'Junk DNA' Evolution Genomics

At Scientific American: Salamander “junk DNA” challenges long-held view of evolution

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One salamander is a very unusual life form:

View the animal up close, and another oddity becomes apparent: its cells are up to 300 times larger than those of a lizard, bird or mammal. You can see, with a simple magnifying glass, individual blood cells zipping through the capillaries in its transparent gills.

The Neuse River waterdog, Necturus lewisi, and other salamanders represent a long-standing conundrum scientists are only now starting to understand. The animal’s strange traits stem from a hidden burden: Each of its cells is bloated with 38 times more DNA than a human cell. The waterdog has the largest genome of any four-footed beast on Earth. The only comparable animals of any kind are lungfish, which also have sluggardly tendencies.

Douglas Fox, “Junk DNA Deforms Salamander Bodies” at Scientific American (February 1, 2022)

They have, we are told, 10 billion to 120 billion base pairs because, it is thought, parasitic DNA has multiplied out of control. They live a slow, dull life and can live about 100 years. They can regenerate not only limbs but brain parts.

And the challenge for evolution?

As for salamanders, one has to wonder why their burden hasn’t dragged them down to extinction. Their very perseverance suggests that our idea of evolution, particularly “survival of the fittest,” has a serious moralistic bias: Work hard, young species, hone your body and brain for high performance, and someday you will succeed. But salamanders owe their success to lying around. They have found a way to cheat the system…

The salamanders would be on death’s door if they were human. “Everything about having a large genome is costly,” Wake told me in 2020. Yet salamanders have survived for 200 million years. “So there must be some benefit,” he said. The hunt for those benefits has led to some heretical surprises, potentially turning our understanding of evolution on its head…

These bloated beasts have demonstrated, time and again, that when it comes to survival of the fittest, our notion of “fitness” is biased toward strength and agility. Genomic parasites have slowed the waterdog’s development, swelled its cells and distorted its anatomy. This odd circumstance has pushed the animal onto a bizarre evolutionary side track that redefines fitness in such a way that hearts and complex brains are reduced to an afterthought. Yet somehow the animal’s lineage persists, even as fires, floods and asteroids obliterate other species—furry, feathered and scaled—that seem more fit.

Douglas Fox, “Junk DNA Deforms Salamander Bodies” at Scientific American (February 1, 2022)

This isn’t schoolbook natural selection, that’s for sure.

6 Replies to “At Scientific American: Salamander “junk DNA” challenges long-held view of evolution

  1. 1
    polistra says:

    “Turning our knowledge on its head” = epicycles.

  2. 2
    bornagain77 says:

    In the article they claim that, “All of this suggests that although transposons are sometimes coopted by the host, they have no inherent purpose.”

    “Transposable elements (transposons, TEs, ‘jumping genes’) are short strands of repetitive DNA that can self-replicate and translocate within the eukaryotic genome, and are generally perceived as parasitic in nature.”
    – per wikipedia

    Yet, once again, empirical science itself disagrees with what Darwinists would want to presuppose to be true beforehand,

    Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni – Sept. 2021
    Discussion
    The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function (Britten and Kohne 1968; Comings 1972; Ohno 1999). This view has fundamentally changed (Biscotti, Canapa, et al. 2015), and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite.
    https://academic.oup.com/gbe/article/13/10/evab204/6361599

    Scientific Paper on Repetitive Elements Slams “Junk DNA”
    Casey Luskin – October 7, 2021
    Excerpt: After reviewing extensive evidence of function in these WEFs, they offer a striking finding:
    “The days of “junk DNA” are over.”,,,,
    What’s striking about this passage is not only that the evidence for function in junk DNA is so overwhelming that they declare “The days of ‘junk DNA’ are over,” but also that these authors remember a day when “the common doctrine was that the nonprotein coding part of eukaryotic genome” consisted of “’useless’ sequences, often organized in repetitive elements.”
    https://evolutionnews.org/2021/10/scientific-paper-on-repetitive-elements-slams-junk-dna/

    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.
    http://phys.org/news/2011-04-s.....y-dna.html

    Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin’ – James Shapiro – Sept. 12, 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.
    http://www.huffingtonpost.com/.....73935.html

    Why repetitive DNA is essential to genome function – James A Shapiro 1 , Richard von Sternberg – 2005
    Abstract excerpt:
    There are clear theoretical reasons and many well-documented examples which show that repetitive DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail.
    https://pubmed.ncbi.nlm.nih.gov/15921050/

  3. 3
    martin_r says:

    no way !
    another Darwinian ‘long-held view’ is challenged ????

    can’t be….

  4. 4
    martin_r says:

    View the animal up close, and another oddity becomes apparent: its cells are up to 300 times larger than those of a lizard, bird or mammal.

    300 times larger than other cells ???

    i was wondering what universal common ancestor would say …

  5. 5
    PaV says:

    From the SA article that’s linked, it appears that the working hypothesis for this huge genome is based on the observation that ‘transposons’ are removed from the salamander’s genome at a slower rate than most all other living beings. Now, why might that be?

    It’s interesting that the other organism with excessively large genomes are the lungfish. Both the salamander and the lungfish are found at the border of water and land. The salamander has many predators. It doesn’t really have any significant defense mechanism. But, apparently, it’s ONE defense mechanism is the ability to reproduce itself, including removed heart valves and portions of their brain. The transposons have the ability to turn genes on and having a whole bunch of them could be handy in the case of losing the lower half of your body.

  6. 6
    Querius says:

    PaV @5,

    From the SA article that’s linked, it appears that the working hypothesis for this huge genome is based on the observation that ‘transposons’ are removed from the salamander’s genome at a slower rate than most all other living beings. Now, why might that be?

    Oh, that’s easy to answer from the perspective of a Darwinist: It musta evolved that way to survive environmental challenges that are “currently not fully understood yet” (pseudo-scientific jargon for “we’re clueless”).

    -Q

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