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What “quote mining” really means to today’s followers of Darwin

At “HGT: Flowering plant genome captures four entire genomes,”  it was noted that

The research also shows, for the first time, that an organelle genome has captured an entire foreign genome, in this case, at least four of them. It is also the first description of a land plant acquiring genes from green algae.

Commenter Mapou writes,

The main prediction of common descent is that branches of the tree of life are strictly nested. Gene sharing between distant branches of the tree are thus forbidden by the theory of evolution.

The Darwinian theory of evolution has been falsified.

No amount of bogus claims of convergent evolution can save the theory now. Read it and weep.

and

Horizontal gene transfers high up in the tree of life is a much bigger problem for the theory of evolution than most people think. It falsifies it. The ID movement should jump on this and make it their primary focus. This is the biggest vulnerability of evolution. Don’t let the Darwinists get away with it with cockamamie pseudoscientific non-explanations like convergent evolution. Let the lay public know about this. Announce it on the rooftops.

Horizontal gene transfers are what software designers call multiple inheritance. It can only occur via intelligent design.

Assume Mapou is right.

It doesn’t matter.

If Darwin’s theory of evolution had ever been just a theory about how life forms change over time, it would have been discredited long ago by lack of evidence for its primary mechanism (natural selection acting on random mutation), together with significant evidence for alternatives like horizontal gene transfer (HGT).

But we live in an age where, while The Onion offers Darwin Christmas kitsch for fun, “evolutionary leaders of the world” apparently think that C.S. Lewis’s mock hymn to evolution is actual praise. And Darwin’s idea is supposed to be the most powerful ever. More powerful than zero, for example, or calculus.

One outcome is that Darwinian evolution is not evaluated according to the normal constraints of logic or evidence. For example, as the recent discussions around claims of quote mining show (see here also), one can quote  exact words with the exact meaning deceitfully if the net effect of the resulting communication is to cause doubts about Darwin.

It’s that simple, really. Niles Eldredge and Ian Tattersall can say, “Change in the manner Darwin expected is just not found in the fossil record” and Barry Arrington can quote them saying “Change in the manner Darwin expected is just not found in the fossil record.”

But the difference is as night and day because every true follower knows that Eldredge and Tattersall would immediately attempt to cover butt whereas Arrington would … well … conclude something unfavourable to the truth status of Darwin’s theory.

Just watch, Mapou, it’ll go the same way with horizontal gene transfer.

Suppose a Darwin notable has said that, on account of the power of Darwinian evolution, HGT seldom happens or only in a very limited way. Neither the fact that he said that nor the fact that it would be incorrect matters. His statement just falls soundlessly into the same memory hole as Kim Jong Un’s uncle. And Arrington’s act of reminding people that the Darwin notable said that would be a thought crime.

Such quotations are a thought crime because they imply that, in relation to Darwinism, facts matter. No. Darwinism is there to tell you when facts matter and when they don’t. You didn’t evolve in such a way as to know that for yourself.

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7 Responses to What “quote mining” really means to today’s followers of Darwin

  1. Hmm. You guys could bother to read the original source for once.

    1. Are these extra genes junk?

  2. A Graveyard of Foreign Genes

    The 197 foreign mitochondrial protein genes in Amborella are predominantly pseudogenes, with only 50 (25%) of them having full-length, intact open reading frames (tables S2 and S8). The intact genes are predominantly short (figs. S22 and S23), suggesting that many of these have remained intact by chance; that is, they are pseudogenes that have yet to sustain an obvious pseudogene mutation. Consistent with this, many of these intact genes are not expressed properly.

    On the basis of phylogenetic, RNA editing, and/or linkage evidence (table S9) (13), Amborella mtDNA is hypothesized to contain a functional, native copy of all but one (rpl10) of the 49 mitochondrial protein and rRNA genes inferred to be present in the ancestral angiosperm (fig. S13) (17). cDNA sequencing of 44 of the 48 native genes showed that, with one apparent exception, they are all transcribed and properly RNA edited (table S10) (13). In contrast, no transcripts were detected for many genes of foreign origin, and 13 of 14 transcribed genes of foreign angiosperm origin (eight of them intact) were poorly edited, suggesting that they are pseudogenes (table S10) (13, 19).

  3. 2. How was this lateral transfer identified? Why, phylogenetics! Part 1:

    Angiosperm Donors

    One class of plastid-derived DNA played a key role in donor identification. Phylogenetic analysis shows that most of the 138 kb of ptDNA present in Amborella mtDNA was acquired through intracellular gene transfer (IGT), that is, from the Amborella plastid genome (Fig. 2, E to H, and fig. S19). Analysis of the remaining 10 kb of ptDNA, which probably entered Amborella from foreign mitochondria, identified donors with much greater specificity than did the mitochondrial gene analyses (13). Four of the HGT plastid regions identified Fagales, Oxalidales, or the predominantly parasitic Santalales as the donor, while a fifth pointed to Magnoliidae (Fig. 2, E to H, and fig. S18). A santalalean origin is also supported by four of the five mitochondrial genes for which multiple Santalales have been sampled (fig. S14, nad1b, and fig. S20). The exceptionally high and specific similarity of two featureless regions to Ricinus communis or Bambusa oldhamii (Fig. 1B and fig. S21) identified transfers from these lineages. Finally, the exceptionally high divergence that diagnosed six angiosperm-like genes as foreign also suggests that they came from additional donors, with high mitochondrial substitution rates.

  4. Part 2:

    Because some angiosperm-HGT tracts in Amborella mtDNA are of mixed phylogenetic origin (Fig. 1) (13), some of its foreign DNA may be the product of serial, angiosperm-to-angiosperm-to-angiosperm HGT (13). In particular, the rbcL gene of santalalean origin (Fig. 2E) resides only 3 kb from the Bambusa-derived sequence on the same 27-kb foreign tract (Fig. 1B). Because all four genes of meaningful length on this tract evidently came from core eudicots (fig. S14), and because parasitic plants are especially active in mitochondrial HGT (5, 7–10), this tract probably came from a santalalean donor that had previously acquired Bambusa DNA through HGT (13). The presence of santalalean DNA in six, mostly long HGT tracts (Fig. 1A) suggests that a large portion of the foreign angiosperm DNA in Amborella came from Santalales. Indeed, RNA-editing data indicate that the 27-kb tract of putative santalalean origin may actually be part of a much larger (>105 kb) HGT tract (13).

    The reason we can identify donors in cases of HGT is precisely because their gene trees stick out like sore thumbs against the massively supported organismal phylogeny.

  5. as to: “their gene trees stick out like sore thumbs against the massively supported organismal phylogeny”

    Would this ‘massively supported organismal phylogeny’ include your literature bluffing, ad hominem attacks, and papers that directly contradict your claims Matzke?

    Does Natural Selection Leave “Detectable Statistical Evidence in the Genome”?
    Casey Luskin August 7, 2013
    Excerpt: These statistical methods that Matzke cites not only don’t demonstrate that selection has occurred, but they also do not demonstrate that stepwise evolutionary pathways are available. For that, experiments are needed. Matzke can call us “juvenile” all he wants, but the fact is, beyond a lot of hand-waving and name-calling, he has not provided an adequate account of how new genes might arise.
    http://www.evolutionnews.org/2.....75171.html

    Hopeless Matzke -David Berlinski & Tyler Hampton August 18, 2013
    http://www.evolutionnews.org/2.....75631.html

    supplemental notes:

    Evolutionist: Plants Are “Driving Me Nuts!” – Cornelius Hunter – July 2012
    Excerpt: Plants also don’t fit into the evolutionary tree very well. Their DNA comparisons are inconsistent with their visible features,,, “The old family tree was now in for a major pruning. Roses were found to be closely related to squash, strawberries to marijuana, this meat-eating pitcher plant to China’s famous rhododendrons. For centuries water lilies were thought to be nearly twins with the lotus—no longer.”
    MARK CHASE: “This, believe it or not, is the closest living relative of the lotus. This is the London plane tree or sycamore. As you can see, this is not a little water plant, this is a big tree.”
    ANDREW DARRAGH (Horticulturist, Kew Gardens): …”driving me nuts!”
    http://darwins-god.blogspot.co.....-nuts.html

    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?
    http://crev.info/2013/05/darwi.....mble-bush/

    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
    http://www.youtube.com/watch?v=MXrYhINutuI

    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.,,,
    http://darwins-god.blogspot.co.....f-how.html

    Logged Out – Scientists Can’t Find Darwin’s “Tree of Life” Anywhere in Nature by Casey Luskin – Winter 2013
    Excerpt: the record shows that major groups of animals appeared abruptly, without direct evolutionary precursors.
    Because biogeography and fossils have failed to bolster common descent, many evolutionary scientists have turned to molecules—the nucleotide and amino acid sequences of genes and proteins—to establish a phylogenetic tree of life showing the evolutionary relationships between all living organisms.,,,
    Many papers have noted the prevalence of contradictory molecule-based phylogenetic trees. For instance:
    • A 1998 paper in Genome Research observed that “different proteins generate different phylogenetic tree[s].”6
    • A 2009 paper in Trends in Ecology and Evolution acknowledged that “evolutionary trees from different genes often have conflicting branching patterns.”7
    • A 2013 paper in Trends in Genetics reported that “the more we learn about genomes the less tree-like we find their evolutionary history to be.”8
    Perhaps the most candid discussion of the problem came in a 2009 review article in New Scientist titled “Why Darwin Was Wrong about the Tree of Life.”9 The author quoted researcher Eric Bapteste explaining that “the holy grail was to build a tree of life,” but “today that project lies in tatters, torn to pieces by an onslaught of negative evidence.” According to the article, “many biologists now argue that the tree concept is obsolete and needs to be discarded.”,,,
    Syvanen succinctly summarized the problem: “We’ve just annihilated the tree of life. It’s not a tree any more, it’s a different topology entirely. What would Darwin have made of that?” ,,,
    “battles between molecules and morphology are being fought across the entire tree of life,” leaving readers with a stark assessment: “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”10,,,
    A 2012 paper noted that “phylogenetic conflict is common, and [is] frequently the norm rather than the exception,” since “incongruence between phylogenies derived from morphological versus molecular analyses, and between trees based on different subsets of molecular sequences has become pervasive as datasets have expanded rapidly in both characters and species.”12,,,
    http://www.salvomag.com/new/ar.....ed-out.php

    Orphan Genes (And the peer reviewed ‘non-answer’ from Darwinists) – video
    http://www.youtube.com/watch?v=1Zz6vio_LhY

    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.
    per nature

    micro-RNAs and Non-Falsifiable Phylogenetic Trees – (Excellent Research) – lifepsy video
    http://www.youtube.com/watch?v=qv-i4pY6_MU

    etc.. etc.. etc..

    Methinks your ‘massively supported organismal phylogeny’ is sinking in quicksand Matzke!

  6. Nick:

    The reason we can identify donors in cases of HGT is precisely because their gene trees stick out like sore thumbs against the massively supported organismal phylogeny.

    Sore thumbs, eh? You take a direct falsification of your religion and turn it around to make it appear as a confirmation. Bam! just like that, blatantly and in your face. The unmitigated gall of some people. Sheesh!

    The fact that they stick out like sore thumbs is precisely why it falsifies both common descent and Darwinian evolution. They cannot be missed. Just one (1) instance of non-nested inheritance is enough to falsify common descent. Statistics has got nothing to do with it. Zilch. Nada.

  7. If Matzke considers it a strong argument that the borrowed genes are considered to be junk (as was in fact noted in the post to which Mapou replied):

    For the record, that’s the very claim that is being steadily undermined in other venues today. (= “lots of the human genome is junk, and that’s good evidence for Darwin’s theory!”)

    If any here lack Matzke’s overriding faith in Darwinism, they should not find his argument a strong one.

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