Home » Intelligent Design » Junk DNA: Yes, paper admits, it WAS thought to be junk

Junk DNA: Yes, paper admits, it WAS thought to be junk

In “Paper Rebuffs Assumption that Pseudogenes Are Genetic ‘Junk,’ Claims Function Is ‘Widespread’” (Evolution News & Views, August 14, 2012), Casey Luskin notes a recent paper trhat discusses “an impressive list of discovered functions for pseudogenes,: observing

After widespread function is discovered for a type of “junk” DNA, we’ve often seen evolutionists respond by trying to rewrite history to suggest no one never had ever maintained that that type of DNA was junk. Lest anyone forget the history of pseudogenes, this paper not only argues for “widespread” function in pseudogenes, but it also makes it clear they have been assumed to be “junk” or “garbage” DNA

(Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J. Ayala and Zhao-Rong Lun, “Pseudogenes are not pseudo any more,” RNA Biology, Vol. 9(1):27-32 (January, 2012).)

You wouldn’t think this would ever be an issue, and normally it wouldn’t be. But that reckons without the cult of Darwinism.

Darwin’s followers considered junk DNA powerful evidence for their theory, which is really a philosophy (often a cult), and that they often expressed that view, often triumphantly. Others insist it is true anyway.

The problem they hope to suppress is that if lots of junk in our DNA is such powerful evidence for their theory, then little junkthrows it into doubt. That is, if it is such a good theory, why was it wrong on a point that was announced so triumphantly?

So it is a good thing that the science-minded public is reminded of the historical fact that Darwinism was supported by junk DNA. And it will be fun when the squirming editorials come out in science mags, warning people not to read too much into this, Darwin is still right.

If it is possible to squirm sonorously and self-righteously,  they will.

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17 Responses to Junk DNA: Yes, paper admits, it WAS thought to be junk

  1. Except the ToE doesn’t explain junk DNA- ya see natural selection was supposed to be a designer mimic, not a design screw-up.

  2. I’ve seen darwinists pull this stunt before. When one of their ‘facts’ (aka assumptions) is later proven to be wrong, they quickly circle the wagons and claim they never said it was a fact… they just ACT like it is and bully and mock those who dare question it without having the evidence to disprove it.

  3. Lest anyone forget the history of pseudogenes, this paper not only argues for “widespread” function in pseudogenes, but it also makes it clear they have been assumed to be “junk” or “garbage” DNA

    If the paper really argues this, then it’s wrong.

    A great many mainstream biologists explicitly said that non-coding DNA likely had function, right from the early days after it was discovered.

    Immediately after Ohno’s very first presentation at the conference proceedings where he coined the term “junk DNA” he gave an interview describing his expectation that Darwinian adaptation should remove non-functional DNA, and therefore by implication remaining DNA is likely functional, even if we don’t know what the function is. The transcript is published in Ohno, S. (1973) “Evolutional reason for having so much junk DNA” in Modern Aspects of Cytogenetics: Constitutive Heterochromatin in Man (ed. R.A. Pfeiffer), pp. 169-173. F.K. Schattauer Verlag, Stuttgart, Germany:

    Ohno: “If there is any gene which is doing some good for your general well-being, you will suffer when you lose that gene. For this very reason a fraction of randomly sustained mutations of that locus would be deleterious. There is simply no way of having a useful gene without paying a certain price for the cost of natural selection. If, on the other hand, there is a gene which is totally irrelevant, you will lose that gene sooner or later, for natural selection would not police that gene.”

    In fact, way back in 1971 before Ohno coined the term “junk DNA”, biologists were discovering large portions of the genome that did not code for proteins and/or was repetitive, and had no known function. Nonetheless, they were proposing numerous possible functions for such, and subsequent research has shown some of their proposals to be correct:

    Ever since the initial demonstration of the existence of repetitive DNA there has been no dearth of theories on the function of this material. … Following is a list of functions that have been proposed …

    1. Recognition of centromeres of common origin.
    2. Recognition between homologous chromosomes during pairing.
    3. Regions involved in the initiation of replication and/or transcription.
    4. Sites concerned with specifying the folding patterns of chromosomes.
    5. Recognition sites for the process of genetic recombination.
    6. Provision of raw material for genetic divergence.
    7. Reflection of similarities in the structure of different proteins.
    8. DNA concerned with the regulation of gene expression (regulatory DNA).
    9. Reflection of multiplicity of repeated genes, as for example, in the master and slave or multistranded chromosome hypothesis.

    None of the recognition functions, i.e., recognition of centromeres, initiation sites, pairing sites, recombination sites, folding sites, or regulatory sites, that we have discussed is mutually exclusive of the others. They all relate to cellular phenomena that have been demonstrated or inferred from other data. All these phenomena probably exist within every higher organism. Therefore, DNA involved in each of these functions could contribute in varying degrees to the repeated portion of the genome.

    – Bostock, C. (1971) “Repetitious DNA” Advances in Cell Biology 2: 153-223.

    And there are many, many more papers over subsequent decades describing the expectation that much “junk” DNA actually has function; some examples appear below.

    1974 — E. Southern, “Eukaryotic DNA” in MTP International Review of Science, Biochemistry Series One, Volume 6, Biochemistry of Nucleic Acids, (1974) University Park Press, Baltimore. pp. 101 – 139:

    “.. large variations in genome size could readily be accomodated if a high proportion of the DNA were used for functions other than coding for proteins. A number of such functions have been proposed and incorporated into hypothetical structures for the eukaryotic genome.”

    1977 — D.M. Skinner, “Satellite DNAs” BioScience 27 (1977) pp. 790-796:

    Satellites [tandemly repeating, non-coding DNA] constitute from 1% to 66% of the total DNA of numerous organisms, including that of animals, plants, and prokaryotes. Their existence has been known for about 15 years but, although it is thought that they must be biologically important … their functions are still largely in the realm of speculation.

    1980 — Orgel & Crick, Nature (284: 604-607), p. 606:

    Thus, some selfish DNA may acquire a useful function and confer a selective advantage on the organism.

    1982 — R. Lewin, “Repeated DNA still in search of a function” Science 217 (1982) pp. 621-623:

    Some repetitive DNA will undoutedly be shown to have a function, in the formal sense, some will likely be shown to exert important effects, and the remainder may well have no function or effect at all and can therefore be called selfish DNA. Repetitive DNA constitutes a substantial proportion of the genome (up to 90% in some cases), and there is considerable speculation on how it will eventually be divided between these three groups.

    So it is simply not the case that biologists only started to acknowledge function for “junk” DNA in recent times. Rather, function has been expected ever since the term “junk” DNA entered the scientific literature.

    Cheers

  4. Darwinism explains junk DNA and it explains functional DNA as well. Finding function in most DNA will surely highlight the false prediction, but false predictions are easy to swallow and assimilate into ToE. It’s been done before and will be done again. ToE is so flexible that it can be made to explain anything and everything, even contradicting results like junk DNA and functional DNA. The fall of the junk DNA paradigm will embolden IDers and creationists but it probably won’t phase too many Darwinists because they already “know” they are right. It is just the mechanisms and details that need to be worked out.

    As more and more function is found, they will have to start backtracking, re-interpreting their past comments and beliefs to fit reality, and come up with new ideas to hold to. I doubt there will be any admission of defeat. I don’t hold out too much hope for change in the Darwinist camp as a result of the junk DNA paradigm falling.

    What does everyone else think? How will the collapse of the junk DNA paradigm effect Darwinists?

    Nevertheless, we need to keep putting the truth out there for those who have eyes to see and ears to hear.

  5. tjguy @ 4

    As more and more function is found, they will have to start backtracking, re-interpreting their past comments and beliefs to fit reality…

    tjguy, did you read any of the quotes I provided above? They show biologists have expected function for non-coding DNA for decades and decades — ever since it was discovered. You’ll have to do better than just claim “backtracking” and “re-interpretation” when the documentary evidence shows otherwise.

    Cheers

  6. CLAVDIVS- The OP refers to PSEUDOGENES, not just any non-coding DNA. Also blind and undirected chemical processes cannot account for regulatory sequences.

  7. Joe @ 6

    The OP refers to PSEUDOGENES, not just any non-coding DNA.

    Oh, okay. The term “pseudogene” dates from 1977 (Jacq et al) and that original paper mentions a possible function for them — see …

    1977 — Jacq, C et al “A pseudogene structure in 5S DNA of Xenopus laevis” Cell 12: 109-120:

    …it has been suggested (Brownlee, 1976) that the pseudogene may be a “transcribed spacer” corresponding to a primary transcript of 5s RNA … This function, if true, would provide the necessary selective pressure to conserve the sequence of the “linker” and pseudogene region so that the correct processing of the postulated 300-long precursor was maintained.

    1980 – Proudfoot, N.J. and T. Maniatis (1980) “The structure of a human ?-globin pseudogene and its relationship to ?-globin gene duplication”. Cell 21: 537-544:

    Although the presence and similar location of pseudogenes in all the mammalian globin gene clusters suggest that pseudogenes may have some as yet unidentified function, the simplest explanation for their existence is that they are the natural consequence of the mechanisms of gene amplification and sequence divergence.

    1980 — Vanin, E.F., et al (1980) “A mouse ?-globin-related pseudogene lacking intervening sequences” Nature 286: 222-226.

    The general hypothesis that pseudogenes control the productive genes in some fashion, nevertheless, remains attractive and we are investigating the hypothesis further, including tests in non-erythroid tissues. Certainly, the widespread occurrence of globin pseudogenes argues strongly for their functional importance.

    So my point still stands that biologists have expected function for non-coding DNA, including pseudogenes, ever since they entered the scientific literature.

    Cheers

  8. It’s okay, guys. If fossil rabbits are found in the Cambrian, CLAVDIVS will say that Darwinism predicted it.

  9. News @ 8

    It’s okay, guys. If fossil rabbits are found in the Cambrian, CLAVDIVS will say that Darwinism predicted it.

    Of course, even if I was a double-talking ideologue, that’s irrelevant to my argument, which is based on documentary evidence — it’s got nothing to do with what CLAVDIVS says, but with what the evidence shows.

    And what the evidence shows is that biologists have expected functions for non-coding DNA all along.

    Cheers

  10. And what the evidence shows is that biologists have expected functions for non-coding DNA all along.

    So biologists are IDists, then. I say that because accumulations of genetic accidents doesn’t predict such a thing.

  11. It’s okay, guys. If fossil rabbits are found in the Cambrian, CLAVDIVS will say that Darwinism predicted it.

    That was somehow in doubt?

  12. CLAVDIVS:

    And what the evidence shows is that biologists have expected functions for non-coding DNA all along.

    If you define “function” as “non-functional.”

    Do tell, CLAVDIVS.

    Where are the predictions of functionality for non-coding DNA?

  13. I wouldn’t dispute CLAVDIVS’ references showing that some biologists proposed functionality for junk DNA long ago. However, stating that biologists in general expected function for non-coding DNA seems at odds with empirical evidence. If that was the case, then how on earth could Richard Dawkins, Ken Miller, Francis Collins, Jerry Coyne, etc. write explicitly and repeatedly that the presence of nonfunctional junk DNA provides a compelling argument against ID? It wouldn’t make sense to argue that noncoding DNA invalidates ID theory if one holds that the noncoding DNA actually possesses function. That would be like arguing, “What sort of designer would waste space by littering the genome with noncoding (but functionally important) DNA?”
    That many evolutionists have used the junk DNA argument against ID (a version of the hackneyed argument from imperfection) is not something that can be seriously disputed by rational people. A brief trip to a library or bookstore provides abundant evidence that this is the case. I find it childish and intellectually dishonest that instead of simply being adults and admitting error, committed Darwinists will attempt to revise history, waving their hands like Jedi masters to make us forget what happened five minutes ago. Such rank distaste for truth is simply appalling.

  14. The point is, Optimus, no one said non-protein-coding DNA is all junk so ID is wrong. In fact, at the time non-coding DNA was discovered it was generally thought to serve some purpose.

    But, it turns out, there is good evidence that some, and probably most non-coding DNA is junk. I’m not sure that’s a great argument against ID, but ID-proponents obsession with denying the existance or almost any junk DNA does suggest ID folks do think it’s a threat.

  15. The point is, wd400, the current theory of evolution has no testable explanation for functioning non-protein-coding DNA

  16. yeah it does Joe, RNAs do chemistry spacers space…

  17. no it doesn’t wd400- and it is very telling that you didn’t post the testable explanation…

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