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"The case for junk DNA"

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  • Jorge
    replied
    Originally posted by TheLurch View Post
    Well, knowing the book and having talked with Wells a number of times, the conclusion i reach is that Wells himself is not a reasonable, fair-minded person. He makes fundamental errors about biology when discussing junk DNA, and all indications are that he's doing so in order to reach the conclusions that he desires.
    Okay ... that's interesting. I myself have read the book and could not find anything like what you say. Perhaps it's because I do not have a PhD in genetics and cell biology. Oh well ...


    That's completely orthogonal to junk DNA. The "multiple codes" papers are about areas that encode proteins. Nobody considers those junk.
    Nope - you missed the point - in fact, several points. First, it is not known exactly how many codes there are in all. The sixteen that we listed in our paper are just the ones that we have been able to identify. It would be illogical to assume that we have identified all of them. It is certainly possible (and likely) that other codes operate with noncoding portions of the DNA and/or that codes that operate within the coding portion of the DNA make use of noncoding portions (see next) . Second, we certainly don't know everything (in most cases anything) about how those codes work. It may well be that, like a subroutine in a computer program, they branch off into other parts of the DNA (coding or noncoding).

    In any event, it is well beyond the observable facts to dogmatically claim that "junk DNA" is truly "junk" as certain Evolutionists do. They are merely speaking from ignorance.
    One thing is indisputable: if most of the genome truly is "junk DNA" then that would support Evolutionism. If there is a miniscule, insignificant or no "junk DNA" in the genome then that would not support Evolutionism. In other words, there is undoubtedly an ideological motivation towards promoting the notion of junk DNA. I'll let you draw your own conclusions from that.

    So, again, when your travels allow, i'd like to hear some of the evidence you feel has supported your position.
    In his book, Wells presents much of the evidence that you request - links, references, etc. are plentiful in his book. I referred you to that book. You have summarily dismissed it as if with a magic wand - POOF! If you did that to Wells, who does have equal academic standing with you, for me you won't even bother to pull out your magic wand. Anywho ... I get back home next week.

    Jorge

    Leave a comment:


  • rwatts
    replied
    Originally posted by Jorge View Post
    The authors (Palazzo and Gregory - P&G) have either forgotten their history ...
    Unlikely.

    A lot of their paper referred back to the history of the idea of "junk DNA". They reference associated material.

    Originally posted by Jorge
    ... or, in typical Evolutionist less-than-honest fashion, are giving us an 'Revised Evolutionist Version' in which the Evolutionists don't have egg on their face regarding all of the things that they believed, claimed and published in prestigious scientific journals about "junk DNA" in years past.
    Again that makes no sense, given that this junk/no junk argument as mostly been one between evolutionists. After all, unlike most of the creation scientists, evolutionists do actual research. So naturally, they would find evidence for junk DNA which would spark the skepticism of other evolutionists, and various evolutionists, as science progresses, would find evidence for so called junk DNA having actual functionality.

    Originally posted by Jorge
    The 'proof' of this is simple: why would so much effort have been spent by so many people to demonstrate -based on scientific observations - that the "junk DNA" claim is wrong if that claim wasn't there to begin with? It WAS there - I witnessed it and so did most of you people here on TWeb (you're old enough). You were there when "junk DNA" was loudly being trumpeted as "proof" of Evolution. Heck, O-Mudd repeats as much in an earlier post here. Now it appears that your recollections have 'morphed' into the REV (Revised Evolutionist Version).
    ???

    But the authors of that paper you claim to have read, show why the idea of junk DNA is still very relevant. And nothing has morphed. These authors are simply pointing out that too much is being made of the no junk DNA claim. They take a swipe at ENCODE for its bloated claims about 80% or more being functional.

    Are you sure you actually read it Jorge?

    Originally posted by Jorge
    I agree that P&G state many things in the paper that are scientifically true - I do not dispute that. What I am saying is that much in the paper is revised history, backpedaling and hindsight. Just another instance of the ethics that Evolutionists often employ. For example:

    "It has now become something of a cliché to begin both media stories and journal articles with the simplistic claim that most or all noncoding DNA was “long dismissed as useless junk.” The implication, of course, is that current research is revealing function in much of the supposed junk that was unwisely ignored as biologically uninteresting by past investigators. Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant”..."

    Only a person that has forgotten how it was 15-25 years ago (i.e., what was being said, taught and published) could write those words. I distinctly remember titles such as "JUNK DNA - Evolutionary Remnants" in which the authors boldly spoke of "junk DNA" as all but "proof" of an Evolutionary history. Now it's, "Oh, we knew it all along ... nobody said that ... repugnant". Yeah, rrrrrrright.

    Jorge
    But Jorge, they cite references to researchers (evolutionists) who were against the notion of junk-DNA. That is, it was not universally accepted. Nevertheless, as these authors point out, there is good scientific reason to maintain that it does exist, in vast quantities. They point out that the no junk DNA claim does not have a good pedigree. The evidence continues to weight against such a claim.

    So, are you able to address that evidence?
    Last edited by rwatts; 05-14-2014, 07:23 PM.

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  • Jorge
    replied
    Originally posted by rwatts View Post
    It looks to me as if you did not read the paper Jorge. It's reasonably readable for laymen like you and me.

    They provide good reasons for thinking there is still a lot of junk.
    Just returned from dinner having left TWeb "on" ...

    As always, you speak and judge without proper basis. Just what part of the paper do you think I haven't read (or understood)? I'll summarize for you what I picked up in the paper:

    The authors (Palazzo and Gregory - P&G) have either forgotten their history or, in typical Evolutionist less-than-honest fashion, are giving us an 'Revised Evolutionist Version' in which the Evolutionists don't have egg on their face regarding all of the things that they believed, claimed and published in prestigious scientific journals about "junk DNA" in years past. The 'proof' of this is simple: why would so much effort have been spent by so many people to demonstrate -based on scientific observations - that the "junk DNA" claim is wrong if that claim wasn't there to begin with? It WAS there - I witnessed it and so did most of you people here on TWeb (you're old enough). You were there when "junk DNA" was loudly being trumpeted as "proof" of Evolution. Heck, O-Mudd repeats as much in an earlier post here. Now it appears that your recollections have 'morphed' into the REV (Revised Evolutionist Version).

    I agree that P&G state many things in the paper that are scientifically true - I do not dispute that. What I am saying is that much in the paper is revised history, backpedaling and hindsight. Just another instance of the ethics that Evolutionists often employ. For example:

    "It has now become something of a cliché to begin both media stories and journal articles with the simplistic claim that most or all noncoding DNA was “long dismissed as useless junk.” The implication, of course, is that current research is revealing function in much of the supposed junk that was unwisely ignored as biologically uninteresting by past investigators. Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant”..."

    Only a person that has forgotten how it was 15-25 years ago (i.e., what was being said, taught and published) could write those words. I distinctly remember titles such as "JUNK DNA - Evolutionary Remnants" in which the authors boldly spoke of "junk DNA" as all but "proof" of an Evolutionary history. Now it's, "Oh, we knew it all along ... nobody said that ... repugnant". Yeah, rrrrrrright.

    Jorge
    Last edited by Jorge; 05-14-2014, 07:07 PM.

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  • TheLurch
    replied
    Originally posted by Jorge View Post
    I'm on travel now but I can think of no better source to give you than The Myth of Junk DNA by J. Wells. Any reasonable, fair-minded person reading that book would immediately and forevermore abandon the notion of DNA being "junk" in whole or in part.
    Well, knowing the book and having talked with Wells a number of times, the conclusion i reach is that Wells himself is not a reasonable, fair-minded person. He makes fundamental errors about biology when discussing junk DNA, and all indications are that he's doing so in order to reach the conclusions that he desires.

    Originally posted by Jorge View Post
    Also, and quickly, I'm likely nowhere near your level of expertise in molecular and cell biology. I'm more versed in information theory and it is on that basis that I've determined that the notion of "junk DNA" is unsupportable. Specifically, you are aware, I presume, of the multiple codes in the DNA - also known as poly-functional DNA. Trifanov identified no fewer than twelve separate codes in DNA (1-2). In a paper that I co-authored (3) we listed sixteen codes with others possible.
    That's completely orthogonal to junk DNA. The "multiple codes" papers are about areas that encode proteins. Nobody considers those junk.

    So, again, when your travels allow, i'd like to hear some of the evidence you feel has supported your position.

    Leave a comment:


  • rwatts
    replied
    Originally posted by oxmixmudd View Post
    That it does 'nothing' is overreaching.
    A lot of what was considered junk, does appear to get transcribed and even translated.

    However, they think this is still junk in the sense that it fails to produce useful protein. With the stuff that gets transcribed but not translated, it gets broken down. The stuff that goes to translation is open to selection. There is a possibility that new genes evolve this way:-

    The Continuing Evolution of Genes

    Proto-genes and de novo gene birth

    Leave a comment:


  • rwatts
    replied
    Originally posted by Jorge View Post
    Yes, an insignificant portion of DNA may become "junk" due to deleterious mutation(s) but, ....
    Getting ready for the backpedal?

    Originally posted by Jorge
    ... overall, there is no "junk" in the DNA due to an Evolutionary history.
    But there would be. Once a gene turns to junk you have a modification which gets passed on by common descent. (Common descent with modification.).

    It would become part of a phylogenetic signal, which could be used to construct trees illustrating degrees of relatedness.

    Leave a comment:


  • rwatts
    replied
    Originally posted by Roy View Post
    It's worth expanding on one of the points made briefly in the article.

    Genetic fingerprinting works by measuring the number of copies a person has of each of several repeated DNA sequences. The number of repetitions of each of these sequences varies widely among individuals, and there are trillions of possible combinations of copy numbers, making the chance that any two random people have the same combination very small. Since the DNA in these repeated sequences can vary in length without any apparent effect, it's clear that the repetitions beyond the minimum number found for each of these sequences are unnecessary. Or, to put it another way, if there was no 'junk' DNA, genetic fingerprinting would not work. Since it does work, there is 'junk' DNA.

    Roy
    I thought the "Onion test" was a beauty as well.

    Leave a comment:


  • Jorge
    replied
    Originally posted by Roy View Post
    That's not falsifiable. Failure can always be dismissed as being due to the significance not having been discovered yet.

    Roy
    True. HOWEVER ...

    You people are always bringing up the "God of the gaps" nonsense, saying that the "gaps are decreasing inversely with knowledge" (a stupid remark, but that's another story).

    Well, okay, as more and more is observed/discovered, much of what was once believed (by the Evos) to not have significance/play a part is now known to be significant/play a part. Ergo, my claim IS falsifiable.

    Spelling it out for you (as I know of your logic handicap) - if since the 1990's (when I made my prediction) the opposite would have been observed (i.e., NO function for the "junk" would have been observed/discovered) then I would have been falsified. Instead, what has been observed/discovered to date supports my claim (my claim is not proven, but certainly supported and most certainly not falsified). Furthermore, I predict that this trend will continue. If it doesn't then I stand falsified.


    Pay the lady a buck and do try again, Roy - it's always amusing.

    Jorge

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  • rwatts
    replied
    Originally posted by Jorge View Post
    ********************************

    I told this story before (in the 'old' TWeb) that now, thanks to Roland, bears repeating:

    Back in the early 1990's (going on memory here) I was debating an Atheist on Evolution v. Creation. At that time, "junk DNA" was being loudly touted by Evolutionists as "clear proof of Evolution". This Atheist brought the argument up proudly and loudly. As a Creationist, I of course think that that claim is nonsense. IMO, they call it "junk" because, (1) it supports their ideological beliefs and, (2) they are clueless as to its function.

    So I expressed this to the Atheist and made a falsifiable prediction: I said, "Based on my model (Creationism), I predict that in the upcoming years - as more and more is learned about this "junk DNA" - it will be discovered to be as significant, if not more significant, than the coding DNA."

    The rest is history - my prediction is becoming more and more confirmed.

    Of course, there are Die-Hard-Fanatical Evolutionists that refuse to give up. In spite of the large and growing body of evidence that the "junk DNA" claim is, well, JUNK, some Evolutionists will continue promoting this concept. This article that Roland brings up testifies towards that fact.

    I will merely repeat my falsifiable prediction: watch as the drama unfolds - as the body of scientific observations continues to mount - and you'll see the notion of "junk DNA" take the route of the Dodo Bird.

    Then, also predictably, the Evolutionists will continue parroting their other beliefs.

    Jorge
    It looks to me as if you did not read the paper Jorge. It's reasonably readable for laymen like you and me.

    They provide good reasons for thinking there is still a lot of junk.

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by Jorge View Post
    I'm on travel now but I can think of no better source to give you than The Myth of Junk DNA by J. Wells. Any reasonable, fair-minded person reading that book would immediately and forevermore abandon the notion of DNA being "junk" in whole or in part.

    Also, and quickly, I'm likely nowhere near your level of expertise in molecular and cell biology. I'm more versed in information theory and it is on that basis that I've determined that the notion of "junk DNA" is unsupportable. Specifically, you are aware, I presume, of the multiple codes in the DNA - also known as poly-functional DNA. Trifanov identified no fewer than twelve separate codes in DNA (1-2). In a paper that I co-authored (3) we listed sixteen codes with others possible.

    BOTTOM LINE: I believe that anyone promoting any significant portion of the DNA as "junk" will find egg on their face in the future. Yes, an insignificant portion of DNA may become "junk" due to deleterious mutation(s) but, overall, there is no "junk" in the DNA due to an Evolutionary history. Future scientific observations will falsify or support this claim.


    (1) Trifanov, EN (1989) Multiple Codes of Nucleotide Sequences, Bull of Mathematical Biology 51:417-432
    (2) Trifanov, EN (1997) Genetic Sequences as Products of Compression by Inclusive Super-position of Many Codes, Mol Biol 31:647-654
    (3) Montanez, Marks, Fernandez & Sanford, Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation, Biological Information: New Perspectives, Symposium Proceedings, World Scientific, 2013, pp. 139-167

    Jorge
    I think the point is that there are large portions of non-coding DNA in our genomes that are common to other lineages and which, in many cases, are leftovers from evolution.

    That it does 'nothing' is overreaching. What is happening is a set of chemical reactions (i.e. a non-abstract system). It is very unlikely ANY of it sits around and does 'nothing' in the most literal sense. Nevertheless, there are large portions that don't do very much and show all the signs of having once been active coding DNA in the past:

    http://abcnews.go.com/Technology/story?id=1666805

    or having been inserted by a retro virus or (long list of things not expected by YEC inserted here)

    That there exist genes for making teeth in an animal that no longer grows them but whose ancestry as implied by the fossils AND the genetics DID grow them is a MAJOR problem for a non-evolutionary hypothesis. That DNA someone classified as "Junk" is now discovered not to be "Junk" is really only a problem for the fellow that classified it as "Junk" in the first place.



    Jim

    Leave a comment:


  • Roy
    replied
    Originally posted by rwatts View Post
    It's worth expanding on one of the points made briefly in the article.

    Genetic fingerprinting works by measuring the number of copies a person has of each of several repeated DNA sequences. The number of repetitions of each of these sequences varies widely among individuals, and there are trillions of possible combinations of copy numbers, making the chance that any two random people have the same combination very small. Since the DNA in these repeated sequences can vary in length without any apparent effect, it's clear that the repetitions beyond the minimum number found for each of these sequences are unnecessary. Or, to put it another way, if there was no 'junk' DNA, genetic fingerprinting would not work. Since it does work, there is 'junk' DNA.

    Roy

    Leave a comment:


  • Roy
    replied
    Originally posted by Jorge View Post
    So I expressed this to the Atheist and made a falsifiable prediction: I said, "Based on my model (Creationism), I predict that in the upcoming years - as more and more is learned about this "junk DNA" - it will be discovered to be as significant, if not more significant, than the coding DNA.
    That's not falsifiable. Failure can always be dismissed as being due to the significance not having been discovered yet.

    Roy

    Leave a comment:


  • klaus54
    replied
    Originally posted by Jorge View Post
    You really must learn to read more carefully.

    I do not believe that "junk DNA" exists so why are you asking for me to define it? YOU are the ones that believe that "junk DNA" exists - YOU define it. E.g., some of you refer to it as "junk" if it does not code for anything (that you can determine) and/or if you believe it to be "unnecessary for the function of the organism". Take it from there if you like.

    Well, I got'ta go. In Omaha, Nebraska now, heading towards Coralville, Iowa later today.

    P.S. Be sure to look at Post # 6 just above and try not to choke on it. Ta-ta ...

    Jorge
    Jorge,

    Duh! So what do call the parts of the human genome that were craptastically called "junk" DNA?

    K54

    P.S. Do you treat "junk" DNA in the same despicable manner that creationists snarked about "vestigial structures"?
    Last edited by klaus54; 05-14-2014, 10:12 AM. Reason: P.S.

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  • Jorge
    replied
    Originally posted by klaus54 View Post
    Jorge,

    Could tell us in a couple of sentences what you think "junk" (a term that never should have been coined) DNA is?

    How does your notion of junk DNA support your creationism "model" (another terrible misuse of language)?

    Donkey Schern!

    K54
    You really must learn to read more carefully.

    I do not believe that "junk DNA" exists so why are you asking for me to define it? YOU are the ones that believe that "junk DNA" exists - YOU define it. E.g., some of you refer to it as "junk" if it does not code for anything (that you can determine) and/or if you believe it to be "unnecessary for the function of the organism". Take it from there if you like.

    Well, I got'ta go. In Omaha, Nebraska now, heading towards Coralville, Iowa later today.

    P.S. Be sure to look at Post # 6 just above and try not to choke on it. Ta-ta ...

    Jorge

    Leave a comment:


  • klaus54
    replied
    Jorge,

    Could tell us in a couple of sentences what you think "junk" (a term that never should have been coined) DNA is?

    How does your notion of junk DNA support your creationism "model" (another terrible misuse of language)?

    Donkey Schern!

    K54

    Leave a comment:

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