Genomics Intelligent Design

Researchers discover sophisticated hospital system for DNA in cells

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DNA illustration (stock image). | Credit: (c) Design Cells / stock.adobe.com
DNA art/© Design Cells, Adobe Stock

Challenging the belief that DNA “floats aimlessly”:

An elaborate system of filaments, liquid droplet dynamics and protein connectors enables the repair of some damaged DNA in the nuclei of cells, researchers at the University of Toronto have found. The findings further challenge the belief that broken DNA floats aimlessly — and highlight the value of cross-disciplinary research in biology and physics.

Double-strand DNA breaks are especially toxic to cells, and researchers had assumed for decades that these breaks floated inside cell nuclei without direction, until they trigger other cellular changes or happen on a fixer mechanism.

That thinking began to change in 2015, when Karim Mekhail and his lab showed that damaged DNA can be intentionally transported by motor protein ‘ambulances’ to DNA ‘hospitals,’ areas enriched with certain repair factors in the nuclei. The researchers later worked with U of T aerospace engineers to show that after a single double-strand break, DNA travels for repair via long ‘autobahns’ of thread-like microtubules, which are also moving…

The most surprising finding came after several cycles of droplet fusion, the researchers found. “It was very bizarre and totally unexpected, I still remember the day,” Mekhail says. Oshidari observed that the larger droplets initiate an internal concentration of filament building blocks, forcing creation of a kind of self-interlocking brick road, which together with the spidery webs allow DNA to hook onto the longer autobahn filaments.

The complex process is easy to miss when looking at DNA damage sites, says Mekhail, largely because imaging in the field has become highly automated. Most software has been set up to see what has already been seen. “We can’t rely on the old ways of observing,” he says. “We need to update our software and also go back to looking with the human eye, guided by simulations when needed.” University of Toronto, “Genome stability: Intricate process of DNA repair discovered” at ScienceDaily

The researchers, fearing that their media release was too long already, never got around to explaining intracellular health care policy, which would have easily run to 30,000 pages of administrese… 😉

Funny how the new finds never seem to support natural selection acting on random mutations (Darwinism) but always intricate nests of patterns inside patterns.

Hat tip: Philip Cunningham

3 Replies to “Researchers discover sophisticated hospital system for DNA in cells

  1. 1
    jawa says:

    The ScienceDaily paper review says “The findings further challenge the belief that…”
    Do they have “beliefs” in science? Do scientists believe things related to their research?
    🙂

  2. 2
    bornagain77 says:

    Here are a few more of the sophisticated repair systems found for DNA:

    A proofreading system that catches almost all errors
    A mismatch repair system to back up the proofreading system
    Photoreactivation (light repair)
    Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase
    Base excision repair
    Nucleotide excision repair
    Double-strand DNA break repair
    Recombination repair
    Error-prone bypass
    http://www.newgeology.us/presentation32.html

    A Look at the Quality Control System in the Protein Factory – JonathanM – March 2012
    Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed.
    http://www.evolutionnews.org/2.....57791.html

    Researchers discover how key enzyme repairs sun-damaged DNA – July 2010
    Excerpt: Ohio State University physicist and chemist Dongping Zhong and his colleagues describe how they were able to observe the enzyme, called photolyase, inject a single electron and proton into an injured strand of DNA. The two subatomic particles healed the damage in a few billionths of a second. “It sounds simple, but those two atomic particles actually initiated a very complex series of chemical reactions,” said Zhong,,, “It all happened very fast, and the timing had to be just right.”
    http://www.physorg.com/news199111045.html

    etc.. etc…

    The following paper on DNA repair is simply jaw dropping..

    Extreme Genome Repair – 20 March 2009
    Excerpt: If its naming had followed, rather than preceded, molecular analyses of its DNA, the extremophile bacterium Deinococcus radiodurans might have been called Lazarus. After shattering of its 3.2 Mb genome into 20–30 kb pieces by desiccation or a high dose of ionizing radiation, D. radiodurans miraculously reassembles its genome such that only 3 hr later fully reconstituted nonrearranged chromosomes are present, and the cells carry on, alive as normal.
    http://www.sciencedirect.com/s.....7409002657

    In the lab, scientists coax E. coli to resist radiation damage – March 17, 2014
    Excerpt: ,,, John R. Battista, a professor of biological sciences at Louisiana State University, showed that E. coli could evolve to resist ionizing radiation by exposing cultures of the bacterium to the highly radioactive isotope cobalt-60. “We blasted the cultures until 99 percent of the bacteria were dead. Then we’d grow up the survivors and blast them again. We did that twenty times,” explains Cox.
    The result were E. coli capable of enduring as much as four orders of magnitude more ionizing radiation, making them similar to Deinococcus radiodurans, a desert-dwelling bacterium found in the 1950s to be remarkably resistant to radiation. That bacterium is capable of surviving more than one thousand times the radiation dose that would kill a human.
    http://www.news.wisc.edu/22641

    As to how the bacterium knows exactly how to ‘miraculously reassemble its genome’ into ‘fully reconstituted nonrearranged chromosomes’ no one, especially including Darwinists, has a clue. In fact, such a ‘miraculous’ feat of ‘fully reconstituted’ reassembly of DNA is completely inexplicable to the reductive materialistic presuppositions of Darwinists, Presuppositions that hold that random mutations to DNA are the primary means by which all species on earth have originated.

    Modern Synthesis
    Excerpt: The Modern Synthesis introduced several changes in how evolution and evolutionary processes were conceived. It proposed a new definition of evolution as “changes in allele frequencies within populations , ” thus emphasizing the genetic basis of evolution.,,,
    Mutation is a weak evolutionary force but is crucial because all genetic variation arises originally from mutation, alterations in the DNA sequences resulting from errors during replication or other factors.,,,
    Advantageous mutations may be incorporated into the population through the process of natural selection. Changes in species therefore occur gradually through the accumulation of small changes. The large differences that are observed between species involve gradual change over extensive time periods.
    https://www.encyclopedia.com/earth-and-environment/ecology-and-environmentalism/environmental-studies/modern-synthesis

    As sophisticated DNA repair in general, and Deinococcus radiodurans in particular, make clear, DNA repair is completely incompatible with Darwinian evolution in principle.

    The Darwinism contradiction of repair systems
    Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.
    http://www.uncommondescent.com.....r-systems/

    Contradiction in evolutionary theory – video – (The contradiction between extensive DNA repair mechanisms and the necessity of ‘random mutations/errors’ for Darwinian evolution)
    http://www.youtube.com/watch?v=dzh6Ct5cg1o

    The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011
    Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce.
    http://www.benthamscience.com/.....OEVOLJ.pdf

  3. 3
    bornagain77 says:

    And as Deinococcus radiodurans in particular made clear, and as Dr. Jonathan Wells states in the following article, 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.”

    Ask an Embryologist: Genomic Mosaicism – Jonathan Wells – February 23, 2015
    Excerpt: humans have a “few thousand” different cell types. Here is my simple question: Does the DNA sequence in one cell type differ from the sequence in another cell type in the same person?,,,
    The simple answer is: We now know that there is considerable variation in DNA sequences among tissues, and even among cells in the same tissue. It’s called genomic mosaicism.
    In the early days of developmental genetics, some people thought that parts of the embryo became different from each other because they acquired different pieces of the DNA from the fertilized egg. That theory was abandoned,,,
    ,,,(then) “genomic equivalence” — the idea that all the cells of an organism (with a few exceptions, such as cells of the immune system) contain the same DNA — became the accepted view.
    I taught genomic equivalence for many years. A few years ago, however, everything changed. With the development of more sophisticated techniques and the sampling of more tissues and cells, it became clear that genetic mosaicism is common.
    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.
    http://www.evolutionnews.org/2.....93851.html

    Contrary to expectations, genes are constantly rearranged by cells – July 7, 2017
    Excerpt: Contrary to expectations, this latest study reveals that each gene doesn’t have an ideal location in the cell nucleus. Instead, genes are always on the move. Published in the journal Nature, researchers examined the organisation of genes in stem cells from mice. They revealed that these cells continually remix their genes, changing their positions as they progress through different stages.
    https://uncommondescent.com/intelligent-design/researchers-contrary-to-expectations-genes-are-constantly-rearranged-by-cells/

    Darwinists simply have no clue why this should be, nor do they have any evidence supporting their primary claim that mutations to DNA can generate new biological forms and/or new species.

    As Jonathan Wells states in the following article, Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.

    Jonathan Wells: Far from being all-powerful, DNA does not wholly determine biological form – March 31, 2014
    Excerpt: Studies using saturation mutagenesis in the embryos of fruit flies, roundworms, zebrafish and mice also provide evidence against the idea that DNA specifies the basic form of an organism. Biologists can mutate (and indeed have mutated) a fruit fly embryo in every possible way, and they have invariably observed only three possible outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly.
    https://uncommondescent.com/intelligent-design/jonathan-wells-far-from-being-all-powerful-dna-does-not-wholly-determine-biological-form/

    Response to John Wise – October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12. None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–,,,
    (As Jonathan Wells states),,, We can modify the DNA of a fruit fly embryo in any way we want, and there are only three possible outcomes:
    A normal fruit fly;
    A defective fruit fly; or
    A dead fruit fly.
    http://www.evolutionnews.org/2.....38811.html

    Thus in conclusion, finding multiple layers of sophisticated DNA repair mechanisms in life is yet another falsification of the core Darwinian presupposition of reductive materialism.

    Darwinists, with their reductive materialistic framework, simply are not even on the correct theoretical foundation in order to properly understand molecular biology in the first place.

    Darwinian Materialism vs. Quantum Biology – Part II – video
    https://www.youtube.com/watch?v=oSig2CsjKbg

    Darwinism vs Biological Form – video
    https://www.youtube.com/watch?v=JyNzNPgjM4w

    Of supplemental note, this irresolvable dilemma for reductive materialists was anticipated thousands of years ago by Aristotle’s argument for final causality.

    Final Causation, var. Final Causality
    Excerpt: Efficient causation is that kind of causation whereby the parts compose the whole; final causation is that kind of causation whereby the whole calls out its parts. Final causation without efficient causation is helpless; mere calling for parts is what a Hotspur, or any man, may do; but they will not come without efficient causation. Efficient causation without final causation, however, is worse than helpless, by far; it is mere chaos; and chaos is not even so much as chaos, without final causation; it is blank nothing.
    http://www.commens.org/diction.....-causation

    “If you have no God, then you have no design plan for the universe. You have no prexisting structure to the universe.,, As the ancient Greeks held, like Democritus and others, the universe is flux. It’s just matter in motion. Now on that basis all you are confronted with is innumerable brute facts that are unrelated pieces of data. They have no meaningful connection to each other because there is no overall structure. There’s no design plan. It’s like my kids do ‘join the dots’ puzzles. It’s just dots, but when you join the dots there is a structure, and a picture emerges. Well, the atheists is without that (final picture). There is no preestablished pattern (to connect the facts given atheism).”
    Pastor Joe Boot – quote taken from 13:20 minute mark of the following video:
    Defending the Christian Faith – Pastor Joe Boot – video
    https://youtu.be/wqE5_ZOAnKo?t=797

    The fact that ‘the whole’ can never be reduced to ‘the parts’, as is assumed within the reductive materialism of Darwinian evolution, also plays out with Gödel’s incompleteness theorem as well it plays out with recent findings in quantum mechanics:
    https://uncommondescent.com/evolution/huge-mystery-why-are-embryos-timed-correctly/#comment-692122

    Psalm 139: 13-16
    For you created my inmost being;
    you knit me together in my mother’s womb.
    I praise you because I am fearfully and wonderfully made;
    your works are wonderful,
    I know that full well.
    My frame was not hidden from you
    when I was made in the secret place,
    when I was woven together in the depths of the earth.
    Your eyes saw my unformed body;
    all the days ordained for me were written in your book
    before one of them came to be.

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