Junk DNA: The Real Story

_{Cornelius Hunter

March 25, 2010

Intelligent Design}

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By now you have probably heard about so-called junk DNA. In recent decades the genomes of a growing number of species have been mapped out. Not surprisingly, scientists did not understand how many of these DNA sequences worked. For instance, repetitive sequences are common, but what do they do? As these data accumulated evolutionists increasingly viewed such sequences as useless junk. Then, years later, various functions began to emerge as our knowledge grew. This junk DNA story is the latest version of what seems like a repeating bad dream that goes like this. Scientists discover something new in biology but don’t understand it. Evolutionists, unaware that they are staring at a design whose complexity dwarfs their puny understanding, decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Later, when the function is eventually uncovered, evolutionists automatically claim the design as an evolutionary achievement. The structure goes from junk to treasure without a second thought. Read more

Comments

Yes, especially when they're jokes, not misunderstandings. Barry Commoner knew exactly what it meant to be "born again", and so do I. He was making a joke, specifically about the apparent necessity to profess being a "born again" Christian when running for president (in 1980, anyway). But, as I said (in a comment that apparently has not made it through moderation), it's hard to make jokes that are understood by the ideologically committed...Allen_MacNeill_{March 25, 2010
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BA77:Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are. Deal?
I'm not Nakishima nor do I intend to speak for him but here is one of many references in relation to DNA and body plans.
Studies of DNA damage and cell death in embryonic limb buds induced by teratogenic exposure to cyclophosphamide Dr. Jeanne M. Manson *, Linda Papa, Marian L. Miller, Christine Boyd Department of Environmental Health, University of Cincinnati, Cincinnati *Correspondence to Jeanne M. Manson, Associate Professor of Environmental Health, University of Cincinnati, 3223 Eden Avenue, Cincinnati, OH 45267 Keywords teratogen • cyclophosphamide • limb buds • DNA damage • cell death Abstract Many teratologic investigations have shown that certain types of chemical insults to the embryo (those altering replication, transcription, and translation) can cause excessive cell death in tissues destined to become malformed. Chemical carcinogens also induce cell death in target tissues, but the critical event is believed to be heritable alteration in the DNA of surviving cells. In the present study, an attempt was made to study the interaction between cell death and DNA damage in the initiation of birth defects. The pattern of DNA damage induced by cyclophosphamide was examined at time intervals before, during, and after the necrotic episode in mouse embryo limb buds. The alkaline elution assay was used to measure alkali-labile sites in single-strand DNA due to its adaptability to small tissue samples. An ip dose of 20 mg/kg of cyclophosphamide induced forelimb malformations in 85% of surviving mouse fetuses and 30% embryolethality when administered at 9 am on Day 11. As early as 5 hr after exposure, a slight excess of necrosis was observed in treated limbs by light microscopy, while at 24 hr, massive necrosis was evident. By 48 and 72 hr, excess necrosis was not observed in treated limbs. When alkaline elution analysis was conducted at prenecrotic (1-, and 5-hr), necrotic (24-hr), and postnecrotic (48-, and 72-hr) intervals, a trend toward increasing DNA damage in treated limbs with time was observed. The greatest differences in elution values occurred during the postnecrotic period. Although mean retention values were not significantly different, significantly increased variance was obtained in retention values of treated limbs at all time intervals other than 1 hr. This may reflect the actual in vivo situation where relatively few cells within a heterogeneous population of cells carry sublethal DNA damage into the postnecrotic period. These results suggest that not all limb bud cells affected by teratogenic exposure to cyclophosphamide die, but that some persist to the postnecrotic period carrying heritable alterations in their DNA.
I'm looking forward to yoru commentary! Hopefully there will be no videos.Acipenser_{March 25, 2010
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Allen_MacNeill,
BTW, I have always liked Barry Commoner’s response to the question of whether he was “born again” (when running for president on the Citizens’ Party ticket back in 1980): “I was born 63 years ago in Brooklyn, New York, and I don’t intend to repeat the process.”
That's just a silly misunderstanding of what it means to be "born again." Do you normally like silly misunderstandings?Clive Hayden_{March 25, 2010
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McNeill, taking cheap shots? What's the deal? Are you angry at me for publicly calling your bluff on your umpteen variations of deception? Hey don't get mad at me! Just falsify Abel's null hypothesis with any one of the numerous variations (besides point mutations) you have listed? If you want to get mad, get mad, but at least rightly place your anger, and get mad at yourself for lying to yourself and others with no empirical evidence to back yourself up. Hmm Nak, seems that the peer review evidence you alluded to was refuted by, of all people Voice coil in 221 As of the 2006 review cited above there were five instances of interspecies nuclear transfer resulting in live births (read, “fully developed”). All such cross species transfers occurred within the same genus. All resulted in animals of the species donating the nuclei. Therefore these within genus differences are determined by DNA. https://uncommondescent.com/intelligent-design/ic-all-the-way-down-the-grand-human-evolutionary-discontinuity-and-probabilistic-resources/#comment-342112 Which for me, clearly indicates that the body plans are strictly constricted to a morphological pattern, whereas the DNA provides the parts necessary for the body plan, with the Gaur example you merely provided more building material for the "cow' to build the body plan with since you reached up higher on the originally created kind of the cow that had been diversified from in the first place And since it is in fact the major body plans of phyla that appear abruptly in the Cambrian, with lack of transitions, I believe the onus is on you to show morphological novelty from overriding body plans rather than just solidifying the already established point that body plans are not encoded in DNA.. Now Nak if you do decide to provide relevant peer-review that does show body plans are decided by DNA I wi8ll gladly look at it to show you where your flaws in thinking are. Deal?bornagain77_{March 25, 2010
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A recent finding of "junk" DNA function involves repetitive elements which have been found to be active in certain tissues. The researchers concluded that this activity "has a key influence" on the overall activity of the mammalian genome. As one evolutionist admitted, "As a class [repetitive elements] are not just a junk DNA. They're not just parasites, but they can shape the architecture of the genome."
So does this mean gene duplications increase information?CLAVDIVS_{March 25, 2010
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Nakashima-san, bornagain 77 isn't interested in evidence, and certainly not evidence from the peer-reviewed scientific literature. Bits and pieces copied willy nilly from various creationist and ID videos, plus selected quote-mines lifted from various creationist and ID quote-mine lists, strung together in an incoherent and meaningless sequence, then paste-bombed into threads so long that even the most committed ID partisan can barely wade through them – yes, by all means, but actual scientific research reports complete with references cited? Don't be ridiculous... BTW, I have always liked Barry Commoner's response to the question of whether he was "born again" (when running for president on the Citizens' Party ticket back in 1980):
"I was born 63 years ago in Brooklyn, New York, and I don't intend to repeat the process." [ http://news.google.com/newspapers?nid=1916&dat=19800926&id=IFgpAAAAIBAJ&sjid=G24FAAAAIBAJ&pg=1153,5380977 ]
Commoner was running against Ronald Reagan, Jimmy Carter, and John Anderson, all three of whom had stated that they were "born again Christians".Allen_MacNeill_{March 25, 2010
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Mr BA^77, Nak, and just why should I ever trust anything you say? The point of linking to the original thread was that I don't expect you to take my word for it. I'm helping you and anyone else interested in following up on the discussion go look, read and decide for themselves. Comment 198 in that thread cites a peer reviewed scientific research paper on interspecies nuclear transfer. Wells is wrong.Nakashima_{March 25, 2010
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Nak, I read through that link and you provided no peer review, the basic Jest is Joseph paitently tried to correct you, you did not listen, Joseph left (apparently tired of talking to the deaf) then you went on for a few more post with nothing relevant to say nor evidence presented. Then you thumped your chest and declared victory as if that is how truth is found in science. It would be funny but it is too sad for me to muster a laugh. I believe the one line out of the whole exchange sums it up, and is the most truthful, is this quote by Joseph in 273: "IOW you have proven your dishonesty beyond any reasonable doubt." Here is another video for you to ignore the implications of Nak; Fearfully and Wonderfully Made - Glimpses At Development In The Womb http://www.metacafe.com/watch/4249713bornagain77_{March 25, 2010
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Nak, and just why should I ever trust anything you say? especially since you have twisted evidence countless times before? Am I suppose to just forgive and forget all the times you have tried to deceive people on UD with your extremely biased, "slight of hand", presentation of evidence??bornagain77_{March 25, 2010
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Mr BA^77, The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact.” The Design of Life – William Dembski, Jonathan Wells Pg. 50 If you want to see how a discussion of Wells' position turned out, just hit that link and check the comments from 198 onwards. The Cliff Notes (TM) version is: Rabbit egg + human DNA, combined in a particular way = human stem cells, the contradiction of Wells, and the limerick of Nakashima!Nakashima_{March 25, 2010
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hrun: 1: Kimura (1968) developed the idea of “Neutral Evolution”. If “Haldane’s Dilemma” is correct, the majority of DNA must be non-functional. The slow, painful death of junk DNA: Junk DNA is not just a label that was tacked on to some DNA that seemed to have no function; it is something that is required by evolution. Mathematically, there is too much variation, too much DNA to mutate, and too few generations in which to get it all done. This was the essence of Haldane’s work....Junk DNA is a necessary mathematical extrapolation... Without Junk DNA, evolution runs into insurmountable mathematical difficulties.(on top of already insurmountable mathematical difficulties) http://creation.com/junk-dna-slow-death Susumu Ohno, a leader in the field of genetics and evolutionary biology, explained in 1972 in an early study of non-coding DNA that, "they are the remains of nature's experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?" 2. The Unseen Genome, Gems Among the Junk: “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this—particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules—may well go down as one of the biggest mistakes in the history of molecular biology.” (John S. Mattick Scientific American (November, 2003) http://www.evolutionnews.org/ 3. Concluding statement of the ENCODE study: "we have also encountered a remarkable excess of experimentally identified functional elements lacking evolutionary constraint, and these cannot be dismissed for technical reasons. This is perhaps the biggest surprise of the pilot phase of the ENCODE Project, and suggests that we take a more 'neutral' view of many of the functions conferred by the genome." http://www.genome.gov/Pages/Research/ENCODE/nature05874.pdf A 'scientific revolution' is taking place, as researchers explore the genomic jungle: "The science of life is undergoing changes so jolting that even its top researchers are feeling something akin to shell-shock. Just four years after scientists finished mapping the human genome - the full sequence of 3 billion DNA "letters" folded within every cell - they find themselves confronted by a biological jungle deeper, denser, and more difficult to penetrate than anyone imagined." http://www.boston.com/news/globe/health_science/articles/2007/09/24/dna_unraveled/?page=1 you want to know what is really funny hrun? Genetic Reductionism is falsified in the first place! Cortical Inheritance: The Crushing Critique Against Genetic Reductionism - Arthur Jones - video http://www.metacafe.com/watch/4187488 DNA: The Alphabet of Life - David Klinghoffer Excerpt: But all this is trivial compared to the largely unheralded insight gained from the Human Genome Project, completed in 2003. The insight is disturbing. It is that while DNA codes for the cell's building blocks, the information needed to build the rest of the creature is seemingly, in large measure, absent. ,,,The physically encoded information to form that mouse, as opposed to that fly, isn't there. Instead, "It is as if the 'idea' of the fly (or any other organism) must somehow permeate the genome that gives rise to it." Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681 "There is now considerable evidence that genes alone do not control development. For example when an egg's genes (DNA) are removed and replaced with genes (DNA) from another type of animal, development follows the pattern of the original egg until the embryo dies from lack of the right proteins. (The rare exceptions to this rule involve animals that could normally mate to produce hybrids.) The Jurassic Park approach of putting dinosaur DNA into ostrich eggs to produce a Tyrannosaurus rex makes exciting fiction but ignores scientific fact." The Design of Life - William Dembski, Jonathan Wells Pg. 50bornagain77_{March 25, 2010
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hrun, for you to not see how evolutionary thinking has hindered research, for over 30 years, into the apparent “complexity that dwarfs our puny understanding” is the height a metaphysical bias blinding objective judgment on the matter.
Okay. Included in this accusation is a clear statement: "Evolutionary thinking has hindered research for over 30 years." See, I thought that this was one of the points CH was making. Now, is there any factual support for this? Another clear statement is: "As well, Evolutionary thinking continues to impede meaningful progress in this area by its continued insistence in misleading the researchers with totally unwarranted conjectures belittling the genome of function." Again, do you have factual support, or does this remain an assertion? Finally, embedded in this "Conjectures that arise from nothing more than a belief that evolution must be true rather than from what the empirical evidence such as ENCODE has suggested." is the assertion that empirical evidence of ENCODE runs counter to 'a belief that evoluion is true'. Again, a bold statement without any factual support. Okay, here we have three assertions without any support. Since you made them, and not CH, I ask you: Support them with facts.hrun0815_{March 25, 2010
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Dr Hunter, Thank you for writing a blog post that I actually come close to agreeing with. I strongly agree that all apologetics are religious. I think the "junk DNA as negative apologetic" stance accurately describes the reactions of some people to the Paleyite apologetic "beauty/efficiency/wonder is evidence of God". By itself, junk DNA cannot be used as a blanket apologetic against creation, only against creation by an omni-(scient, potent, benevoloent) deity who thinks like we do. Knock out experiments on the 'omni' genes of the deity can lead to junk DNA. A tri-omni deity that thinks like a praying mantis instead of man might create junk DNA. Angra Mainyu might create junk DNA. So we can see that the negative apologetic of junk DNA is quite limited in power. I don't know the intertwined history of evolution and religion well enough to know when was the first use as an apologetic device of Ohno's back-of-the-envelope calculation that a large part of the human genome was not under any strong selection pressure. However, it should be clear that such use is an 'exaptation' of a legitimate scientific question - if Ohno's assumptions are accurate, how do we account for all that DNA? Finding function for a very small amount of repeated sequences (according to the paper you reference, those REs just 5'-ward or embedded in the 3' UTR of a protein coding gene) is to some the tip of the iceberg of junk DNA function. To others it the tip of the icecube. As long as there is new science emerging from this area, some on each side will appropriate the result for polemic use.Nakashima_{March 25, 2010
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hrun, for you to not see how evolutionary thinking has hindered research, for over 30 years, into the apparent "complexity that dwarfs our puny understanding" is the height a metaphysical bias blinding objective judgment on the matter. As well, Evolutionary thinking continues to impede meaningful progress in this area by its continued insistence in misleading the researchers with totally unwarranted conjectures belittling the genome of function. Conjectures that arise from nothing more than a belief that evolution must be true rather than from what the empirical evidence such as ENCODE has suggested.bornagain77_{March 25, 2010
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CH these guys are proving your point at every turn in that their metaphysics is driving their science.,,, You must be gently laughing and shaking your head in disbelief as you type responses,
What do you know about my (or hdx's) science? In any case, how are we proving a point? I am simply trying to discern WHAT exactly CS is trying to claim in his posts about 'junk DNA'. I thought I knew, yet, I was told that I did not read carefully engouh. You, apparently, know as well. Would you like to hazard a guess as to what exactly he is trying to claim about 'junk DNA'?hrun0815_{March 25, 2010
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CH these guys are proving your point at every turn in that their metaphysics is driving their science.,,, You must be gently laughing and shaking your head in disbelief as you type responses,bornagain77_{March 25, 2010
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hdx:
This has got to be one of the most ridiculous things I have ever read. Duplications, deletions and insertions of genomes are occurring all the time. Are you saying that every time a duplication/insertion occurs, it has an important function? This is obviously ridiculous
Responses of evolutionists to criticism of their theory are often a good example of how steeped they are in their own metaphysics. You can point it out to them, but they are unmoved. They automatically read their own metaphysical issues into the criticism, and then criticize you for not adequately handling their metaphysical concerns. These responses we're seeing here are typical, and they speak volumes about what evolution is all about.Cornelius Hunter_{March 25, 2010
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This has got to be one of the most ridiculous things I have ever read. Duplications, deletions and insertions of genomes are occurring all the time. Are you saying that every time a duplication/insertion occurs, it has an important function? This is obviously ridiculous and would go against ID concepts about increasing information. Or are all of these changes harmful? Which wouldn't make sense since plenty of organism are still around with multiple insertions/duplications. Or are many of the duplications/insertions functionless. If so...there's your junk DNA.hdx_{March 25, 2010
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Again, you should try reading before criticizing with unfounded preconceptions about what the evolution skeptic must be saying.
Yes. Thanks. Again, no support. Just the claim that now somebody who actually read the text misunderstood it. Rather than criticizing me, you might want to consider that what you wrote is in fact very misleading. And, rather than criticizing me, you might want to take the time to erradicate such misunderstanding. Just a thought.hrun0815_{March 25, 2010
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hrun:
Ahh, now you are at least agreeing that it might be ‘SOME evolutionists’ rather than ‘evolutions’.
Ah, you've caught me, and now you can see me backpedaling to try to save face from my obvious inaccuracies you have cogently pointed out.
So if you never disputed that evolutionary biologists study and discover function in ‘junk DNA’ then what the point of your statement above? In fact, what is the point of the whole post?
Again, you should try reading before criticizing with unfounded preconceptions about what the evolution skeptic must be saying.Cornelius Hunter_{March 25, 2010
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Some evolutionists use the strategy of tossing out unfounded criticisms as fast as possible.
Ahh, now you are at least agreeing that it might be 'SOME evolutionists' rather than 'evolutions'. So if you never disputed that evolutionary biologists study and discover function in 'junk DNA' then what the point of your statement above? In fact, what is the point of the whole post?hrun0815_{March 25, 2010
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hrun:
You keep forgetting that all those scientists that studied the function of ‘junk DNA’ were actually evolutionists.
Again, I never said otherwise. Some evolutionists use the strategy of tossing out unfounded criticisms as fast as possible.Cornelius Hunter_{March 25, 2010
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aqeels:
I have always believed that if design is ultimately responsible for the complexity found in life, then junk DNA does not make any sense at all.
I can't argue with you there. This is a classic metaphysical argument for evolution which is not falsifiable. Evolution must be true.
The problem I have though is this; Why would the genome of certain onion species be about 5 times bigger than a humans?
Darwin's book, and the evolution genre, is full of "Why would's". Design is falsified and therefore evolution, in one way or another, must be true. It is a fact and a theory. The fact tells us it is true. The theory tries to explain how in the world the absurdity could actually have happened. And we call this science. :-(
This presents a real problem for design proponents as finding uses for some previously thought junk DNA sequences is fine, but how many novel functions can you expect to find for something as relativity simple as an onion?
I have no idea, but I can tell you that even if uses were found for all of it, evolution would not be harmed, for this is just one example of many biological structures that evolutionists mandate must not have been designed. Indeed, in cases where function is found, even there evolutionists don't give up their contention -- they say even if function if found, a designer would not have done it in such a strange way. That's religion for you.Cornelius Hunter_{March 25, 2010
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In fact, the OP doesn’t say otherwise. Did you actually read the OP, or is this just an evolutionary canard? You keep forgetting that all those scientists that studied the function of 'junk DNA' were actually evolutionists. And yet, I did read the OP. For starters, like so many times before, you misrepresent the term 'junk DNA'. And take for example this paragraph:
Evolutionists, unaware that they are staring at a design whose complexity dwarfs their puny understanding, decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Later, when the function is eventually uncovered, evolutionists automatically claim the design as an evolutionary achievement. The structure goes from junk to treasure without a second thought.
It's fiction, until you actually are able to support it with actual facts. That will be very hard for you.
hrun0815_{March 25, 2010
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hrun (3):
This OP is again riddled with assertions– none of which are actually supported by any evidence. For starters, junk DNA is a colloqial term. If you actually learn about what Cornelius calls ‘junk DNA’ you get much more info about what types there are, where it is found, how it likely came to be, and what its potential function could be. Among other things, you learn about the long history of experiments on ‘junk DNA’ by biologists (none of which is an ID proponent). What you find is, that in some cases function is found for stretches of this DNA. In very rare cases (like RNAi) completely new functions are found. However, biologists looked for those functions, no matter what the OP says.
In fact, the OP doesn't say otherwise. Did you actually read the OP, or is this just an evolutionary canard?Cornelius Hunter_{March 25, 2010
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This OP is again riddled with assertions-- none of which are actually supported by any evidence. For starters, junk DNA is a colloqial term. If you actually learn about what Cornelius calls 'junk DNA' you get much more info about what types there are, where it is found, how it likely came to be, and what its potential function could be. Among other things, you learn about the long history of experiments on 'junk DNA' by biologists (none of which is an ID proponent). What you find is, that in some cases function is found for stretches of this DNA. In very rare cases (like RNAi) completely new functions are found. However, biologists looked for those functions, no matter what the OP says. And the reason they were only found late is not because some biologists decided to go against some form of 'prevailing dogma'. The function if this DNA has continually be studied. And johnnyb's interjection about genome size would be spot on: If he had any evidence whatsoever that the onion is capable of genomic adaptation due to its 'junk DNA' while humans are capable of such adaptations because of their mind. A quick google search (e.g. here ) can be extremely informative. (It has a link to look at all the research on the onion genome as well. Read it here and compare that to the post by johnnyb.)hrun0815_{March 25, 2010
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aqeels - Why should humans be more complex? Humans have the least variability of just about any species on the planet. Plants, on the other hand, have to deal with a huge variety of biochemical situations. The human mind can adapt its environment to what it needs. Plants have no ability to adapt their environment, and therefore have to adapt themselves to whatever environment the find themselves in. Therefore, their biochemistry library (i.e. genome) is much bigger. I think your view of life is overly genocentric, and that is why it is causing difficulties.johnnyb_{March 25, 2010
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I have always believed that if design is ultimately responsible for the complexity found in life, then junk DNA does not make any sense at all. The problem I have though is this; Why would the genome of certain onion species be about 5 times bigger than a humans? This presents a real problem for design proponents as finding uses for some previously thought junk DNA sequences is fine, but how many novel functions can you expect to find for something as relativity simple as an onion? Evolutionists have made this point many times and readily accept that whilst certain sequences previously thought to be useless might show function, it is unwise to commit to the thesis that all DNA has purpose. This is a serious point. Onions are just one example amongst a vast list of simple organisms that have comparatively large genomes. Speaking as a computer scientist, the analogy would be to say that a simple password acceptance routine (the onion) has more lines of code when compared to a full blown operating system (the human). The premise of this problem is that complexity is directly proportional to size of genome. This might not be the case but if it is not then as design proponents what are we suggesting?aqeels_{March 25, 2010
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