale. That rationale may be dubious, but at least there is some underlying reasoning. Yet none of these strategies worked. In fact they sometimes exacerbated the incongruence problem. What the evolutionists finally had to do, simply put, was to select the subset of the genes or of the problem that gave the right evolutionary answer. They described those genes as having “strong phylogenetic signal.”
    And how do we know that these genes have strong phylogenetic signal. Because they give the right answer.
    This is an example of a classic tendency in science known as confirmation bias.,,,

    Phylogeny: Rewriting evolution – Tiny molecules called microRNAs are tearing apart traditional ideas about the animal family tree. – Elie Dolgin – 27 June 2012
    Excerpt: “I’ve looked at thousands of microRNA genes, and I can’t find a single example that would support the traditional tree,” he says. “…they give a totally different tree from what everyone else wants.” (Phylogeny: Rewriting evolution, Nature 486,460–462, 28 June 2012) (molecular palaeobiologist – Kevin Peterson)
    Mark Springer, (a molecular phylogeneticist working in DNA states),,, “There have to be other explanations,” he says.
    Peterson and his team are now going back to mammalian genomes to investigate why DNA and microRNAs give such different evolutionary trajectories. “What we know at this stage is that we do have a very serious incongruence,” says Davide Pisani, a phylogeneticist at the National University of Ireland in Maynooth, who is collaborating on the project. “It looks like either the mammal microRNAs evolved in a totally different way or the traditional topology is wrong.

    micro-RNAs and Non-Falsifiable Phylogenetic Trees – (Excellent Research) video

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.

    Orphan Genes (And the peer reviewed ‘non-answer’ from Darwinists) – video

  9. 9
    Mapou says:

    JLAfan2001 @7,

    I’m not in a good mood right now. So this means you can kiss my asteroid, if you know what I mean. All of you atheists/Darwinists and Christianity haters are the same, a bunch of lying sacks of feces, weavers of lies and deception. Take your smelly buddy Kevin for example. Here’s what the hatemonger wrote to justify accusing Casey Luskin of dishonesty:

    As the authors show, the clear majority of the gene quartets supporting tree B (8-3) fall in the slower-evolving half of these gene quartets, whereas the majority of those supporting tree A (14-10) are in the faster half, indicating that evolutionary rate heterogeneity between genes, combined with the generally faster-evolving rates in the rhabditid nematode lineage, have created artifacts that make tree A superficially seem more well-supported than tree B, and we should prefer the latter.

    In other words, that deceiving little jerk is telling us with a straight face that we should use statistics as a measure of whether or not experimenters should jettison all the observed lineages except one, so as to remain faithful to his little insignificant god, Darwin. Now, how dishonest is that? A lineage either exists or it does not. If there is any confusion or doubt, the experiment should be conducted over and over with independently obtained genomes, if necessary, and replicated by others. Code sequences don’t just appear in a genome by chance. They are either in or they are not.

    Like I said, you goats should stay downwind from the rest us. We don’t like the way you smell.

  10. 10
    Mapou says:


    Are you familiar with the concept of ‘first take the plank out of your own eye, and then you will see clearly to remove the speck from your brother’s eye.’?

    JLAfan2001 ain’t my brother. He’s a smelly goat. 🙂

  11. 11
    Mung says:

    A better metaphor? A forest of trees, where each tree represents a family/kind.

    There were no trees on the ark.

  12. 12
    Timaeus says:

    jlafan2001 wrote:

    “You guys should take a look at the three comments made under the article at Salvo. Luskin gets schooled real good.”

    Perhaps if you spent less time reading Justice League comics, and more time reading good literature, your grammar would be better. “Gets schooled real good”?

    Also, since you have at best minimal scientific training yourself — apparently no science beyond high school — and Luskin has two degrees in the natural sciences, how are you qualified to assess whether his or his critics’ arguments are valid?

    Finally, I note that you never replied to the detailed response to your theological position on the “Bowling with God” thread. I guess that critique hit dead center.

  13. 13
    Sebestyen says:

    Does anybody know how the 19+ different genetic codes are supposed to fit together with a common tree of life?

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