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Another layer of protection for DNA that just happened to evolve…

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Probably in a short period of time, in relation to life on Earth:

Researchers from Case Western Reserve University have identified a new mechanism by which a protein known for repairing damaged DNA also protects the integrity of DNA by preserving its structural shape.

The discovery, involving the protein 53BP1, offers insight into understanding how cells maintain the integrity of DNA in the nucleus, which is critical for preventing diseases like premature aging and cancer…

53BP1 is a large protein known for determining how cells will repair a particular type of DNA damage—DNA double-strand break (DSB), in which the two strands of DNA are both broken, leaving a free DNA end floating around in the cell’s nucleus.

When DSB occurs, if not repaired, DNA ends could fuse to what it should not under normal conditions, which leads to the disruption of genetic information. In the short term, cells with unrepaired DNA may kill themselves off; but if a cell lost this self-surveillance, it may start the journey toward cancer.

In this study, the team discovered 53BP1 has a biological function in mediating the structure of DNA, specifically at a highly compacted region called heterochromatin.

The researchers found that this new function involves a new form of activity of 53BP1, in which the protein accumulates at the condensed DNA regions and forms small liquid droplets—a process called liquid-liquid phase separation, similar to mixing oil with water for salad dressing.

Case Western Reserve University, “Case Western Reserve University research team identifies new mechanism for protecting DNA” at The Daily (January 18, 2022)

Darwinism was easier back when cells were just blobs of protoplasm.

The paper is open access.

Comments
"It's simply a matter of the other side waving the "white flag." True. But to them it's a matter of hanging on until they find another theory to try to hold up the materialist paradigm (which maybe they'll come up with something... but it isn't real hopeful, and still not probably or plausible really) Never conflate the issue... this is a contention on worldviews, not science/truth.zweston
January 28, 2022
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Jerry:
Several things. No one is underestimating Mendel. Certainly not me.
But modern genetics is the heritability of characteristics. That is all the modern synthesis really is. They may claim more but that’s what it is. (Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms – Wikipedia) But Jerry, it was Mendel who demonstrated that genetics works via inheritance. This is what hybrids are all about. The Modern Synthesis is the work of Darwinists trying to survive the discovery of Mendelian genetics--not the other way around; that is, they didn't "add" genetics to Darwinism but "added" Darwinism to genetics. Hence, R.A. Fisher's, "The Genetical Theory of Natural Selection."
Variation comes in many forms. I believe Allen McNeill when he used to post here had 50+ engines of variation. But all to DNA.
Yes, I remember the exchange well. But what has become clear is that "evolution" has more to do with the "loss" of genetic material than any gain. Almost six years ago I declared victory because of this new discovery--for Darwinism had nothing left. ( See, The War Is Over; We Won)
Horizontal gene transfer and directed mutations are just a subset of them and work on DNA. Therefore they are genetics.
This makes you sound like a "materialist." Maybe you are; I don't know. And, it's not really important. Here's a 'for instance': They are building a levitating train system. Through the use of strong magnetic fields, the train is powered and actually 'hovers' over the rails. Now, is the metal in the train "causing" the train to hover, or, is the metal in the train simply reacting to the magnetic field? If you were someone from the 17th century, you would describe this as some kind of metal that is able to defy gravity. You would be convinced, in your ignorance of electro-magnetism, that this metal is some kind of special metal that has the property whereby it can defy gravity. "Correlation is not causation," even when it comes to genomes. Any "effect" of intelligence MUST BE realized in the genome--where else could it take place.
PaV: You seem almost enamored with the study of genetics. Its charms have deceived you, I’m afraid. Just the opposite. I’m saying genetics and DNA is irrelevant. I’ve made that statement several times. But Darwinian processes are just genetic processes and very important but irrelevant in the Evolution debate.
Maybe we're saying the same thing, then.
I’m interested in winning the argument and denigrating Darwin is a way to loose the debate. Framing his discovery in terms of its actual relevance is a way to win.
But this implies that Darwinists can be persuaded. To a Darwinist, anyone espousing ID thoughts is ignorant and an IDiot. I declared we had "won the war" back in 2016 because I knew that they had no sensible argument to be made, but, that they would never admit to that. As I said back in 2016, paraphrasing Max Planck, “a theory does not prove itself right; it’s just that the scientists who opposed it eventually die.” We simply have to wait for those who are in charge of the scientific oligarchy to pass from this world so as to let a younger generation, able and willing to deal with the obvious failings of Darwinian theory, to relegate Darwinism to the "dust heap of history." Currently, Lamarckism is being lifted out of this "dust heap" and finding its proper place. But, of course, Lamarckism, like Darwinism, is a 19th century theory. Jerry, you can argue all you want with EBs/Darwinists, but it will get you nowhere. I don't waste my time on that anymore. Since 2016, I have posted relatively little here at UD. The war was won. I put away my military gear. It's simply a matter of the other side waving the "white flag."PaV
January 26, 2022
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You are not giving Mendel his due and, in my opinion, while you’ve overinflating the importance of genetics when it comes to the Modern Synthesis. Horizontal gene transfer and directed mutations make the Modern Synthesis an almost meaningless scientific point of view.
Several things. No one is underestimating Mendel. Certainly not me. But modern genetics is the heritability of characteristics. That is all the modern synthesis really is. They may claim more but that’s what it is. (Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms - Wikipedia) Variation comes in many forms. I believe Allen McNeill when he used to post here had 50+ engines of variation. But all to DNA. Horizontal gene transfer and directed mutations are just a subset of them and work on DNA. Therefore they are genetics.
You seem almost enamored with the study of genetics. Its charms have deceived you, I’m afraid
Just the opposite. I’m saying genetics and DNA is irrelevant. I’ve made that statement several times. But Darwinian processes are just genetic processes and very important but irrelevant in the Evolution debate I’m interested in winning the argument and denigrating Darwin is a way to loose the debate. Framing his discovery in terms of its actual relevance is a way to win. Aside: Mendel never gets mentioned in the Evolution debate.jerry
January 26, 2022
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Jerry: You make Darwin out to sound like Mendel. Lamarck, and other naturalists in Darwin's time, understood "inheritability." That is NOT, Darwin's "contribution." His "contribution" is two-fold, but linked: (1) Natural Selection and (2) the Principle of Divergence. It was Wallace's co-discovery of the "Principle of Divergence" in the Malay Archipelago that, in fact, caused Darwin to publish. Darwin tells us that it is (external) nature itself (unlike Lamarck where it is "internal" nature at work) that selects advantageous traits which are then handed down to its descendants with this process finally reaching the point where the 'descendant' it so better adapted to an environment that it takes over the niche of the progenitor species, with the progenitor species now going extinct and disappearing. That's his theory. He knew nothing of genetics. Naturalist of his day, and Lamarck in particular, accepted the notion of the inheritance of traits: what else does "acquired characteristics" mean? You are not giving Mendel his due and, in my opinion, while you've overinflating the importance of genetics when it comes to the Modern Synthesis. Horizontal gene transfer and directed mutations make the Modern Synthesis an almost meaningless scientific point of view. You seem almost enamored with the study of genetics. Its charms have deceived you, I'm afraid. :)PaV
January 26, 2022
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No problem Martin_r, Another interesting tidbit that brings the “mutation protection paradox” for Darwinists into even more stark relief are these findings from ancient bacteria. Ancient bacteria spores recovered from amber crystals and salt crystals, which are tens to hundreds of millions of years old, have been 'revived'. And these ancient 'revived' bacteria have been compared to their living descendants of today. To the disbelieving shock of Darwinists, “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.”
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; - 2002 “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637
Moreover, in terms of morphology, billion year old bacteria "surprisingly looked exactly like modern species," and the similarity in morphology is widespread among fossils of [varying] times,”
Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330
Of related note:
Scientists find signs of life in Australia dating back 3.48 billion years - Thu November 14, 2013 Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”... “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,” http://www.cnn.com/2013/11/13/world/asia/australia-ancient-life/ Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13 Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages. http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1
To say that these findings from ancient bacteria are unexpected under Darwinian presuppositions is a gross understatement. It is, basically, a straight up refutation of the core Darwinian presupposition that biological form and genetic sequences are (fairly) 'plastic' and that existing biological forms and genetic sequences are able to (fairly) easily morph into new biological forms and new genetic sequences. Quote: "You, (materialistic philosophers), place matter before life and you decide that matter has existed for all eternity. How do you know that the incessant progress of science will not compel scientists to consider that life has existed during eternity, and not matter?" - Louis Pasteur - has been honoured as the "father of bacteriology" (per wikipedia)
Louis Pasteur on life, matter, and spontaneous generation - June 21, 2015 "Science brings men nearer to God.,, Posterity will one day laugh at the foolishness of modern materialistic philosophers. The more I study nature, the more I stand amazed at the work of the Creator. I pray while I am engaged at my work in the laboratory.,, The Greeks understood the mysterious power of the below things. They are the ones who gave us one of the most beautiful words in our language, the word enthusiasm: a God within.,,, I have been looking for spontaneous generation for twenty years without discovering it. No, I do not judge it impossible. But what allows you to make it the origin of life? You place matter before life and you decide that matter has existed for all eternity. How do you know that the incessant progress of science will not compel scientists to consider that life has existed during eternity, and not matter? You pass from matter to life because your intelligence of today cannot conceive things otherwise. How do you know that in ten thousand years, one will not consider it more likely that matter has emerged from life? You move from matter to life because your current intelligence, so limited compared to what will be the future intelligence of the naturalist, tells you that things cannot be understand otherwise. If you want to be among the scientific minds, what only counts is that you will have to get rid of a priori reasoning and ideas, and you will have to do necessary deductions not giving more confidence than we should to deductions from wild speculation." [en francais, Pasteur et la philosophie, Patrice Pinet, Editions L’Harmattan, p. 63.] https://uncommondescent.com/intelligent-design/louis-pasteur-on-life-matter-and-spontaneous-generation/
Verse: "In him was life, and that life was the light of all mankind."
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind.
bornagain77
January 26, 2022
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BA77 thanks for bringing the "mutation protection paradox’" to my attention ... I am glad that at least one Darwinist noticed :))) ha ha ... i like this part (from that Darwinian paper you posted above ):
This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation. https://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf
needs further investigation ? no kidding...martin_r
January 25, 2022
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Poor Jerry one-note sang out with "gusto" And just overlorded the place Poor Jerry one-note yelled willy nilly Until he was blue in the face For holding one note was his ace Couldn't hear the brass Couldn't hear the drum He was in a class by himself, by gum!Belfast
January 25, 2022
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What will it take to dethrone him?
Stop criticizing him. Give him his due. How can one criticize someone who was so obviously right about heritability. But then point out heritability has nothing to do with Evolution. His ideas are extremely relevant to genetics and thus important. And DNA is only about genetics. Every time ID or this site discusses DNA it reinforces that is what Evolution is about and that Darwin got it right. It’s guaranteed not to win the argument.jerry
January 25, 2022
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Where are the darwinists with their counter arguments and complaints about hell?zweston
January 25, 2022
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Random wasn't a whole lot easier in Darwin's era. Optical microscopes and the craft of staining were pretty well developed. The inner workings of cells, and the behaviors of cells, were visible and often drawn. Every advance in magnification has found MORE design, but there was already no excuse to assume randomness.polistra
January 25, 2022
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Yes. Darwin knew nothing of Mendelian genetics, nor of the complexity of cells (just protoplasm), nor of DNA and its correction mechanisms, nor of the complete lack of fossils in deep time, yet his theory still remains with us. Incredible. What will it take to dethrone him? I'm guessing a miracle.PaV
January 25, 2022
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Martin_r, you might appreciate just how clearly the following experiments demonstrated the fact that "repair mechanisms are incompatible with Darwinism in principle", "miraculously" incompatible at that,
Extreme Genome Repair - 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.ncbi.nlm.nih.gov/pmc/articles/PMC3319128/ 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
bornagain77
January 25, 2022
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The bottom line is that repair mechanisms are incompatible with Darwinism in principle.
exactly ... in my opinion, any repair mechanism is an ultimate proof of intelligence / engineering ... and like i said, if you want to repair something, first, you need to know it is broken... and indeed, there are DNA damage sensors inside the cell ... But the main question is, how a blind unguided natural process knows, that something is broken ??? How a blind unguided process with no foresight knows, that this is not the way it is supposed to be ... As we can see In Darwinian fantasy world, everything is possible ...martin_r
January 25, 2022
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BA77
Yet, finding such (very) sophisticated repair mechanisms maintaining the ‘integrity of DNA’ in the cell is fundamentally at odds with Darwinian claim that ‘mutations/errors’ to DNA are ultimately responsible for all the diversity of life we see on earth.
yes, this fundamental Darwinian claim/idea is absurd in the highest possible degree ... and like i said, it is very disturbing, that smart well educated Darwinian scientists accept such absurd claims ...martin_r
January 25, 2022
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as to, "cells maintain the integrity of DNA in the nucleus, which is critical for preventing diseases like premature aging and cancer…" The (very) sophisticated and overlapping repair mechanisms found for maintaining the 'integrity of DNA" thus far include, (but are not limited to), the following:
Debunking Evolution - the clash between theory and reality Excerpt: 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 40,,, http://www.newgeology.us/presentation32.html
Yet, finding such (very) sophisticated repair mechanisms maintaining the 'integrity of DNA' in the cell is fundamentally at odds with Darwinian claim that 'mutations/errors' to DNA are ultimately responsible for all the diversity of life we see on earth. As the preceding article went on to note, "But the (sophisticated repair) mechanisms not only remove harmful mutations from DNA, they would also remove mutations that evolutionists believe build new parts. The evolutionist is stuck with imagining the evolution of mechanisms that prevent evolution,"
Harmful mutations happen constantly. Without repair mechanisms, life would be very short indeed and might not even get started because mutations often lead to disease, deformity, or death. So even the earliest, "simple" creatures in the evolutionist's primeval soup or tree of life would have needed a sophisticated repair system. But the (sophisticated repair) mechanisms not only remove harmful mutations from DNA, they would also remove mutations that evolutionists believe build new parts. The evolutionist is stuck with imagining the evolution of mechanisms that prevent evolution, all the way back to the very origin of life. http://www.newgeology.us/presentation32.html
And in the following study, this contradiction between the necessity of mutations/errors in Darwinian theory, and the reality of sophisticated repair mechanisms that prevent unwanted mutations/errors from happening to DNA, is termed the 'mutation protection paradox'.
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. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." https://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf
So again, finding (very) sophisticated repair mechanisms protecting the 'integrity of DNA' is fundamentally at odds with the Darwinian belief that mutations/errors are ultimately responsible for all the diversity of life we see on earth. As the following article states, "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."
The Darwinism contradiction of repair systems - 2009 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. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/
Of supplemental note: the following articles give us a (small) glimpse into just how (very) sophisticated some of these repair mechanisms for DNA actually are,
The Chromosome in Nuclear Space – Stephen L. Talbott Talbott: If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled? Obviously it must be possible, however difficult to conceive — and in fact an endlessly varied packing and unpacking is going on all the time.,,, Managing the Twists Perhaps none of this helps us greatly to understand how the extraordinarily long chromosome, tremendously compacted to varying degrees along its length, can maintain itself coherently within the functioning cell. But here’s one relevant consideration: there are enzymes called topoisomerases, whose task is to help manage the forces and stresses within chromosomes. Demonstrating a spatial insight and dexterity that might amaze those of us who have struggled to sort out tangled masses of thread, these enzymes manage to make just the right local cuts to the strands in order to relieve strain, allow necessary movement of individual genes or regions of the chromosome, and prevent a hopeless mass of knots. Some topoisomerases cut just one of the strands of the double helix, allow it to wind or unwind around the other strand, and then reconnect the severed ends. Other topoisomerases cut both strands, pass a loop of the chromosome through the gap thus created, and then seal the gap again. (Imagine trying this with miles of string crammed into a tennis ball — without tying the string into knots!) I don’t think anyone would claim to have the faintest idea how this is actually managed in a meaningful, overall, contextual sense, although great and fruitful efforts are being made to analyze isolated local forces and “mechanisms”. http://natureinstitute.org/txt/st/mqual/genome_2.htm Quantum Dots Spotlight DNA-Repair Proteins in Motion – March 2010 Excerpt: “How this system works is an important unanswered question in this field,” he said. “It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It’s akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour.” – Dr. Bennett Van Houten – http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Quote and Verse
“applying Darwinian principles to problems of this level of complexity is like putting a Band-Aid on a wound caused by an atomic weapon. It’s just not going to work.” – David Berlinski Psalm 139:13-14 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.
bornagain77
January 25, 2022
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one thing is to repair something, but another thing is to know, that there is something broken ... What a surprise - inside a cell there are DNA damage sensors ...
DNA Damage Sensing by the ATM and ATR Kinases In eukaryotic cells, maintenance of genomic stability relies on the coordinated action of a network of cellular processes, including DNA replication, DNA repair, cell-cycle progression, and others. The DNA damage response (DDR) signaling pathway orchestrated by the ATM and ATR kinases is the central regulator of this network in response to DNA damage. Both ATM and ATR are activated by DNA damage and DNA replication stress, but their DNA-damage specificities are distinct and their functions are not redundant. Furthermore, ATM and ATR often work together to signal DNA damage and regulate downstream processes. Here, we will discuss the recent findings and current models of how ATM and ATR sense DNA damage, how they are activated by DNA damage, and how they function in concert to regulate the DDR. https://cshperspectives.cshlp.org/content/5/9/a012716.full
Of course, when you want to repair something, first you need to know that it is broken. They you need to know how to repair it ... and then, eventually, to check that the repair was successful ... And that is exactly what we see inside the cell ... What level of faith is required to believe that all this were invented by some mysterious blind unguided process ? Really, what level of faith is required ? Darwinists are the most religious people in the universe :)))))martin_r
January 24, 2022
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let me also add:
a new mechanism by which a protein known for repairing damaged DNA also protects the integrity of DNA by preserving its structural shape.
Darwinists discover more and more mechanisms by which a cell protects the information/integrity of DNA ... but, after all these discoveries, Darwinists still BELIEVE, that mutations created millions of kinds of species we see today ... so how absurd it is ? What is wrong with these people ? These people are very smart, no doubts, so what is wrong with them ?martin_r
January 24, 2022
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Darwinism was easier back when cells were just blobs of protoplasm
touche ... ... but Darwinists stay the same .... doesn't matter what they discover ... still the same ... still in 19th century .... anyway, it is very disturbing what smart educated Darwinian scientists are willing to accept ...martin_r
January 24, 2022
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