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"The case for junk DNA"

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  • klaus54
    replied
    Originally posted by Catholicity View Post
    Clearly Jim doesn't talk about the length of time he's been married to his wife. And you obviously don't have a clue about logic and reason if you believe that a conclusion and then a person believes he/she should take revenge or something. In fact I think the ONLY issue Jim has with a person believing in YEC is the insistence that its somehow a requirement for salvation. Which you seem to believe. So you might want to come down from that stupid tree you climbed up.
    Jorge,

    Is this true? Do you really believe your scientifically risible position is a salvific issue??

    And in a previous thread you weren't even able to support your belief Biblically; you couldn't even get past Ge 1:3!!!

    Amazing hubris...!

    I think I'll ping that thread again -- just for you!

    K54

    P.S. Do you really believe that the various large impact structures are not formed by meteor impacts but rather by steam explosions???!

    Have you ever heard of shocked quartz and shatter cones?

    Leave a comment:


  • Catholicity
    replied
    Originally posted by Jorge View Post
    I am convinced - convinced! - that a YEC stole your teenage girlfriend and you now have a vendetta against anyone even remotely connected to YEC.

    Your statement that "... science is a continuous process of learning" is a bunch of unethical hogwash. First, what "science" are you speaking of? Evolution? Physics? Second, ALL areas of study involve a continuous process of learning. Why do 'you people' believe that you've cornered the market of learning? Worse yet, you think you've cornered that market and have locked OUT anyone that doesn't agree with your views. Yeah, that's "good science" alright; more like Medieval dogmatism if you ask me.

    Anyway, you remain clueless, O-Mudd. But do keep trying.

    Jorge
    Clearly Jim doesn't talk about the length of time he's been married to his wife. And you obviously don't have a clue about logic and reason if you believe that a conclusion and then a person believes he/she should take revenge or something. In fact I think the ONLY issue Jim has with a person believing in YEC is the insistence that its somehow a requirement for salvation. Which you seem to believe. So you might want to come down from that stupid tree you climbed up.

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by Jorge View Post
    I am convinced - convinced! - that a YEC stole your teenage girlfriend and you now have a vendetta against anyone even remotely connected to YEC.

    Your statement that "... science is a continuous process of learning" is a bunch of unethical hogwash. First, what "science" are you speaking of? Evolution? Physics? Second, ALL areas of study involve a continuous process of learning. Why do 'you people' believe that you've cornered the market of learning? Worse yet, you think you've cornered that market and have locked OUT anyone that doesn't agree with your views. Yeah, that's "good science" alright; more like Medieval dogmatism if you ask me.

    Anyway, you remain clueless, O-Mudd. But do keep trying.

    Jorge
    Well - you were also "convinced - convinced!", sylas was a TE posting on these pages and he deconverted before your eyes. Likewise your are "convinced - convinced!" all the major meteor impacts are steam explosions, and likewise you are "convinced - convinced!" that somehow 100 mile wide craters made by steam explosions is somehow 'better' for YEC than 100 mile wide craters made by meteor impacts, and of course, you were likewise "convinced -convinced!" it would be YEARS before we ever saw a picture of an extra-solar planet and so on and so on.

    Oh yeah, and you are also "convinced - convinced!" that the world must be <10,000 years old.



    Somehow I'm not thinking you are particularly 'convincing' ....



    Jim

    Leave a comment:


  • klaus54
    replied
    Originally posted by Jorge View Post
    I am convinced - convinced! - that a YEC stole your teenage girlfriend and you now have a vendetta against anyone even remotely connected to YEC.

    Your statement that "... science is a continuous process of learning" is a bunch of unethical hogwash. First, what "science" are you speaking of? Evolution? Physics? Second, ALL areas of study involve a continuous process of learning. Why do 'you people' believe that you've cornered the market of learning? Worse yet, you think you've cornered that market and have locked OUT anyone that doesn't agree with your views. Yeah, that's "good science" alright; more like Medieval dogmatism if you ask me.

    Anyway, you remain clueless, O-Mudd. But do keep trying.

    Jorge
    Jorge's response to Jim's cogent post is a sight to behold. No content, just insults.

    If this is what Fundamentalist YEC Christianity does to your brain, ... Ughh...

    K54

    Leave a comment:


  • Wally
    replied
    Originally posted by Jorge View Post
    I didn't "duck" anything, you Yo-Yo.

    I commented directly to the point of "Wells does not reliably present science in his book."


    Jorge
    The problem here, is that you are demonstrably unqualified to make the judgment.

    Leave a comment:


  • JonF
    replied
    Originally posted by Jorge View Post
    I didn't "duck" anything, you Yo-Yo.

    I commented directly to the point of "Wells does not reliably present science in his book."
    I also clearly stated - "clearly" except to the comprehension-impaired as yourself - that I have to
    wait until I'm home where I will have access to Wells' book and evidence contained therein.

    Jorge
    Wotta maroon. You failed to respond directly to the reason given for that evaluation. If you could not until you get home, shut yo' mouth until you are home.

    You also lied about the reason for his evaluation. It was not because Wells criticized mainstream science, it was because he cited one example of egregious error. I bet he can post more.

    Slimy even by Jorge standards.

    Leave a comment:


  • Jorge
    replied
    Originally posted by oxmixmudd View Post
    Does it even matter? And look at the Kettle calling the Pot black. There is not a more forgetful bunch in terms of seeping under the rug what they got WRONG than the YEC crowd. So what is the 'set of evidences for YEC' du jour Jorge over against those in 2000, or 1990, or 1980?

    What you fail to realize Jorge is that science is a continuous process of learning. Learning, refining, getting better, more accurate, this is what its all about.

    Your side, OTOH, is all about codifying and dodging the appearance of error. Because you ostensibly think your position is God revealed, and therefore nothing can be wrong, so 'correction' is NOT part of the process.

    So to you, pulling back from the idea of junk DNA is some kind of major faux pas that prooooooves you were right, right, right. To anyone with half a brain it just means we are learning more. The aspects of DNA that produced the observation 'junk' are still there. We just understand more about how it all fits together. And not only that, when new data contradicts old conclusions, it gets published and talked about, not buried and ignored as it does in YEC land (e.g. Sarfati STILL tries to claim their aren't any SNR's older than 10,000 years).

    What YOU can't deal with is the fact that at least some of the 'junk' DNA is in fact RE-PURPOSED DNA. And as I pointed out in my post which you ignored, we have observational proof that DNA once coded for artifacts known to be a part of the animal's ancestry (Activated genes producing teeth in a bird - a chicken - your mascot) now sits buried in its DNA in a more or less inactive state. This simply DOES NOT FIT any sort of YEC paradigm - BUT IS EXPECTED IN AN EVOLUTIONARY ONE. And you know it. But then again, that is why you 'missed' the post where I pointed this little snag out earlier.



    Jim
    I am convinced - convinced! - that a YEC stole your teenage girlfriend and you now have a vendetta against anyone even remotely connected to YEC.

    Your statement that "... science is a continuous process of learning" is a bunch of unethical hogwash. First, what "science" are you speaking of? Evolution? Physics? Second, ALL areas of study involve a continuous process of learning. Why do 'you people' believe that you've cornered the market of learning? Worse yet, you think you've cornered that market and have locked OUT anyone that doesn't agree with your views. Yeah, that's "good science" alright; more like Medieval dogmatism if you ask me.

    Anyway, you remain clueless, O-Mudd. But do keep trying.

    Jorge

    Leave a comment:


  • Jorge
    replied
    Originally posted by JOnF View Post
    We all see how you ducked the issue and tried to change the subject there.
    I didn't "duck" anything, you Yo-Yo.

    I commented directly to the point of "Wells does not reliably present science in his book."
    I also clearly stated - "clearly" except to the comprehension-impaired as yourself - that I have to
    wait until I'm home where I will have access to Wells' book and evidence contained therein.

    Jorge
    Last edited by Jorge; 05-15-2014, 03:56 PM.

    Leave a comment:


  • oxmixmudd
    replied
    Originally posted by Jorge View Post
    If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

    jorge
    Does it even matter? And look at the Kettle calling the Pot black. There is not a more forgetful bunch in terms of seeping under the rug what they got WRONG than the YEC crowd. So what is the 'set of evidences for YEC' du jour Jorge over against those in 2000, or 1990, or 1980?

    What you fail to realize Jorge is that science is a continuous process of learning. Learning, refining, getting better, more accurate, this is what its all about.

    Your side, OTOH, is all about codifying and dodging the appearance of error. Because you ostensibly think your position is God revealed, and therefore nothing can be wrong, so 'correction' is NOT part of the process.

    So to you, pulling back from the idea of junk DNA is some kind of major faux pas that prooooooves you were right, right, right. To anyone with half a brain it just means we are learning more. The aspects of DNA that produced the observation 'junk' are still there. We just understand more about how it all fits together. And not only that, when new data contradicts old conclusions, it gets published and talked about, not buried and ignored as it does in YEC land (e.g. Sarfati STILL tries to claim their aren't any SNR's older than 10,000 years).

    What YOU can't deal with is the fact that at least some of the 'junk' DNA is in fact RE-PURPOSED DNA. And as I pointed out in my post which you ignored, we have observational proof that DNA once coded for artifacts known to be a part of the animal's ancestry (Activated genes producing teeth in a bird - a chicken - your mascot) now sits buried in its DNA in a more or less inactive state. This simply DOES NOT FIT any sort of YEC paradigm - BUT IS EXPECTED IN AN EVOLUTIONARY ONE. And you know it. But then again, that is why you 'missed' the post where I pointed this little snag out earlier.



    Jim
    Last edited by oxmixmudd; 05-15-2014, 01:07 PM.

    Leave a comment:


  • JonF
    replied
    You also say that, "Wells does not reliably present science in his book." I am always amazed at how anyone no toeing the Evolutionary line is immediately dismissed as a "non-scientist"
    We all see how you ducked the issue and tried to change the subject there.

    Leave a comment:


  • Jorge
    replied
    Originally posted by TheLurch View Post
    The problems are pretty fundamental. Wells implies that any non-coding sequence was considered junk. The concept of junk DNA originated in the 70s; Jacob and Monot got their Nobel for the discovery of non-coding regulatory DNA in 1965; the results clearly were significantly earlier than that. So, the concept of noncoding regulatory DNA was already firmly established before the junk DNA discussion even started.

    This is pretty fundamental stuff; the Lac operon is in every basic biology text. I can't possibly imagine why Wells chose to pretend it wasn't known about in writing his book.


    Having gone through the list, it's very clear that the vast majority of that number are either part of or would need to function in immediate proximity to the coding portions of a gene. The only exceptions appear to be structural functions, like binding to the nuclear scaffold. If you look into these in detail, they're relatively uncommon and only a few hundred bases long. Therefore, they cannot account for more than a tiny fraction of the DNA in eukaryotic genomes that is not conserved across species.


    I'd agree with this. The evidence is that a significant portion of most eukaryotic genomes are what has been termed junk DNA, but that's a tentative conclusion, subject to further revision.


    Where as this, i suspect, is wrong. My only doubt is focused on the term "evolutionism", which i'm not familiar with. Assuming it means "someone who accepts the evidence for evolution", then the statement is false.

    The relative percentage of junk DNA, within an evolutionary model, depends on the strength of selective pressure and effective population size. Things like copy number variations are constantly adding non-functional DNA to the genome, which has a very small, but non-zero energetic cost. There can be strong selective pressure to minimize the genome - examples include things like bacteria, where the minimizing energy expenditures is strongly selected for, or the bladderwort, which lives in an environment that doesn't provide it with much of a chemical that's essential to DNA (Phosphorous, i think). A large effective population size ensures that deletions that get rid of non-essential DNA occur with a reasonable frequency. Combine the two, and you get an organism with a compact, largely junk-free genome through standard evolutionary processes.


    As described above, Wells does not reliably present science in his book. So, it's not a summary dismissal; more of a critical evaluation.
    Okay, I'll have to be back home where I have Wells' book and can refute with evidence some of your claims here (e.g., if memory serves me, Well's is fully aware that just because it's non-coding does not make it "junk".)

    You also say that, "Wells does not reliably present science in his book." I am always amazed at how anyone no toeing the Evolutionary line is immediately dismissed as a "non-scientist". Examples are legion: Dean Kenyon was considered one of the top scientists in his field UNTIL he went against the Materialistic Evolutionary Paradigm at which point he was downgraded into 'basically' a lab technician. Same story for Mike Behe - regarded as a top-level scientist UNTIL he published Darwin's Black Box after which he was 'magically' transformed into a "pseudo-scientist". Here you say that "Wells does not reliably present science ..." Let me hazard a wild guess : Wells opposes the Evolutionary Paradigm. Yup, that'll do it every time.

    As for the term "Evolutionism" - odd that you aren't familiar with it given that you subscribe and practice it. Evolutionism, concisely stated, is simply the metaphysical stance that Evolution explains the entire spectrum of flora and fauna in existence today as well as every aspect of intra- and inter-species phenomena. Evolutionism, taken to its logical implications, must also account for the emergence of life itself (although this is adamantly denied by the practitioners of Evolutionism). In a nutshell, that is Evolutionism.

    Anyway, I got'ta get going - next stop Chicago, IL. I'll consider this after I'm back home but I will confess that it won't be on my priority list.

    Jorge

    Leave a comment:


  • rwatts
    replied
    Originally posted by Jorge View Post
    If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

    jorge
    Because Jorge disagrees with the paper, it must be wrong, no matter what evidence it brings to bear to support its argument.

    Is this what you are trying to argue Jorge?


    Here you go, some of the references the authors used to show that not every one was happy with the term 'junk DNA":-

    10. Aronson AI, Bolton ET, Britten RJ, Cowie DB, Duerksen JD, et al.. (1960) Biophysics. Year book - Carnegie Institution of Washington (1960). Volume 59. Baltimore, MD: Lord Baltimore Press. pp. 229–289.

    16. Britten RJ, Kohne DE (1968) Repeated sequences in DNA. Science 161: 529–540. doi: 10.1126/science.161.3841.529 View Article

    17. Gregory TR (2008) Junk DNA – the quotes of interest series. Available: http://www.genomicron.evolverzone.co...series​/. Accessed 10 April 2014.

    That last link is worth scrounging through.

    However, this (your grumbling) is all somewhat irrelevant.

    The point is, the authors of the paper I linked to in the OP are maintaining that the non coding DNA is likely to be mostly junk or have a large component of junk. That is, they are countering the perception that evidence points to the non-coding DNA being all functional or mostly functional. They are pointing out that the evidence does not support this idea.

    You haven't read the paper at all, have you. I find it odd, but typical, that your only argument to date, is to cry "revisionism" when all these guys are doing is remphasizing orthodoxy. Supporting orthodoxy is hardly revisionism.

    So, would you like to address the science behind their claims that orthodoxy is correct, namely that a lot, if not most DNA is junk? I think they make a good case. I really liked their "Onion test" section. Look at their figure 1. The star represents the size of the human genome. Now look at the spread of mammalian genomes and look at the spread for other organisms. If the human genome is mostly, if not all functional, then how do you explain* this graph in the context of organismal complexity and genome size?


    * Irrelevant rants are not "explainations" in my world. In your world they might be, but not mine.
    Last edited by rwatts; 05-14-2014, 10:28 PM.

    Leave a comment:


  • TheLurch
    replied
    Originally posted by Jorge View Post
    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 ...
    The problems are pretty fundamental. Wells implies that any non-coding sequence was considered junk. The concept of junk DNA originated in the 70s; Jacob and Monot got their Nobel for the discovery of non-coding regulatory DNA in 1965; the results clearly were significantly earlier than that. So, the concept of noncoding regulatory DNA was already firmly established before the junk DNA discussion even started.

    This is pretty fundamental stuff; the Lac operon is in every basic biology text. I can't possibly imagine why Wells chose to pretend it wasn't known about in writing his book.

    Originally posted by Jorge View Post
    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) .
    Having gone through the list, it's very clear that the vast majority of that number are either part of or would need to function in immediate proximity to the coding portions of a gene. The only exceptions appear to be structural functions, like binding to the nuclear scaffold. If you look into these in detail, they're relatively uncommon and only a few hundred bases long. Therefore, they cannot account for more than a tiny fraction of the DNA in eukaryotic genomes that is not conserved across species.

    Originally posted by Jorge View Post
    In any event, it is well beyond the observable facts to dogmatically claim that "junk DNA" is truly "junk" as certain Evolutionists do.
    I'd agree with this. The evidence is that a significant portion of most eukaryotic genomes are what has been termed junk DNA, but that's a tentative conclusion, subject to further revision.

    Originally posted by Jorge View Post
    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.
    Where as this, i suspect, is wrong. My only doubt is focused on the term "evolutionism", which i'm not familiar with. Assuming it means "someone who accepts the evidence for evolution", then the statement is false.

    The relative percentage of junk DNA, within an evolutionary model, depends on the strength of selective pressure and effective population size. Things like copy number variations are constantly adding non-functional DNA to the genome, which has a very small, but non-zero energetic cost. There can be strong selective pressure to minimize the genome - examples include things like bacteria, where the minimizing energy expenditures is strongly selected for, or the bladderwort, which lives in an environment that doesn't provide it with much of a chemical that's essential to DNA (Phosphorous, i think). A large effective population size ensures that deletions that get rid of non-essential DNA occur with a reasonable frequency. Combine the two, and you get an organism with a compact, largely junk-free genome through standard evolutionary processes.

    Originally posted by Jorge View Post
    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!
    As described above, Wells does not reliably present science in his book. So, it's not a summary dismissal; more of a critical evaluation.

    Leave a comment:


  • klaus54
    replied
    Originally posted by Jorge View Post
    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
    Jorge,

    What does any of your blathering have to do with "God of the Gaps"? GoG is BTW a fairly good explanation for Dembski's notion of "irreducible complexity." Something or other is too complicated so "the designer" musta done it.

    Surely you agree. If not, why not?

    K54

    Leave a comment:


  • Jorge
    replied
    Originally posted by rwatts View Post
    Unlikely.

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



    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.



    ???

    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?

    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?
    If you also are going to make use of REV and deny that such Historical Revisionism is taking place then there's really not much more to say. I could, of course, (after returning home) spend hours or days of my time digging up article after article from the 1980's and 1990's in which the history as I state it is there in black and white for you to see but, no, I've been down that road before. After spending (wasting!) all that time you will merely pull something else out of your hat. Believe as you wish. I am sure that some of you here remember well enough but you'd be booted out of the Evolutionists-R-Us Club should you dare say anything.

    jorge

    Leave a comment:

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