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No coherent “narrative” for transposable elements (jumping genes)?

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Transposable elements (transposons, jumping genes) From Genome Biology and Evolution:

At the most basic level of inquiry, the percent of a genome derived from TEs, vertebrate genomes can vary from 6 to 60%. If one takes into account aspects of TE diversity, accumulation histories, and even variation in repeat annotations themselves, it becomes difficult to build a coherent narrative that adequately explains repeat variation across vertebrates. Generally, higher levels of TE diversity correlate with the age of vertebrate lineages; lineages that have existed for longer periods, such as fishes, and deep-branching tetrapods tend to have higher TE diversity than more recent radiations, such as birds and mammals. However, as the number of vertebrate genome assemblies increases, exceptions to this pattern will become more common. Known outliers within each vertebrate lineage include the lungfish with a genome dominated by two types of non-LTR retrotransposons, and the western clawed frog whose TE content is highly biased towards DNA transposons. Woodpeckers contain almost half a million more TE copies than other birds. Among mammals, vespertilionid bats is the sole lineage exhibiting DNA transposon activity. Indeed, our view of what is ‘normal’ for broad lineage such as mammals or birds continues to expand and our understanding of TEs and their role in vertebrate genome evolution benefits greatly from understanding both general trends and outliers. Identification of the contribution of TEs to the uniqueness of each genome will be key to unravelling the impact of genome architecture on organismal evolution. [colour emphasis added] Paper. (public access) – Evolution and Diversity of Transposable Elements in Vertebrate Genomes
Cibele G Sotero-Caio Roy N Platt, II Alexander Suh David A Ray Genome Biol Evol (2017) evw264. DOI: https://doi.org/10.1093/gbe/evw264 More.

Note: From the definition of transposons at Nature: “For decades, scientists dismissed transposable elements, also known as transposons or “jumping genes”, as useless ‘junk DNA.’ But are they really?” No. But Darwinism needed that “narrative.”

See also: Jumping genes make the tree of life a bush


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2 Replies to “No coherent “narrative” for transposable elements (jumping genes)?

  1. 1
    J-Mac says:

    I’m pretty sure professor Larry Moran has some experimental evidence to explain this. After all, him and Coyne are the masters of deceit when it comes to reality and their own “reality” which is much different than the reality we live in…

  2. 2
    bornagain77 says:

    There is a ‘coherent narrative’ but it is not one that Darwinists will ever accept since it undermines Darwinian evolution and points to intelligent design.

    Firstly, Darwinists ‘predicted’ that repetitive elements were “genomic parasites” that were regarded as useless ‘junk DNA’. Yet, as with practically every other major prediction that Darwinists have made, that prediction was found to be false.

    Safeguarding genome integrity through extraordinary DNA repair – April, 2011
    Excerpt: Unlike euchromatin, where most of an organism’s genes reside and where most DNA consists of long, unrepetitive sequences of base pairs, DNA in heterochromatin consists mostly of short repeated sequences that don’t code for proteins; indeed, heterochromatin was long regarded as containing mostly “junk” DNA.
    Heterochromatin is now known to be anything but junk, playing a crucial role in organizing chromosomes and maintaining their integrity during cell division. It is concentrated near centromeres, where chromatids are in closest contact, which are required to transmit chromosomes from one generation to the next. Maintaining heterochromatin structure is necessary to the normal growth and functions of cells and organisms.

    Mutation Protocols: Cut-And-Paste DNA with Built-In Tuning Knobs – johnnyb – September 15, 2012
    Excerpt: Tuning knobs are generally implemented in the cell through short sequences of repetitive DNA (called SSRs) — one of the types of DNA previously thought to be junk.,,,
    The second mutation protocol discussed by King is the copy-and-paste protocol implemented by Transposable elements. These were previously considered “genomic parasites”, but have recently been shown to play a role in providing robust variation in organisms. In other words, transposons can import necessary functions into new sites.

    A Key Evidence for Evolution Involving Mobile Genetic Elements Continues to Crumble – Cornelius Hunter – July 13, 2014
    Excerpt: A study published last week found strong signs of function in mobile repetitive DNA elements. Mobile genetic elements have been heavily recruited by evolutionists in recent years as powerful, undeniable proofs of common ancestry. An underlying assumption in those proofs, aside from the usual non scientific metaphysics, is that such mobile elements insert themselves into the genome at random.,,,
    “The biological roles of these place-jumping, repetitive elements are mysterious.
    They are largely viewed (by Darwinists) as “genomic parasites,” but in this study, researchers found the mobile DNA can provide genetic novelties recruited as certain population-unique, functional enrichments that are nonrandom and purposeful.
    “The first shocker was the sheer volume of genetic variation due to the dynamics of mobile elements, including coding and regulatory genomic regions, and the second was amount of population-specific insertions of transposable DNA elements,” Michalak said. “Roughly 50 percent of the insertions were population unique.”

    “Most of the mammalian genome is transcribed. This generates a vast repertoire of transcripts that includes protein-coding messenger RNAs, long non-coding RNAs (lncRNAs) and repetitive sequences, such as SINEs (short interspersed nuclear elements). A large percentage of ncRNAs are nuclear-enriched with unknown function. Antisense lncRNAs may form sense-antisense pairs by pairing with a protein-coding gene on the opposite strand to regulate epigenetic silencing, transcription and mRNA stability.
    (Carrieri et al., “Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat,” Nature (2012), doi:10.1038/nature11508 )

    ENCODE Reveals Incredible Genome Complexity and Function by Jeffrey Tomkins, Ph.D. – Sept. 2012
    Excerpt: Tom Gingeras, one of the senior scientists on the ENCODE project said, “Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more.”4,,,

    Moreover, repetitive DNA was predicted to have function in 2005

    Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116.
    Excerpt: Employing an information science model, the “functionalist” perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.

    Shapiro and Sternberg Anticipated the Fall of Junk DNA – Douglas Axe – September 13, 2012
    Excerpt: “In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”
    These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.
    The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.”
    – James Shapiro

    How life changes itself: the Read-Write (RW) genome. – 2013
    Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

    Finding a read/write genome, as Shapiro terms it, directly undermines the central dogma of Darwinian evolution since it shows that it is the organism controlling the DNA and not the DNA controlling the organism as Darwinists believe in their reductionist view of biology

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: I now know as an embryologist,,,Tissues and cells, as they differentiate, modify their DNA to suit their needs. It’s the organism controlling the DNA, not the DNA controlling the organism.

    Here is a recent powerpoint presentation by Dr. Wells, starting around the 15:00 minute mark of the following video, showing that the central dogma of Darwinian evolution, i.e. “DNA makes RNA makes protein makes us”, is incorrect at every step. As well, at about the 42:00 minute mark of the video, Dr. Wells demonstrates that, during embryological development, information must somehow be coming into the developing embryo ‘from the outside’, by some ‘non-material’ method:

    Design Beyond DNA: A Conversation with Dr. Jonathan Wells – video (14:36 minute mark) – January 2017

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