Saturday, August 3, 2013

More Functions For “Junk” DNA

Introns Can Regulate Gene Expression

In the aftermath of Dan Graur’s claim that either our genome is mostly junk or evolution is false, new research is finding yet more ways that the so-called junk DNA is, in fact, functional. This time it is the introns which have been found to help with regulation of gene expression. As one of the researchers explained:

This discovery, involving what was previously referred to as "junk," opens up a new level of gene expression control that could also play a role in the development of many other tissue types. Our observations were quite surprising and they open entirely new avenues for potential treatments in diverse diseases including cancers and leukemias.

But as we explained, not only does Graur’s claim vastly underestimate the malleability of evolutionary theory—evolutionists could easily accommodate a largely functional genome—it will never even be tested.

For evolutionists will never allow the genome to be viewed as functional or mostly functional, no matter what the evidence. Instead, any and all functions—and there will be many—for “junk” DNA will never alter its status of junk but merely will be viewed as lucky function which the “junk” DNA happened to stumble upon.

As with the so-called vestigial structures—another evolutionary construct—function is, ultimately, irrelevant. A structure is “vestigial,” or DNA is “junk,” not by virtue of any objective criterion dealing with function, but because evolutionists say so.

Evolutionary conclusions are driven by evolutionary assumptions, not by the evidence. Junk DNA does not support the claims of evolution; rather, evolution supports the claims of junk.

Religion drives science and it matters.

49 comments:

  1. This may be of interest also > http://link.springer.com/article/10.1186%2F1877-6566-7-2

    Larry Moran and crowd seem very concerned > http://sandwalk.blogspot.com/2013/08/the-junk-dna-controversy-john-mattick.html

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    1. Wow! Mattick's paper published in a peer reviewed journal. His conclusions that "we suggest that resistance to these findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design." must be true!

      "HUGO is a peer-reviewed open access journal published under the brand SpringerOpen. HUGO is the Official Journal of the Human Genome Organisation and publishes original papers and articles on all aspects of genomic medicine. "

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    3. @ awstar:

      No, anyone with a fair mind would draw the conclusion the Junk DNA ideologues are having a hissy fit, as demonstrated on Moran's blog, especially by the character "Diogenes"

      And further demonstrated by Shapiro > http://www.huffingtonpost.com/james-a-shapiro/further-thoughts-on-the-e_b_1893984.html


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    4. misc, why did you start your response to awstar with the word "No"? What is it that you don't agree with?

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    5. "Larry Moran and crowd seem very concerned > http://sandwalk.blogspot.com/2013/08/the-junk-dna-controversy-john-mattick.html"

      LOL. I got my popcorn out. These are great days to watch the darwinists do exactly what they accuse IDist of - fighting against the evidence. They placed too much weight on the Junk DNA argument to the public and its spinning around to bite them in the rear.

      funny stuff....need another bucket of popcorn. Moran's head is about to spin off :)

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    6. Oh my they are ready to rip him a new one for this as Moran summarizes -

      "The last two references are to Michael Behe's paper about functional pseudogenes and to Jonathan Wells' book The Myth of Junk DNA. I don't think I've ever see a legitimate scientific paper that references that book by Jonathan Wells.

      Mattick also uses IDiot terminology when he says that, "...the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution." As you should all know by now, the accumulation of junk DNA is the antithesis of "Darwinian evolution." You should also note that it's mostly IDiots who get confused about the difference between junk DNA and "non-protein-coding" DNA.

      I find that very troubling."

      I bet you do Moran Not because its an endorsement but because

      A) Someone was willing to say a major argument against ID is less than devastating and likely is terribly wrong.
      B) Someone was honest enough to admit the bias.

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    7. @ Elijah2012

      I have my bag of popcorn in hand also. :) Lee Bowman is making a strong argument here with Dr. Hurd > http://chronicle.com/article/Ball-State-U-Bars-Teaching-of/140777/

      Keep hitting 'load more comments' toward end of comment thread.

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    8. rjop

      Lee Bowman is making a strong argument here with Dr. Hurd > http://chronicle.com/article/Ball-State-U-Bars-Teaching-of/140777/


      LOL! Hardly. Bowman is just regurgitating the same old tired ID talking points - ID isn't about religion blah blah blah, whining about the Kitzmiller v. Dover decision, etc. Dr. Hurd is both a competent scientists and qualified as an expert scientific witness in legal cases. He's mopping the floor with Bowman's blustering rhetoric.

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    9. rjop,

      To be honest the whole Ball State thing doesn't interest me much. Its not like similar universities haven't had the same positions but less public. The way that "junk" DNA research is going situations like that may well be taken care of by the science. IF the ENCODE scientists (and others as well) prove to be right it will change forever the effectiveness of the Darwinian rhetoric as far as the public is concerned. In fact the way the die hard atheistic community is trying to rag on ENCODE scientists its creating a split that will allow a lot more honesty to come out of the debate.

      Moran's blog comments are particularly amusing because if you read them you can see them trying the same tactics of claiming a well known respected scientists doesn't know anything about the science (a couple people had to reign that silliness in).

      This is a GAME CHANGER where Ball State is just another ruckus. Atheistic Darwinists are going all in with defending Junk DNA and IF ENCODE wins out it will have sweeping repercussions all of which would benefit ID.

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    10. @ Thorton,

      The only whining would be coming from you here day after day.

      @ Elijah2012. I have read the comments, I posted the link.(under different handle). Yes, quite amusing at Moran's blog, same thing happened with Shapiro and Birney when ENCODE was first announced.

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    11. rjop

      The only whining would be coming from you here day after day.


      LOL! I see, you're another one of those brave Creationists who only crawls out from under his rock just long enough to toss some mud, then scuttles quickly back into the shadows.

      At least you know your limitations.

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    13. @ Thorton,

      I really see no difference in occasionally tossing mud in comparison to those who do it on an hourly, daily and yearly basis. The only difference is the later would suggest Psychosis. Perhaps you should also consider your limitations, or shall I say hypocrisy, and take a hard look the in mirror..

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    14. *in the mirror.. (comment section needs edit feature ;)

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    15. rjop

      (crawls out from under rock)

      (tosses some mud)

      (scuttles quickly back into the shadows)


      Exactly as predicted.

      Here's the thing you Fundies never get - your continual egregious lying about scientists and their work is every bit as insulting to the scientists as any ad hom you may toss. You you idiots think insulting honest scientists is perfectly OK as long as you use polite flowery language to do it.

      Pity you guys don't follow a book that teaches "Thou shalt not lie".

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  2. The humble onion has around 12 times as much DNA as we do, the microscopic amoeba something like 200 times. Now, unless they're secretly doing a whole lot of super-intelligent stuff we haven't seen yet (how about a movie called "The Revenge of the Killer Onions") there's a whole lot of DNA in there not doing much.

    Add to that the experiments where substantial parts have been cut out of the genomes of test animals without any observable effect and you get the distinct impression that a goodly portion of it is just along for the ride.

    Finding that some introns may be involved in tweaking gene expression don't really change that.

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    1. I have a theory that the extra DNA of onion stores bootleg copies of Left Behind.

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    2. Clearly justifying the use of the term "junk".

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    3. IH Spedding:

      Now, unless they're secretly doing a whole lot of super-intelligent stuff we haven't seen yet (how about a movie called "The Revenge of the Killer Onions") there's a whole lot of DNA in there not doing much.

      ID is often denigrated because it is supposed to cut-off further investigation and research. You know: "God-did-it," so, end of story.

      How untrue this is. ID is but simply a guide as to how and what to investigate.

      Here, Ian, you present, in contradistinction to the ID perspective, an evolutionary mindset that indeed "cuts-off" further research.

      What do I mean?

      You tell us that the onion has 12 times as much DNA as humans do. Therefore, it MUST be "junk." End of discussion.

      Now here's the ID perspective:

      WHY does the "humble onion" have 12 times as much DNA as humans?

      Two possible reasons:
      (1) There is a built in effeciency in the human genome that exists because of very tight embryonic constraints, or
      (2) the onion, unable to move, and so subject to all sorts of environmental constraints, needs added copies of its DNA in order to survive extreme environmental conditions. Part of this strategy might be to have a number of extra copies wherein a higher level of mutations occur due to NS not 'reining in' the genome in. I.e., neutral drift. And then, when the environment demands it, the needed mutations are ready at hand.

      The evolutionists point of view given the same set of facts: it's "junk"! No need to study it any further.

      Now who are the true scientists here?

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    4. Maybe it's time to think up a new definition of "junk".

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    5. Mistake number 1:
      Assuming the onion is "humble".

      Recent research has shown that the onion is a formidable organism not to be taken so lightly. They have been cultivating humans for thousands and thousands of years to the point where they no longer have to do the work for themselves. In their DNA is code for complex body plans including a very large brain! They just don't need to express those anymore as their cultivation project worked and the humans are doing all the hard work for them!

      Mistake number 2:
      Well I lost track so I will stop there on the mistakes front.

      On a more serious note I am curious as to the experiment you mentioned; removing DNA segments from animals. Do you recall how much was taken out, substantial could be anything really? Also did it mention if any DNA was repaired, or was it all permanently lost?

      Thanks

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    6. Lino,
      Here, Ian, you present, in contradistinction to the ID perspective, an evolutionary mindset that indeed "cuts-off" further research


      Perhaps you should link those ID inspired studies preformed by IDists.

      There is a built in effeciency in the human genome that exists because of very tight embryonic constraints,

      So would proof of inefficiencies be evidence For non intelligent design theory? After all per DrHunter, is a theory accommodates both A and Not A then A cannot be evidence for the theory. More generally what could be Not A for an intelligent design theory?

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    7. bw August 3, 2013 at 10:31 AM

      Mistake number 1:
      Assuming the onion is "humble".


      Okay, I'll give you that one. If we are ever taken out of the picture then, with all that DNA, onions could eventually rule the world.

      Or the amoeba.

      Or Christmas trees.

      Mistake number 2:
      Well I lost track so I will stop there on the mistakes front.


      Phew!

      On a more serious note I am curious as to the experiment you mentioned; removing DNA segments from animals. Do you recall how much was taken out, substantial could be anything really? Also did it mention if any DNA was repaired, or was it all permanently lost?

      I think this is the one:

      Nabrega, M. Y. Zhu, I. Plajzer-Frick, V. Afzal and E. M. Rubin. 2004. Megabase deletions of gene deserts result in viable mice. Nature 431:988-993.

      It was apparently only about 3% which doesn't sound like much but if it's all functional as EID proponents believe then deleting it should have made a difference.

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    8. Lino Di Ischia August 3, 2013 at 9:44 AM

      [...]

      ID is often denigrated because it is supposed to cut-off further investigation and research. You know: "God-did-it," so, end of story.


      It's the creationist wing of the movement that indulges in the "Goddidit" cop-out rather than the EIDers, although there's considerable overlap between the two.

      The problem for EID is that, for scientific purposes, there really isn't much difference between God and an Extraterrestrial Intelligent Designer of unspecified nature and powers. They're both suggestions - or just labels, really - for 'who' not 'how'. That's not an explaantion.

      How untrue this is. ID is but simply a guide as to how and what to investigate.

      Not unless you say something about the nature of the designer it isn't.

      Here, Ian, you present, in contradistinction to the ID perspective, an evolutionary mindset that indeed "cuts-off" further research.

      What do I mean?

      You tell us that the onion has 12 times as much DNA as humans do. Therefore, it MUST be "junk." End of discussion.


      Who said anything about "end of discussion"?

      Now here's the ID perspective:

      WHY does the "humble onion" have 12 times as much DNA as humans?

      Two possible reasons:
      (1) There is a built in effeciency in the human genome that exists because of very tight embryonic constraints, or
      (2) the onion, unable to move, and so subject to all sorts of environmental constraints, needs added copies of its DNA in order to survive extreme environmental conditions. Part of this strategy might be to have a number of extra copies wherein a higher level of mutations occur due to NS not 'reining in' the genome in. I.e., neutral drift. And then, when the environment demands it, the needed mutations are ready at hand.


      Good start. Now all you have to do is get into the laboratory or out in the field and find evidence to support those claims.

      The evolutionists point of view given the same set of facts: it's "junk"! No need to study it any further.

      Now who are the true scientists here?


      In case you hadn't noticed, all the research - past and ongoing - cited by CH, all the information we now have about DNA, the sizes of different genomes and the functions - or lack thereof - of the genes within - has come from evolutionary biology. Not so much from EID.

      I'd say it's pretty obvious who the real scientists are.

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    9. Lino,
      the onion, unable to move, and so subject to all sorts of environmental constraints, needs added copies of its DNA in order to survive extreme environmental conditions. Part of this strategy might be to have a number of extra copies wherein a higher level of mutations occur due to NS not 'reining in' the genome in. I.e., neutral drift. And then, when the environment demands it, the needed mutations are ready at hand.


      Interesting, but " Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum? "

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    10. I'll add to what velikovskys said and mention that the great variability in genome size exists in many living organisms other than onions. Most notably, it exists in amphibians and flowering plants. This graph gives a general overview of the genome sizes of different groups of organisms.

      But the onion example illustrates the picture very well. Since you see great variability in the genome size of closely related species.

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    11. pav-lino said:

      "The evolutionists point of view given the same set of facts: it's "junk"! No need to study it any further."

      Au contraire mon IDiot, lots of scientists (most or all of which you would call "evolutionists") are studying all aspects of DNA.

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    12. ShadiZ1:

      you see great variability in the genome size of closely related species.

      Which is unexpected on evolutionary theory.

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    13. Cornelius Hunter

      ShadiZ1: "you see great variability in the genome size of closely related species."

      Which is unexpected on evolutionary theory.


      It's also not precluded by evolutionary theory.

      What is Intelligent Design Creationism's explanation for the observed great variability in genome size of closely related species?

      Anyone?

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    14. DrHunter,
      Which is unexpected on evolutionary theory


      The unexpected is normal, but it sort of deflates everything is purposeful conjecture, though junk DNA or no Junk DNA are both equally possible with a designer, so the existence or non existence of junk" DNA is no evidence for design, correct?

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    15. "It was apparently only about 3% which doesn't sound like much but if it's all functional as EID proponents believe then deleting it should have made a difference."

      Weak....The paper itself admits that it did not test for enough functions to rule out any function whatsoever.

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    16. "This graph gives a general overview of the genome sizes of different groups of organisms. "

      I don't suppose any one noticed that the organism types that have the narrowest bands were on the ark, and those with the wider bands had to make their way through the flood on their own.

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  3. At least in the case I'm aware of, the "parts" "cut out ... without any observable effect" were inferred (per their assumptions about indicators of relatedness and time of origin) to be surprisingly "conserved." Thus those "parts" are not explained plausibly by theory. They could be functional in ways we are yet ignorant of. For example, they could be functional in ways specific to only certain conditions, thereby explaining at least the surprising "conserved" feature.

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  4. And yet again conflating non-coding DNA with junk DNA. Dr. Hunter, how many times did Dan Graur emphasize in his lecture at the SMBE the mistake that many people make in conflating junk DNA with non-coding DNA? And why are you unwilling to engage with the many population genetics arguments for the existence of junk DNA? Did you sufficiently address the onion test that T. Ryan Gregory proposed?

    Besides, can you tell your readers how much of the introns did the researchers analyze? Even if all introns in the genome turned out to be functional, which is obviously and unambiguously not the case, they don't make more than 30% of the genome (which is well under Graur's minimum estimate for junk in the genome -- since he puts the estimate at at least 65%).

    And if you really do care about science not getting influenced or driven by ideology or media hype, I hope that you do take a look at the paper that Graur has been digging through and tell us your opinion on the quality of the science that the ENCODE project has been doing.

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    1. ShadiZ1:

      Did you sufficiently address the onion test that T. Ryan Gregory proposed?

      I made no such claim of universal function for non-coding DNA.

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    2. Cornelius Hunter

      I made no such claim of universal function for non-coding DNA.


      We know CH. Weasel wording and plausible deniability are among the most useful skills of a Creationist professional propagandist.

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  5. "And yet again conflating non-coding DNA with junk DNA. Dr. Hunter, how many times did Dan Graur emphasize in his lecture at the SMBE the mistake that many people make in conflating junk DNA with non-coding DNA?"




    So what difference does it make how many times Graur said anything? What is the significance of that? Graur can say anything he wants. Whether or not that has scientific support needs to be tested. So, whoever conjectures whatever, has to stand to real scientific scrutiny, or else it might as well be classified as BS.

    You nde proponents need to be REMINDED OF THE REALITY OF REAL SCIENCE, or get the F out of here. You imbeciles.

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  8. "I'll add to what velikovskys said and mention that the great variability in genome size exists in many living organisms other than onions."

    So the F what? Just show how nde was able to construct the basis for what you call genomic variability. You simpleton.

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    1. bpragmatic,
      So the F what? Just show how nde was able to construct the basis for what you call genomic variability. You simpleton.


      Very persuasive argument . How did the designer construct the genome?

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    3. Drunk and angry teenage Fundy spotted.

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    4. What an IDIOTIC comment. Who knows how a hypothetical designer would have constructed the genome.

      Good point, who could know?

      What a lame argument. You should know better than that. But knowing the philosophy your mind is so entrenched in, I can understand why you would ask such a dipshit question

      It was a question, not an argument. I just assumed you were capable of curiosity. Apologies.

      I doubt you understand anything about me, bg, but I am interested in hearing your theory if you can string a couple of complete thoughts together.

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  9. "Au contraire mon IDiot, lots of scientists (most or all of which you would call "evolutionists") are studying all aspects of DNA."


    Au contraire you clown. Those who you claim are "lots of scientists" are so concerned about their jobs and pensions that they absolutely do not want to upset the STATUS QUO because they want to be comfortable until they die. The majority of them will turn their heads to any kind of real evidence that, even if they really agree with, will put their comfort in jeopardy. THIS IS NOT SCIENCE!

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    1. I'm not following you.

      Are you saying all the papers being published by scientists on DNA are not the result of scientist studying DNA?

      If not, then what exactly are you saying?

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