Junk DNA hires a PR firm

_{Denyse O'Leary

March 9, 2015

'Junk DNA', Intelligent Design, News}

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Fights back.

Well, that seems to be what’s happening. Further to: New York Times science writer defends junk DNA (Old concepts die hard, especially when they are value-laden as “junk DNA” has been—it has been a key argument for Darwinism), one of the conundrums on which the junk DNA folk rely heavily is the “onion test” (why does the onion have such a large genome?). Without waiting to answer the question, the junk DNA folk assume that that’s because most of it is junk.

But let’s face it, when even Francis Collins, the original Christian Nobelist for Darwin, is abandoning ship, they really need to double down on that junk.

From Evolution News & Views:

What’s so striking about Zimmer’s current piece is his explicit worry that — should “junk” DNA turn out to be functional — the “creationists” (as he calls the baddies) would be vindicated. At least twice in this long article, Zimmer raises the alarm that genomes had BETTER be junky, OR…the bad guys will win. It’s the same anxiety driving Dan Graur and Lawrence Moran into their fits of rage about ENCODE.

Hence in a not-so-subtle way, project ENCODE researchers are put on notice that, should they continue looking for function in non-coding DNA, they will be traitors to evolution and science.

Doubtless, the ENCODE guys have already begun to stammer and splutter. That’s what tends to happen when Darwin’s boys arrive (except here). For ENCODE, when they could afford to be open, see, for example:

Latest ENCODE Research Validates ID Predictions On Non-Coding Repertoire

Junk DNA’s defender doesn’t “do” politeness (No, we bet not.)

and

At least Forbes.com’s John Farrell, while trashing Jonathan Wells’ The Myth of Junk DNA, doesn’t threaten to actually read the book, the way some do.

For free highlights of the junk DNA uproar, see:

Anyone remember ENCODE? Not much junk DNA? Still not much. (Paper is open access.)

Yes, Darwin’s followers did use junk DNA as an argument for their position.

Another response to Darwin’s followers’ attack on the “not-much-junk-DNA” ENCODE findings

Hey, by the time you can’t tell the difference between Darwin’s elite followers and his trolls, you know something is happening.

Plus, pass the chocs, will you?

Anyone else for the myth of junk DNA? Richard Dawkins, for one (Reliable Source Central 😉 )

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Comments

Well Curly, I gather that you hold that I fabricate e-mail correspondence. I do not. However I'm the only one who knows this for a fact. Consequently I also know for a fact that you are the one who is still not getting it.Box_{March 10, 2015
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#83 PaV Is there a difference between "Some Alu elements, pseudogenes, ERVs, TEs, etc., have been co-opted for a function" and "Most/all DNA has a function"? For what percentage of those elements has any kind of functionality been demonstrated?Piotr_{March 10, 2015
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Box, I guess you're still not getting it. The "selection" of fragments relies on complementary base pairing and is aided by RecA. The entire mechanism is pretty well explained in the 2006 paper and by studies done in the 1990s-early 2000s and summed up in a mini review by Frenkiel-Krispin & Minsky (2006). Andddd here comes a BA77 regurgitation. Just looking at your first point BA, the cell protects all DNA because the repair systems can't differentiate between protein coding regions, regulatory regions or junk regions. They only recognize broken DNA and fix it as best they can. Molecules can't think, can you? PS-I don't think "quantum computation" is involved at all in the repair process. You didn't just see the word "quantum dots" and immediately go into one of your quantum physics frenzies did you?Curly Howard_{March 10, 2015
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Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video https://vimeo.com/81930637 Concluding powerpoint of the lecture (at the 1 hour mark): “Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages.” Edward N. Trifonov – 2010 Astonishing DNA complexity update Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. https://creation.com/images/pdfs/tj/j21_3/j21_3_111-117.pdf Multidimensional Genome – Dr. Robert Carter – video http://www.metacafe.com/watch/8905048/ The Extreme Complexity Of Genes – Dr. Raymond G. Bohlin – video http://www.metacafe.com/watch/8593991/ Duality in the human genome - Nov. 28, 2014 Excerpt: The gene, as we imagined it, exists only in exceptional cases. "We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel's time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,",,, "Our investigations at the protein level have shown that 96 percent of all genes have at least 5 to 20 different protein forms.,,, http://medicalxpress.com/news/2014-11-duality-human-genome.html
Towards the latter half of the following podcast, Dr Sternberg, who has a PhD in evolutionary biology, elucidates how the overturning/loss of the ‘gene’ as the central unit of inheritance turns the modern synthesis of neo-Darwinism from a science into no better than the discarded alchemy or Ptolemy astronomy of yesteryear.
Podcast – Richard Sternberg PhD – On Human Origins: Is Our Genome Full of Junk DNA? Part 5 (emphasis on ENCODE and the loss of the term ‘gene’ as a accurate description in biology and how that loss undermines the modern synthesis of neo-Darwinism) http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-5/
etc.. etc.. etc..bornagain77_{March 10, 2015
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Inferring functionality for virtually 100% of the genome, even though we do not know the precise function of all of the sequences of all the elements of the genome, is relatively easy. One way to infer widespread functionality, despite not having knowledge of precise function, is to note that the entire genome, contrary to Darwinian presuppositions, is subject to multiple layers of DNA repair thus raising the obvious question of 'why is the cell so jealously protecting so much dead weight junk?'
Repair mechanisms in DNA include: 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
The following repair mechanism is my favorite since it indicates, (due to the traveling salesman problem which is a notoriously difficult problem in classical computation), that quantum computation is somehow involved in the repair process:
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 – of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
Moreover sophisticated repair mechanism in place for DNA are incompatible with Darwinism 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. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/
Another way to infer widespread functionality across the entire genome, despite not having knowledge of precise function, is empirically. In the following study the entire genome is transformed into a optical device:
Shoddy Engineering or Intelligent Design? Case of the Mouse’s Eye – April 2009 Excerpt: — The (entire) nuclear genome is thus transformed into an optical device that is designed to assist in the capturing of photons. This chromatin-based convex (focusing) lens is so well constructed that it still works when lattices of rod cells are made to be disordered. Normal cell nuclei actually scatter light. — So the next time someone tells you that it “strains credulity” to think that more than a few pieces of “junk DNA” could be functional in the cell – remind them of the rod cell nuclei of the humble mouse. http://www.evolutionnews.org/2009/04/shoddy_engineering_or_intellig.html
In the following study, what was thought to be junk DNA was cut out but, contrary to Darwinian thought, it had a negative effect:
Jonathan Wells on Darwinism, Science, and Junk DNA – November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
Another way to infer widespread functionality across the entire genome, despite lacking knowledge of precise function, is to note the trend in evidence. Every element that Darwinists have insisted to be junk in the past has been now shown to have function of one kind or the other. i.e. There has only been an increase in the amount of the genome known to functional, never a decrease!
Reference Notes For Jonathan Wells’ Book – The Myth Of Junk DNA – Hundreds of Studies Outlining Function for various elements of supposed ‘Junk’ DNA http://www.discovery.org/f/7651
another way to infer widespread functionality across the entire genome is to look at the 'polyfunctionality' of the genome:
3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell – Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip — while avoiding the knots and tangles that might interfere with the cell’s ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm DNA – Replication, Wrapping & Mitosis – video https://vimeo.com/33882804
bornagain77_{March 10, 2015
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CH #84, What exactly seems fishy, Howard? What you quote seems consistent with "Yes, that’s exactly the biggest remaining mystery, how are the homologous fragments brought together." Your quote doesn't say how the fragments are selected and how they are transported.Box_{March 10, 2015
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wd400: Stop being pedantic. It's irritating.PaV_{March 10, 2015
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Something seems fishy Box because as I said, in their 2006 paper they describe the mechanism by which fragments realign. They outline the mechanism in the abstract: "...'extended synthesis-dependent strand annealing' (ESDSA), followed and completed by crossovers. At least two genome copies and random DNA breakage are requirements for effective ESDSA. In ESDSA, chromosomal fragments with overlapping homologies are used both as primers and as templates for massive synthesis of complementary single strands, as occurs in a single-round multiplex polymerase chain reaction. This synthesis depends on DNA polymerase I and incorporates more nucleotides than does normal replication in intact cells. Newly synthesized complementary single-stranded extensions become 'sticky ends' that anneal with high precision, joining together contiguous DNA fragments into long, linear, double-stranded intermediates. These intermediates require RecA-dependent crossovers to mature into circular chromosomes that comprise double-stranded patchworks of numerous DNA blocks synthesized before radiation, connected by DNA blocks synthesized after radiation." Also PaV, everywhere your statement about duplicating chromosomes could have been wrong, it was wrong. Chromosomes are not diploid, genomes are. Duplication of homologous chromosomes (2 independent, single DNA molecules) in eukaryotes still gives you only 2 chromosomes. Only now each chromosome consists of two DNA molecules. You should've paid more attention in bio class.Curly Howard_{March 10, 2015
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That what has been hailed as classic examples of "junk-DNA" are now being found to have function: an omen that the neo-Darwinist evo-bios are losing the battle to ID. It seems a bit odd that if you have an Alu sequence that is shown to have function, and there are loads of other such sequences, that you would think that this entire class of similar Alu sequences would only be limited to a handful of cases. What about pseudogenes? Classic "junk-DNA," and now known to be intimately involved in the developing embryo.PaV_{March 10, 2015
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#80 PaV, Denial of what?Piotr_{March 10, 2015
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If you duplicate a diploid chromosome, you get TWO diploid chromosomes.
... I don't even... what?wd400_{March 10, 2015
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They say that Alu elements make up more than 10% of the human genome. They don’t say that all of them are (or can be) functional.
Sounds like you're in a state of denial.PaV_{March 10, 2015
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If you duplicate a diploid chromosome, you get TWO diploid chromosomes.PaV_{March 10, 2015
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Curly Howard, Thank you for the explanation. Somehow I didn't get that mechanism you have spelled out. If what you describe is indeed the explanation then I must have misinterpreted the words of one the researchers during my e-mail correspondence. On my question "Am I correct when I say that one of the unanswered questions is how the hundreds of overlapping genomic fragments are reordered in the correct sequence? This seems like a miracle to me." the following response:
Yes, that's exactly the biggest remaining mystery, how are the homologous fragments brought together. We know that there is no pre-alignment of the genomic copies, but perhaps alignment occurs before repair takes place. How this happens is a mystery. We wanted to test the possibility of 'post-alignment' (after IR) by tagging a certain locus with GFP and looking at whether we see two dots side by side or fart apart, but the resolution of light microscopy doesn't allow for the GFP foci to be visualized separately.
Of course the selecting and placement still remains mysterious. Something (similar to RNA polymerase?) reads the code of a DNA-fragment (how does it find the "first one"?), remembers it and then starts a search for an overlapping homologue piece and then maneuvers it in the correct position. I don't expect an explanation for that any time soon. Weird that the researcher writes "but perhaps alignment occurs before repair takes place", I mean logic dictates that this must happen. The "post-alignment" idea I did not get. Another perhaps relevant fact is that there are many DNA repeat elements in Drad's genome. That may or may not complicate homologous recombination. In 1999 researchers write:
Another important component may be the presence of DNA repeat elements scattered throughout the genome.These repeats satisfy several expected requirements for involvement in recombinational repair including that they are intergenic, they are ubiquitous in the chromosomes and the megaplasmid, and they occur at a frequency that is comparable to the number of double stranded DNA breaks that can be tolerated by D. radiodurans. A possible function of the repeats may be in regulating DNA degradation after damage. DNA degradation following the introduction of double stranded breaks is an integral part of the DNA repair process in D. radiodurans;
Box_{March 10, 2015
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Hey IDers, You should reply to the onion test by saying that the wildly varying amounts of DNA in onion and other species can be accounted for by whole genome duplications. These are random events that occur in many species, especially plants, and to a non-biologist it might sound like a valid explanation. Of course it doesn't answer the onion test, but explaining why could be difficult and confound some of the science folks.....and that's all that really mattersRodW_{March 10, 2015
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Well, you are certainly being clear about what it is you don't understand! Here's a better, more simple example with the numbers representing the original chromosome. 1. the quick brown fox jumped over the lazy dog 2. the quick brown fox jumped over the lazy dog Fragmented: 1. the quick 1. brown fox jumped 1. over the lazy 1. dog 2. the quick brown 2. fox jumped over the 2. lazy dog Now sequence alignment by complementary base pairing allows you to realign the original sequence based on the different fragments of homologous chromosomes. 1. brown fox jumped over the lazy dog 2. ----------fox jumped over the------------ Do you see how 2 fragments originally from chromosome 1 were rejoined in the correct order based on the homologous sequence of a fragment from chromosome 2? And now another fragment from chromosome 2 can be added in correct sequence based on the homology in the chromosome 1 fragment: 1. --------------brown fox jumped over the lazy dog 2. the quick brown fox jumped over the------------ I don't know how much simpler I can make it. You simply don't know what you are talking about. Homology is always between 2 separate DNA molecules (or their fragments in this case) whereas complementary base pairing doesn't care whether it's within a single DNA molecule or between two different molecules. This is why complementary base pairing can be used to reorder fragments from homologous chromosomes. I know it's complicated, but try to stay with me.Curly Howard_{March 10, 2015
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follow up #71 // The problem is simple. A comparison: Hamlet's Sililoquy (and several copies of this work) is fragmented into thousand of words and parts of words. We now have something like:
sleep Arms or Whether Aye against Arrows outrag eams That Flesh consummation question Slings To die Sea To be, not mind against to eous be, that is the question Sea shuffled mind Whether To be, sleep Aye To b Slings [and so forth]
Now how do we repair things? (just like Drad repairs its shattered genome; see #43)
To be, or not to be, that is the question— Whether 'tis Nobler in the mind to suffer The Slings and Arrows of outrageous Fortune, Or to take Arms against a Sea of troubles, And by opposing, end them? To die, to sleep— No more; and by a sleep, to say we end The Heart-ache, and the thousand Natural shocks [and so forth]
Okay the stitching things back together ONCE THEY HAVE BEEN SEQUENCED IN THE RIGHT ORDER has been explained and part of that stitching process has to do with homology. But homology between the fragments doesn't help finding the correct sequence at all. Am I being clear this time?Box_{March 10, 2015
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#64 PaV, They say that Alu elements make up more than 10% of the human genome. They don't say that all of them are (or can be) functional.Piotr_{March 10, 2015
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"Obviously non-homologous DNA molecule," Box? I don't think you understand the words you are using.Curly Howard_{March 10, 2015
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However, I was not talking about “junk-DNA” in general, but to genome duplication events and increased genome size in plants, specifically
Onions are diploid.wd400_{March 10, 2015
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Curly Howard,
Curly Howard: Box, it seems you don’t have a very good understanding of homologous recombination.
If that is the case, maybe you can help me out here.
Curly Howard: Both 1 and 2 are processes within homologous recombination. The sequences are aligned based on the homology between DNA molecules.
How does homology help sequencing the fragments into an obviously non-homologous DNA molecule? I can understand that homology helps explaining that homologous DNA-fragments face each other during homologous recombination. But I certainly don't understand that fragments are sequenced in the right (non-homologous) order of an entire DNA-molecule. Homology is of help in one dimension (direction) but not in another, so to speak. edit: is this an atheist thing? WD400 also failed to see the mystery. Am I being unclear or what?Box_{March 10, 2015
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wd400:
This is getting comical. There are loads of papers that actually test hypotheses about the evolution of junky genomes, you should read some.
Glad to add to your merriment. However, I was not talking about "junk-DNA" in general, but to genome duplication events and increased genome size in plants, specifically. Also, look at my comment to Bob O'H. Finally, do you really believe that the idea of Darwinism---in your case neo-Darwinism---doesn't drive your decisions about what to look further into, and what not? Being self-critical can help. The physicist Feynman cautioned: "The first principle is that you must not fool yourself and you are the easiest person to fool." And that's a physicist who has all kinds of repeatable experimental evidence.PaV_{March 10, 2015
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Box, it seems you don't have a very good understanding of homologous recombination. Both 1 and 2 are processes within homologous recombination. The sequences are aligned based on the homology between DNA molecules. This is the same reason why crossing over exchanges precise fragments between homologous chromosomes in us. "Tiny" fragments is not a good description in my opinion. 20-30kb is quite large and with the ssDNA overhangs, allows for complementary base pairing between homologous strands that are not fragmented in the same place. Having fragments that overlap allow for reconstruction of the genome based on complementary base pairing of sections of the fragments in a way similar to how a genome would be realigned during shotgun sequencing. When I say recent work, I am referring to: Cox et al. 2010 PLoS Genetics Sugiman-Marangos & Junop. 2010 Nucleic Acids Res. Bent chilly et al. 2010 PLoS Genetics Hickman et al. 2010 EMBO J Motors et al. 2010 J Nucleic Acids Bouthier de la tour et al. 2011 DNA Repair Amst Subhuman-Marangos et al. 2013 Nucleic Acids Res George et al. 2012 J Biol ChemCurly Howard_{March 10, 2015
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Bob O'H:
This hypothesis would suggest that all plants would have large genomes, which would mostly be non-coding DNA. But then why would rice have such a small genome compared to wheat?
It suggests that duplicating the entire genome is an adaptive measure for plants. As to rice, aren't they grown in areas where the ground is flooded with water? This isn't the case for wheat. If my thesis has some merit, then, because the plant has to actually respond more to presence of water than that of 'food,' then the rice would have possibly "lost" its duplicated form, being that it is grown in a flooded state.PaV_{March 10, 2015
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wd400 proudly declares:
There are loads of papers that actually test hypotenuses
How does one test a hypotenuse? Why are so many atheists and Darwinists so insufferably pompous? It's the same refrain: We know something you don't and if you knew what we knew, then you too would believe that living organisms evolve all by themselves into what they are and that life arose from dirt all by itself. What utter crap!Mapou_{March 10, 2015
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I find it interesting that none of this has been thought about before. Evolutionary biologists, I guess, reach the conclusion that the polyploidy is just “junk-DNA,” and they stop asking questions, since this fits their narrative so well.
This is getting comical. There are loads of papers that actually test hypotheses about the evolution of junky genomes, you should read some.wd400_{March 10, 2015
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Diogenes:
As for being sessile, I just listed many animals that have far more DNA than humans but are NOT sessile.
If they are not sessile, then the hypothesis wouldn't apply. And how many "plants" are NOT sessile? I don't there's many. I find it interesting that none of this has been thought about before. Evolutionary biologists, I guess, reach the conclusion that the polyploidy is just "junk-DNA," and they stop asking questions, since this fits their narrative so well. BTW, as I thought a little bit further about this "onion" problem, it came to me that the plants would respond more to the presence and absence of water than simply 'food,' although needing both. I would think, however, that 'water' would be the prime requirement based simply on my experiences in the garden. Interestgingly, the bladderwort has no problem with 'finding' water, since it lives on water. This might be exactly why its genome is so relatively short.PaV_{March 10, 2015
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Diogenes:
Now divide by 3.2 billion. How much of the genome are we talking about, percentage-wise? 0.001%? As usual.
Nice speculation. Just look up the paper. The 10% figure comes from there. (Here's the link.)PaV_{March 10, 2015
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Diogenes @36 All your "why" questions miss the point. What we have is a device the purpose of which is obviously to store digital information, some of which contains the assembly instructions for various functional protein machines. Knowing that, it is reasonable to assume the rest of it will either be functional in some other way not yet understood, or just be unused memory capacity. In a given instance, regardless of how much of the total memory is extra capacity the contents of which are functionally insignificant, and how much memory is functionally significant, what is of major consequence is that a biological digital-information storage device exists at all. Such a device was absolutely necessary, since without the assembly instructions it is obvious that the protein machines required for metabolism and reproduction would have as much chance of getting slopped together accidentally as one would have at arriving at Margaret Mitchell's Gone with the Wind by continually dumping out crates of Scrabble pieces on empty parking lots until the pieces happened to fall such that they were neatly arranged that way. When lifeless, yet self-replicating units of some kind of chemical activity were supposedly mindlessly and accidentally evolving into that first single-celled, reproducing life form, what would have been the selectable advantage of some sort of digital-information storage device, a precursor of the DNA molecule, unless it actually contained functional information that was accessible? Yet how would its contents evolve into such functional information without machinery exterior to it that could read and write the memory? And why would such machinery evolve while the contents of the storage device's memory were still gibberish, and reading and writing it was just a waste of energy? Mindless evolutionary processes can arrive at neither the functional information nor the machinery to access it in the absence of the other. In other words, life just isn't going to happen mindlessly and accidentally. Or did Margaret Mitchell actually come up with Gone with the Wind by randomly selecting letters of the alphabet?harry_{March 10, 2015
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Curly Howard #53,
“D. radiodurans survives 7 kGy of ionizing radiation with marginal lethality (10%). This dose shatters its 3.28 Mb genome into 20–30 kb fragments (…)”
Get the picture: all of the DNA is shattered in small fragments. Next Drad will (1) Align the fragments in the correct order (2) Stitch the DNA fragments together again by a process termed "homologous recombination" Now the mystery rests in (1). Remember that Drad carries multiple copies of its genome, however these copies are also shattered in tiny fragments; making the "puzzle" even more difficult. From this tangle of short DNA-fragments Drad needs to select usable fragments and align them in the CORRECT (original) sequence. Question: How does Drad know the correct sequence? With so many fragments available Drad can align the DNA in many wrong sequences.
Curly Howard: Sequences finding each other is driven by the fact that they are virtually identical.
How is that an answer to the question? What do you even mean? Identical fragments are not socializing at any stage of the repair process. Why would they?
Curly Howard: Also a paper out of their own lab in 2006 showed that realignment of the genome through ESDSA occurs through annealing of complementary 20-30 kilobase single-strand DNA ends.
I know it's complicated, but that is part of the not mysterious phase (2) - stitching DNA fragments together again. You need to address (1) - align the fragments in the correct order.
Curly Howard: Lastly, you should look up some of the more recent work that’s been done as well.
I suppose that you refer to Kisko and Radman, however they don't address the mystery as layed out in (1).Box_{March 10, 2015
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