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"The case for junk DNA"

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  • "The case for junk DNA"

    Thanks to Steviepinhead at TR for bringing this to our attention.

    An online article from PLoS Genetics which puts junk DNA back into context:-

    The Case for Junk DNA

    From the overview (highlighting mine):-

    Originally posted by link above
    With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcriptomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as “junk DNA.” Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the fundamental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation.

  • #2
    Originally posted by rwatts View Post
    Thanks to Steviepinhead at TR for bringing this to our attention.

    An online article from PLoS Genetics which puts junk DNA back into context:-

    The Case for Junk DNA

    "With the advent of deep sequencing technologies and the ability to analyze whole genome sequences and transcriptomes, there has been a growing interest in exploring putative functions of the very large fraction of the genome that is commonly referred to as “junk DNA.” Whereas this is an issue of considerable importance in genome biology, there is an unfortunate tendency for researchers and science writers to proclaim the demise of junk DNA on a regular basis without properly addressing some of the fundamental issues that first led to the rise of the concept. In this review, we provide an overview of the major arguments that have been presented in support of the notion that a large portion of most eukaryotic genomes lacks an organism-level function. Some of these are based on observations or basic genetic principles that are decades old, whereas others stem from new knowledge regarding molecular processes such as transcription and gene regulation."
    ********************************

    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

    Comment


    • #3
      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
      Jorge,

      Regardless of "junk" DNA (terrible term that should never have been coined), DNA is still not your friend. Clades are determined by it as well as evolutionary history in general.

      Put some of your slobber in a vial and send it to 23andMe.com for a little shocker. I'm 2.7% Neanderthal. I'll wager your percent is higher than that.

      https://www.23andme.com/

      K54

      P.S. Oh, and how about that nasty (2p, 2q) thingy and that darn mutated GLO gene in humans and other primates?

      I know it's slightly off topic, but it's high time somebody put you in your place.

      Whadda ya think, Boss?

      Another notch down...
      Last edited by klaus54; 05-14-2014, 07:56 AM. Reason: grammar

      Comment


      • #4
        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."

        The rest is history - my prediction is becoming more and more confirmed.
        Could you provide some of this confirming evidence?

        Separately, the paper linked in the OP indicates that a very significant fraction of many eukaryotic genomes is in fact junk. Could you point out the flaws in the paper's arguments? My PhD is in molecular and cell biology, so feel free to get as technical as you desire.
        "Any sufficiently advanced stupidity is indistinguishable from trolling."

        Comment


        • #5
          Jorge,

          In what sense, other than philosophical, is creationism a "model"? Same deal for ID.

          K54

          Comment


          • #6
            Originally posted by TheLurch View Post
            Could you provide some of this confirming evidence?

            Separately, the paper linked in the OP indicates that a very significant fraction of many eukaryotic genomes is in fact junk. Could you point out the flaws in the paper's arguments? My PhD is in molecular and cell biology, so feel free to get as technical as you desire.
            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

            Comment


            • #7
              Originally posted by klaus54 View Post
              Jorge,

              In what sense, other than philosophical, is creationism a "model"? Same deal for ID.

              K54
              You need to 'hit' them-there books, Santa.

              Creationism is not a "model" in the technical sense of the word - it is an ideological position, a worldview. Exactly in the same way as is Atheism, Humanism, ...

              I was using the term "model" loosely (in the sense that I clarified above) but I forgot that you guys like to strain on gnats while swallowing the entire camel. I'll try to be more careful in the future.

              Jorge

              Comment


              • #8
                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

                Comment


                • #9
                  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

                  Comment


                  • #10
                    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.

                    Comment


                    • #11
                      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
                      Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                      mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

                      Mountain Man: First of all, the Bible is a fixed document.
                      Mountain Man: … this is how liberals argue these days, with labels instead of ideas.

                      Comment


                      • #12
                        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
                        Jorge: Functional Complex Information is INFORMATION that is complex and functional.

                        mikewhitney: What if the speed of light changed when light is passing through water? ... I have 3 semesters of college Physics.

                        Mountain Man: First of all, the Bible is a fixed document.
                        Mountain Man: … this is how liberals argue these days, with labels instead of ideas.

                        Comment


                        • #13
                          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
                          He will reply, ‘Truly I tell you, whatever you did not do for one of the least of these, you did not do for me."

                          "So in everything, do to others what you would have them do to you, for this sums up the Law and the Prophets"

                          Comment


                          • #14
                            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.

                            Comment


                            • #15
                              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

                              Comment

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