Amazing DNA Repair process further detailed

_{David L. Hagen

September 10, 2015

Biophysics, Darwinism, Design inference, Genomics, Intelligent Design, Irreducible Complexity, specified complexity}

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Rockefeller University researchers

found that part of a DNA repair protein known as 53BP1 fits over the phosphorylated part of H2AX “like a glove,” says Kleiner. This interaction helps bring 53BP1 to the site of DNA damage, where it mediates the repair of double-stranded breaks in DNA by encouraging the repair machinery to glue the two ends back together.

New findings shed light on fundamental process of DNA repair

What are the prospects of a DNA self replicating entity surviving with rapid cumulative DNA mutations until it assembles the DNA repair mechanism – by random stochastic processes?

Paper: Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response Ralph E Kleiner et al. Nature Chemical Biology (2015) 07 September 2015 doi:10.1038/nchembio.1908

For context, see John C. Sanford’s “Genetic Entropy and the Mystery of the Genome.”

For such insightful details elegantly explained, see Dr. Howard Glicksman’s Exercise Your Wonder: Beyond Irreducible Complexity. e.g.,
CAUTION: ENZYMES AT WORK: Part III: Anti-Clotting

Comments

Ms. O'Leary, Semi-off topic. My church recently had a biologist publish a blog post on why he thinks evolution does not contradict the bible and he criticized intelligent design. He basically assumed irreducible complexity is the only idea ID has and refuted it by saying that sometimes engineers use evolutionary ideas for making new things. I had a lot of comments that I could have made to him, but I decided to do a quick search online to see if there was any new stuff by Michael Behe. And it seems like he has kind of taken a hiatus from speaking, debating and blogging. Do you know what is up with him? Can we expect any more books or articles on irreducible complexity or the Edge of Evolution? thanks,Collin_{September 18, 2015
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But can't the Diety "DEEP TIME"explain all this?ayearningforpublius_{September 13, 2015
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But can't the deity "DEEP TIME" explain this?ayearningforpublius_{September 13, 2015
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What is the perfect rebuttal to Evolution: DNA, even before these findings. Only a religious fanatic could claim that DNA was not designed. It is even more true now.Peter_{September 11, 2015
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What are the prospects of a DNA self replicating entity surviving with rapid cumulative DNA mutations until it assembles the DNA repair mechanism – by random stochastic processes?
This is, of course, a show stopper for the Darwin parade. But for believers, there is no such thing as a show stopper. Their faith is able to move any mountain necessary. Since a DNA repair mechanism exists, it's obvious it had to have evolved. It's existence is proof! I mean, that's the only "scientific" answer there is, right? Materialist "reasoning"! lol. And, of course, it is us 'creationist fanatics' who are anti-science and hinder the efforts of all real scientists by appealing to some unseen supernatural entity to explain the problem. If we just wait another 1,000 years, certainly "SCIENCE" will figure it out. (This allows them to believe whatever they want without being held accountable for their faith. It allows them to have faith while at the same time criticizing us for faith because their faith is in blind purposeless natural processes. This qualifies their faith as "scientific" and therefore all is well. So, basically, using this approach, there is NO EVIDENCE that will ever convince these adherents to the tenets of Materialism. The problems, no matter how insurmountable they may seem now are irrelevant. Some day, we will figure it out they hope. It's an ingenious way to dismiss any & all evidence that challenges their beliefs. A DNA self repair mechanism? Ho hum! So what! Who cares! No big deal! old news! What's all the fuss about? Some day we'll figure it out.tjguy_{September 11, 2015
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Oh Yeah! :) https://www.youtube.com/watch?v=SU0Ypufo6BMbornagain77_{September 11, 2015
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BA77 #7, Oh yeah! :)Box_{September 11, 2015
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Box at 4 & 5 per Talbott: Top 10 Greatest In Your Face Dunks of All Time https://www.youtube.com/watch?v=epoqTYDzsDU :)bornagain77_{September 11, 2015
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What is it about the word, 'random' you people don't understand, eh? Come on! Out with it! Oh.... it's exemplified in the article above to anyone with an IQ in double figures is it? I see.... Well, we believe in 'meaning horizons', as well as event-horizons. There are circumstances when the meanings of words no longer ... errrr... mean what they're meant to.Axel_{September 11, 2015
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// Follow-up #4
Talbott: 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".
Box_{September 11, 2015
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Semi-on-topic: How to picture DNA? Talbott's writings helped me a lot:
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. The first thing to realize is that chromosomes do not consist of DNA only. Their actual substance, an intricately woven structure of DNA, RNA, and protein, is referred to as chromatin. Histone proteins, several of which can bind together in the form of an extremely complex histone core particle, are the single most prominent constituent of this chromatin. Every cell contains numerous such core particles — there are some 30 million in a typical human cell — and the DNA double helix, after wrapping a couple of times around one of them, typically extends for a short stretch and then wraps around another one. The core particle with its DNA is referred to as a nucleosome, and between 75 and 90 percent of our DNA is wrapped up in nucleosomes. But that’s just the first level of packing; it accounts for relatively little of the overall condensation of the chromosomes. If you twist a long, double-stranded rope, you will find the rope beginning to coil upon itself, and if you continue to twist, the coils will coil upon themselves, and so on without particular limit, depending on the fineness and length of the rope. Something like this supercoiling happens with the chromosome, mediated in part by the histone core particles. As a result the core particles, and the DNA along with them, become tightly packed almost beyond comprehension, in a dense, three-dimensional geometry that researchers have yet to visualize in any detail. This highly condensed state, characterizing great stretches of every chromosome, contrasts with other, relatively uncondensed stretches known as open chromatin. With that background, we can gain our first glimpse of the concerted dynamism in which genes participate. At any one time — and with the details depending on the tissue type and stage of the organism’s development, among other things — some parts of every chromosome are heavily condensed while others are open. Every overall configuration represents a unique balance between constrained and liberated expression of our total complement of 21,000 genes This is because the transcription of genes generally requires an open state; genes in condensed chromatin are largely silenced. The supercoiling has another direct, more localized role in gene expression. Think again of twisting a rope: depending on the direction of your twist, the two strands of the helix will either become more tightly wound around each other or will be loosened and unwound. (This is independent of the supercoiling, which occurs in either case.) And if, taking a double-stranded rope in hand, you insert a pencil between the strands and force it in one direction along the rope, you will find the strands winding ever more tightly ahead of the pencil’s motion and unwinding behind. Recall, then, that the enzyme (RNA polymerase) responsible for transcribing DNA into RNA must separate the two strands as it moves along a gene sequence. This is much easier if the supercoiling of the chromatin has already loosened the strands — and harder if the strands are tightened. So in this way the variations in supercoiling along the length of a chromosome either encourage or discourage the transcription of particular genes. Moreover, by virtue of its own activity in moving along the DNA and separating the two strands, RNA polymerase (like the pencil) tends to unwind the strands in the chromosomal region behind it, rendering that region, too, more susceptible to gene expression. There are proteins that detect such changes in torsion propagating along chromatin, and they read the changes as “suggestions” about helping to activate nearby genes (Lavelle 2009; Kouzine et al. 2008). Picture the situation concretely. Every bodily activity or condition presents its own requirements for gene expression. Whether you are running or sleeping, starving or feasting, getting aroused or calming down, suffering a flesh wound or recovering from pneumonia — in all cases the body and its different cells have specific, almost incomprehensibly complex and changing requirements for differential expression of thousands of genes. And one thing necessary for achieving this expression in all its fine detail is the properly choreographed performance of the chromosomes. This performance cannot be captured with an abstract code. Interacting with its surroundings, the chromosome belongs as much to a living activity as any other element in its cellular environment. Maybe instead of summoning the image of a rope, I should have invoked a snake, coiling, curling, and sliding over a landscape that is itself in continual movement.
Box_{September 11, 2015
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There has been a spate of gun shots on vehicles just outside of Phoenix Az recently. The media have been calling them "random shootings". They must mean "random" in the Darwinian sense - guided and purposeful. Darwinism runs deep:(ppolish_{September 10, 2015
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The DNA repair mechanism defeats Darwinian evolution because it repairs the very mutations that the evotards need for their brain-dead theory. But if you get rid of the DNA repair mechanism, the organism dies. Darwinism: stuck between stupidity and imbecility.Mapou_{September 10, 2015
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What are the prospects of a DNA self replicating entity surviving with rapid cumulative DNA mutations until it assembles the DNA repair mechanism – by random stochastic processes? Zero. You may as well believe in miracles.Mung_{September 10, 2015
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