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Junk DNA hires a PR firm

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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?

File:A small cup of coffee.JPG Anyone else for the myth of junk DNA? Richard Dawkins, for one (Reliable Source Central 😉 )

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Comments
rvb8:
Alternatively birds evolved from land animals that used to have teeth,...
How can that be tested? No one knows what makes a bird a bird...Joe
March 10, 2015
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PaV @ 18 - (sorry for coming in after another 40 comments, but the time zones are not favourable)
(3) And probably it’s because they are generally sessile organisms. I.e., they can’t go scavenge for their food, so they might need duplicate copies of genes so as to ‘multiply’ the amount of certain gene products when the right moment comes—like when it rains, or when its fed plant food, or when some detritus comes its way.
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? There's a nice figure here showing variation in genome size amongst taxonomic groups. Note, for example, that sessile fungi tend to have small genomes, as do a lot of angiosperm plants. EDIT: I wonder how large the genome is of a triffid.Bob O'H
March 10, 2015
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Bet you 50 bucks Diogenes have never thought about it like this, Perhaps we see junk and clutter in the DNA because over time it behaves just like a windows registry? The Registry clutter is a condition in which disorganized data stuffs up over time. In a freshly installed copy of Windows, the clutter is not considerable enough to affect performance. As most of the systems today are protected by Antivirus and Antispyware, complete corruption of Windows to warrant re-installation is less frequent. Hence the same Windows is used for years and therefore accumulates broken links and leftover files in the registry. The more the registry is cluttered, the more loss in speed will be observed. Following is the list of reasons that cause registry clutter: 1.When multiple software are installed and removed over time, they leave some amount of redundant, useless links and files behind. As uninstallations increase, clutter spreads. 2.An incomplete installation (one that is done without an uninstaller) will leave more traces of broken and unwanted files in the registry. 3.A fragmented registry will also bring down a computer’s performance. Empty spaces and sectors will increase the time taken to address the registry (Similar to how a fragmented disk slows down performance, read the article The path to performance loss; How a computer loses speed) 4.Viruses, malware, trojans generate embedded keys. These will cause registry errors and reduce performance. The undesirable clutter and errors in the registry will cause crashes, error messages and screen freezes. At the end of the day we know its software that drives us....... So I have a hypotheses, just like a brand new install of windows we started out pristine but over time even with some maintenance system junk builds up due to frequent use.Andre
March 10, 2015
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Headshot! More function less junk! http://www.nature.com/nsmb/journal/v21/n4/full/nsmb.2799.html Diogenes the official materialist snake oil salesman.....Andre
March 10, 2015
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Diogenes.... Have all the other sites you stalk banned you and now you're pulling your creepy wares here at UD? Junk DNA, aka Darwin style has been falsified, your religion is in tatters rather go do some PR work around the fact that your entire movement is drenched in sex scandals, just like the priests....... Go clean-up your own house!Andre
March 9, 2015
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Of course in some perverse experiments scientists have turned on non-coding DNA in chickens and produced teeth. So the birds have the DNA for teeth but it is not functional. If it were removed the bird would be none the worse off; sounds like pointless junk to me. Then again maybe god did design a chicken to have teeth and after the arc landing they micro-devolved away; that god chap, what a joker. Alternatively birds evolved from land animals that used to have teeth, and as an evolved answer to the problems of weight and aerodynamics in flight, teeth were selected against. Thus the DNA remained, but in junk non-coding form. One of these answers is rational, can you guess which?rvb8
March 9, 2015
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Wd400, As you know, in the C value paradox, C is divided by number of duplicates of genome. So Box's story of bacteria with duplicate genomes is irrelevant. But in their mind, any gap in scientific knowledge vindicates ALL claims of gaps in scientific knowledge, facts be damned-- and then they fill all the gaps with God. Even those which are already, uncomfortably filled with Science.Diogenes
March 9, 2015
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Quest, Different methods (and even definitions of load), and different kinds of data make for better or worse estimates, it's not really possible to answer your question in the abstract. If you have a point, please make it.wd400
March 9, 2015
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Quite frankly Box, I don't believe you. Homologous recombination relies on the complementarity between homologous chromosomes. Sequences finding each other is driven by the fact that they are virtually identical. 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. Lastly, you should look up some of the more recent work that's been done as well.Curly Howard
March 9, 2015
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WD400 #50 (and Curly Howard), the mystery is really easy to explain, but probably I have been unclear. Allow me to try again:
“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 (…)”
Those fragments are "stitched" back together. The paper describes the mechanism by which the fragments are stitched back together. The remaining question is: how are the DNA-fragments reordered in the correct sequence before they are stitched back together. The researcher doesn't know and told me: "Yes, that's exactly the biggest remaining mystery". Something in the cell knows the correct sequence, is capable of solving the puzzle and reorders the many fragments before reconstruction. But what?
WD400: I’ve no idea how this is meant to relate to junk DNA.
Just an example of a large genome (with a lot of apparent redundancy) that pays off in an unexpected way.Box
March 9, 2015
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WU40, How accurate are the calculations of the genetic load...?Quest
March 9, 2015
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Curly, Unfortunately, I've been down this path with Box before. (S)he doesn't seem to want to accept the pedestrian answer. I've no idea how this is meant to relate to junk DNA.wd400
March 9, 2015
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Curly Howard #47, I did. I even had some correspondence with one of the researchers at the time. She explicitly stated that this was exactly the unsolved mystery. I know that the paper doesn't make this clear at first glance, but you can trust me on this one.Box
March 9, 2015
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There are several different ways to calculate or estimate genetic load, Quest. What has this to do with anything?wd400
March 9, 2015
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Box, did you actually read the paper you have cited? It's not as much of an unsolved mystery as you seem to think.Curly Howard
March 9, 2015
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Dionogenesis, Here is the link you couldn't find:http://www.sciencedirect.com/science/article/pii/S0959437X14001002 There is more to come.... lolQuest
March 9, 2015
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Dionogenesis, You haven't answered my very important question; how is genetic load calculated...? I'm going to skip the rest of your embarrassment... You are just too low ball for me...Quest
March 9, 2015
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Diogenes "Look Diogenes, I can see you're really upset about this. I honestly think you ought to sit down calmly, take a stress pill, and think things over. " HAL 9000 Computer "If it helps, I could sing you a song, would you like to here it?" https://www.youtube.com/watch?v=OuEN5TjYRCE CheersCross
March 9, 2015
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Bacterium deinococcus radiodurans carries many copies of its genome - resulting in a 3.3 mb genome - and utilizes that in an amazing way.
Ionizing radiation can damage DNA in various ways, perhaps worst of all by causing double-strand breaks. These are breaks across both strands of the DNA double helix. The familiar bacterium, E.coli, not at all untypically, dies when it suffers about four double-strand breaks per each of its four-to-eight circular DNA molecules. Deinococcus radiodurans,by contrast, can survive over a thousand double-strand breaks. This means that it continues life after its genome is broken into hundreds of small fragments. It does so by proceeding to put its genome back together again when living conditions improve — a daunting task, to say the least. “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 (...)”
All the copies are shattered, but as the breakage is random (i.e., it doesn't occur on both copies at the same place), repair by homologous recombination can occur between the copies. The unsolved mystery is how the homologous fragments are brought together in the correct sequence.Box
March 9, 2015
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Exactly, Mapou, exactly. ID isn't a scientific dead end for tat simple fact- it forces us to ask questions we will try to answer.Joe
March 9, 2015
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Joe, it really does not matter that ID says nothing about the who or the when. There is no harm in analyzing all available evidence (the designed objects) to see what it can tell us about the designers. This, too, should be a scientific field of enquiry in its own right. Design detection as envisioned by Dembsky et al is not the be-all of the entire field of intelligent design.Mapou
March 9, 2015
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ID doesn't have anything to do with God: in "The Design Revolution", page 25, Dembski writes:
Intelligent Design has theological implications, but it is not a theological enterprise. Theology does not own intelligent design. Intelligent design is not a evangelical Christian thing, or a generally Christian thing or even a generally theistic thing. Anyone willing to set aside naturalistic prejudices and consider the possibility of evidence for intelligence in the natural world is a friend of intelligent design.
He goes on to say:
Intelligent design requires neither a meddling God nor a meddled world. For that matter, it doesn't even require there be a God.
In his book "Signature in the Cell" Stephen C. Meyer addresses the issue of Intelligent Design and religion:
First, by any reasonable definition of the term, intelligent design is not "religion".- page 441 under the heading Not Religion
He goes on say pretty much the same thing I hve been saying for years- ID doesn't say anything about worship- nothing about who, how, why, when, where to worship- nothing about any service- nothing about any faith nor beliefs except the belief we (humans) can properly assess evidence and data and properly process information. After all the design inference is based on our knowledge of cause and effect relationships.Joe
March 9, 2015
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Man, go fly a kite or mow the lawn or something.Mapou
March 9, 2015
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Mapou:
Creating truckloads of junk DNA just for silly grins and giggles would not be one of their goals, IMO.
Oh. Now God's back to not being mysterious, and now you DO know God's purposes again.Diogenes
March 9, 2015
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Diogenes, Man, give it a rest. First, I was giving plausible reasons for the onion's huge genome. Second, intelligent designers do work in mysterious ways (of course, since we don't yet know exactly who they are and what their goals were) but not in stupid ways. Intelligence is the key word here. Whoever designed life on earth were not a bunch of goofballs or buttheads. They were extremely disciplined, knowledgeable and methodical with a highly advanced sense of beauty. Creating truckloads of junk DNA just for silly grins and giggles would not be one of their goals, IMO.Mapou
March 9, 2015
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BA77, as I have already pointed out, you IDers started out arguing that all DNA was functional and that the genome was the dictator controlling the organism, and that this falsifies evolution, which means that according to you, evolution predicts non-functional DNA. Now your argument has flipped. Now you argue that DNA is non-functional and that the genome is NOT the dictator controlling the organism, and that this also falsifies evolution, which means that according to you, evolution predicts *FUNCTIONAL* DNA. So which is it? Which prediction is entailed by evolution, according to you? They're opposites. I will return to my still-unanswered questions.
No, no IDer can explain why the onion genome is 5x the size of the human genome… or why the VARIATION in genome sizes within the genus Allium is several times larger than the whole human genome. Why is it that within some genera of frogs, where all the species look equally complex, some species have far less DNA than humans, while other species in the same genus, distinguishable only by experts, have far more DNA than humans? Why? And excluding frogs, all amphibians that have been studied, including caecilians that have no legs nor eyes, have much, much more DNA than humans. Why? Nor can any of you answer Wd400?s frequently repeated question: if every baby born has ~ 100 more mutations than its parents, ~200 more than its grandparents etc. etc., and if all that DNA is functional, and mutations are “catastrophic” as IDcreationists always say, why don’t all babies die? Tell me how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.” Is it not true that to attempt to answer this question, you must know the purposes of God? And if your hypothesis depends on your beliefs about God’s purposes, doesn’t that make ID dependent on religion?
Diogenes
March 9, 2015
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Mapou, A minute ago you said Intelligent Designers were mysterious.
Intelligent designers work in mysterious ways.
Now you say they're not mysterious, you know the purposes of God.
The onion and its cousins can probably be bred into an amazing variety of flavors, shapes and appearances... The advanced designers who designed life on earth seemed to have had an eye for beauty, taste and the good life.
They're not mysterious now. Now you DO know the purposes of God: to make food that tastes good... to those people who like onions. Now many people hate the taste of onions, but they are not like God, huh? God's taste is similar to that of people who like onions. You sure know a lot about the purposes of God-- this minute. The next minute you'll know nothing. If your above hypothesis were true, the variations in taste between onions would track to the regions that are variable within the genus Allium. The variations between the species within Allium are 10 times larger than the entire human genome. Is it necessary to have a variation in genome size 10x larger than that of the whole human genome to create a nearly imperceptible change in taste? Now to the frogs. Within some genera of frogs, some frogs have much more DNA than humans and some species, looking nearly identical, have far less DNA than humans. What was God's purpose there? Since you know his Infinite Mind now. And lastly, consider humans. Consider all our Junk DNA. How do you know that Junk DNA is not beautiful to God? How do you know what is beautiful to an Infinite Mind? Since you allow that God created onions to taste good, how do you know that God didn't create humans as vectors just to carry around beautiful (to Him) broken transposons?Diogenes
March 9, 2015
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Mapou says:
But tell me, Joe, how ID explains why the pufferfish has a genome 1/8 the size of the human genome, and why another fish, the African lungfish, has 50 times more DNA than a human and 400 times more than some other fish, via your hypothesis “God made all genomes by sorcery.”
Intelligent designers work in mysterious ways.
If intelligent designers are mysterious, how did IDers know that God didn't make junk DNA? God didn't work in mysterious ways when IDers said ID predicts there will be NO Junk DNA. Then God was not so mysterious, but rather, his purposes were known. Why were IDers so sure? How do you know that God didn't make us as vectors for carrying around Junk DNA? Or that Junk DNA will have a front-loaded function that will only be revealed in a more advanced successor species to Homo sapiens 1 billion years from now? God didn't work in mysterious ways when IDers said ID predicts there will be NO Junk DNA. Then God was not so mysterious, but rather, his purposes were known. Why were IDers so sure? How do you know that God didn't make us as vectors for carrying around Junk DNA? Or that Junk DNA will have a front-loaded function that will only be revealed in a more advanced successor species to Homo sapiens 1 billion years from now?Diogenes
March 9, 2015
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Pest, what in Heaven's name is your source, and who is the "I" referred to?Diogenes
March 9, 2015
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The distribution of deleterious genetic variation in human populations Population genetic studies suggest that most amino-acid changing mutations are deleterious. Such mutations are of tremendous interest in human population genetics as they are important for the evolutionary process and may contribute risk to common disease. Genomic studies over the past 5 years have documented differences across populations in the number of heterozygous deleterious genotypes, number of homozygous derived deleterious genotypes, number of deleterious segregating sites and proportion of sites that are potentially deleterious. These differences have been attributed to population history affecting the ability of natural selection to remove deleterious variants from the population. However, recent studies have suggested that the genetic load is the same across populations and that the efficacy of natural selection has not differed across human populations. Here I show that these observations are not incompatible with each other and that the apparent differences are due to examining different features of the genetic data and differing definitions of terms.Quest
March 9, 2015
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