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Another important unexpected role for junk DNA

Darwinian “Scientists have called it “junk DNA.” They have long been perplexed by these extensive strands of genetic material that dominate the genome but seem to lack specific functions. Why would nature (or an Intelligent Designer) force the genome to carry so much excess baggage?”

As predicted by Intelligent Design theorists “researchers from Princeton and Indiana University have found that junk DNA may not be so junky after all. They have discovered that DNA sequences from regions of what had been viewed as the “dispensable genome” are actually performing functions that are central for the organism. They have concluded that Darwinian theory was incorrect the genes spur an almost acrobatic rearrangement of the entire genome that is necessary for the organism to grow.”

The term “junk DNA” was originally coined (by Darwinian biologists) to refer to a region of DNA that (they wrongly concluded because of their philosophical committment) contained no genetic information. Scientists are beginning to find, (as predicted by Intelligent Design theorists), that much of this so-called junk plays important roles in the regulation of gene activity.”

Italics are (obviously) my additions.

Source  http://www.princeton.edu/main/news/archive/S24/28/32C04/

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25 Responses to Another important unexpected role for junk DNA

  1. I think this has been covered in a couple previous posts on junk DNA. Not this particular finding but the general finding that researchers have been examining the so called junk DNA for years and the term in no way restricted this group of researchers.

    I am sure there were some researchers who did not pursue investigating it because of the supposed junk DNA designation but it is obviously in full swing now.

    The most likely conclusion is that some of the genome will be junk but how much will not be determined till far in the future. Remember there a single celled eukaryotes with far larger genomes than humans and I don’t think ID or any scientists are willing to count is all as useful. It is not just about humans.

  2. From the UD response to Bad Design Means No Design:

    From a scientific perspective, a cosmic designer could, in principle, be an imperfect designer and, therefore, create a less than perfect design….

    If “junk DNA” truly had no function, the foregoing would be the ID response. So how can functionality of DNA for which no function is presently known be an ID prediction? IDers have put absolutely nothing at stake. When new functions are discovered — something all mainstream evolutionists expect — IDers chime in and say, “We told you so.” And should most of the DNA remain apparently useless for centuries to come, IDers will remind us, “Well, bad design does not mean no design.” You can’t have it both ways.

  3. I suggest that readers look at the entire link that Sal Gal has pointed to and see if they agree with Sal Gal’s convoluted interpretation. Or if ID is being reasonable and logical.

    ID is about evidence of design, not whether junk DNA has 100% use or not. The junk DNA only represents an area that should be pursued to see what it may do. Because of ideological blinders many researchers limited their investigation of it because they could not see the usefulness of almost endless repetitive apparently meaningless sequences of simple patterns. And in the end both groups may be right. It should have been investigated because there was a lot of important uses but a lot of it may end up useless.

    But it should be noted that the vast expanses of the supposedly non functional DNA is purported to be the breeding ground of new elements for the organism. So according to this theory junk DNA has a potential function in the future. That sounds teleological in a way. It is a process that expects change to happen and change in a direction of more complexity.

  4. I am sorry that this post seems repetitive.

    What I see is that the design of life has become even more amazing and has demonstrated even more abstract design principles. These principles are not in any way related to the fundamental physics and chemistry of the constituents.

    They are about language, and language is always the product of intelligence.

    Thinking like Darwinian evolutionary theory is good at explaining things on a basic level like why a stone may be more round by the time it gets to the end of the rapids. It is no good at explaining the Easter Island statues. The trouble for evolutionary biology is that we are not finding round stones, we are finding complicated and integrated coded language. Darwinians simply repeat the mantra “Darwinian evolution can do anything”.

  5. Onlookers,

    Let’s not distract the thread from its very important point on the increasing success of a risky ID prediction from the 1990′s on.

    A prediction that was based on the point that since in our experience designs generally incorporate in the main functional features so most — or at least much — of a credibly designed entity such as DNA as a digital memory storing information vital to the functioning of the cell [cf. the recent "FAQ" 4 discussion here, e.g. at no 122], would be normally expected to be functional.

    So, it is worth citing WmAD from First Things, 1998, on Junk DNA:

    . . . Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.

    By contrast, as late as 2003 – 4, Mr Dawkins was still confidently asserting:

    Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn’t even need scarequotes) get on with their business in a different part of the same genome. And there’s lots more DNA that doesn’t even deserve the name pseudogene. It too is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, ‘tandem repeats,’ and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. . . . Creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudognes and junk tandem repeat DNA. [A Devil's Chaplain, p. 98]

    Looks like the despised ID thinkers (and the even more despised Creationists), are turning out to be right on the functionality of so-called junk DNA; and on what evolutionary materialism led Mr Dawkins and ilk to erroneously perceive and expect!

    GEM of TKI

    PS: Now, to correct SG’s somewhat out of context quote, here is the context:

    ___________________

    24] Bad Design Means No Design

    This argument assumes an infallible knowledge of the design process.

    Some, for example, point to the cruelty in nature, arguing that no self respecting designer would set things up that way. But that need not be the case. It may well be that the designer chose to create an “optimum design” or a “robust and adaptable design” rather than a “perfect design.” Perhaps some animals or creatures behave exactly the way they do to enhance the ecology in ways that we don’t know about. Perhaps the “apparent” destructive behavior of some animals provides other animals with an advantage in order to maintain balance in nature or even to change the proportions of the animal population.

    Under such circumstances, the “bad design” argument is not an argument against design at all. It is a premature — and, at times, a presumptuous — judgment on the sensibilities of the designer. Coming from theistic evolutionists, who claim to be “devout” Christians, this objection is therefore especially problematic. For, as believers within the Judeo-Christian tradition they are committed to the doctrine of original sin, through which our first parents disobeyed God and compromised the harmonious relationship between God and man. Accordingly, this break between the creator and the creature affected the relationship between men, animals, and the universe, meaning that the perfect design was rendered imperfect. A spoiled design is not a bad design.

    Beyond such theodicy-tinged debates, ID as science makes no claims about an omnipotent or omniscient creator.

    From a scientific perspective, a cosmic designer could, in principle, be an imperfect designer and, therefore, create a less than perfect design; indeed, that was precisely the view of many who held to or adapted Plato’s idea of the Demiurge. So, even if one rejects or abandons theism, the “bad design” argument still does not offer a challenge to ID theory as a scientific endeavor.

    The real scientific question is this: Is there any evidence for design in nature? Or, if you like, is a design inference the most reasonable conclusion based on the evidence?

    ____________________

    Plainly, context here makes every difference in the world, so SG please tell your friends over at Anti Evo (or wherever) to correct the out of context cite.

  6. Mr Jerry,

    You are right, we did discuss this research before. I think Mr Cordova brought it up.

    This Oxytricha organism is interesting because it makes a working nucleus that is only 5% the size of the nucleus used in reproduction. (It has two.) It is as if all the splicing out of introns and other non-coding elements takes place at once.

    This might even bear on the discussion from the previous thread on why couldn’t an organism get rid of 90% of its DNA if it was non-functional. Oxytricha seems to have figured out at least part of the trick.

    Points –

    1 – There is some sense in which the non-coding DNA is junk. We can’t ignore the fact that the working nucleus is only 5% of the size, and doesn’t include all that stuffs.

    2 – The article is pointing out that a function of one part of the non-coding DNA is to get rid of the rest of the non-coding DNA and itself when forming the working nucleus. That is certainly a useful function in the presence of lots of non-coding DNA, but doesn’t get at the problem of why the non-coding DNA was there in the first place.

    One further comment on the OP. Mr idnet.au.com is wrong with his editorial insertion “(they wrongly concluded because of their philosophical committment)”. As Mr Cordova provided the link to the website with the PDF of the original paper coining the term Junk DNA, we can see where it came from and why. It has its basis in a mathematical calculation of the size and number of probable genes in the genome. A comparison of the bulk weight of that much DNA to the actual bulk weight of the DNA actually observed leads to the conclusion that there is a lot of DNA that is not part of a gene.

  7. ID is about evidence of design

    If so would it be possible to detect human design in genomes. Actually, it is possible to introduce mutations in genomes without leaving any traces. Would ID be capable to detect such alterations that would be indeed intelligently designed? Or would a human induced change remain a droplet hidden in a sea of sequences designed by a more intelligent designer?
    Just wonderig.
    BTW, if ID researchers go in this direction they should of course not use the tools that only make sense in the light of evolution like sequence databases or programs like fasta, blast or Phylip.
    And don’t ask Smith, Waterman, Needle or Wunsch for help.

  8. the bad design argument comes form ignorance of ID. In Dr Sanford book states that genome is in decay and nature selection can not stop it. this leads to the idea design was perfect once. Also logically leads that there must a designer because natural processes can not improve anything or even maintained it. The reason Darwinist have to come idea of junk Dna because of neutral mutations. if neutral did noting than there was no concern but if neutral mutations were not truly neutral and just near neutral it would be death nail for Neo Darwin evolution because it shows that natural selection is flawed. if there are no truly neutral mutations also means that all genes have effects even if they are deleterious.

  9. spark,

    In Dr Sanford book states that genome is in decay and nature selection can not stop it. this leads to the idea design was perfect once.

    Interesting view. I haven’t read Dr. Sanford’s book, but is he saying that this so-called junk DNA is caused by deterioration of genomes? And that ID therefore predicts junk DNA? (and I mean true junk DNA here, not just DNA which might have yet undiscovered functions).

  10. Sal Gal @2:

    And should most of the DNA remain apparently useless for centuries to come, IDers will remind us, “Well, bad design does not mean no design.” You can’t have it both ways.

    My position as a (non-YEC) Christian and ID supporter is that the designers (Elohim) had millions of years to perfect their creation. We are told that, after they were done, they took a step back and said, “It is very good”.

    From this perspective, I would expect that bad designs would show up mainly in the distant fossil record. Having said that, even good designs can deteriorate over the years due to disease or incestuous mating. Still, I would expect junk DNA to be a very rare occurrence.

  11. in Dr Sanford book he supports the ID prediction that all DNA has some function or effect. Meaning the prediction is that there is no junk DNA.

  12. 12

    My position as a (non-YEC) Christian and ID supporter is that the designers (Elohim) had millions of years to perfect their creation. We are told that, after they were done, they took a step back and said, “It is very good”.

    Excellent. Design by committee. That makes more sense (to me) than a single omnipotent actor, considering the inelegance of many of the products.

    Christians are woefully ignorant of the wisdom of the Torah.

  13. spark,

    In Dr Sanford book he supports the ID prediction that all DNA has some function or effect. Meaning the prediction is that there is no junk DNA.

    Thanks for clarifying. This has got me to wondering, however, whether the Fall has any implications on the issue of junk DNA. I have to confess that I used to follow organizations like AIG more closely than I do now, and IIRC it that their view that Creation itself had decayed nearly to the point of collapse in these end times. Might that be consistent with our DNA being full of broken or completely nonfunctional genes?

  14. Spark and herb

    Brian Sykes claims that the y chromosome is deteriorating (might have been a reference to some research on the radio, but I do not remember who or where) which supports Sanford’s position. Sykes also claims that mtdna can be traced back to 4 women and that y chromosome dna can be traced to 1 man. (Seven Daughter of Eve)

    Sanford’s book was discussed in June of 2006 on UD.

  15. Thanks, merlin. That y chromosome stuff is fascinating.

  16. I normally ignore Preacher Prolix, but it’s worth noting that he’s done something I’ve never seen an ID rhetorician do before — pick cherries from the writing of an ID authority, and then appeal to authority:

    Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function.

    “DNA, as much as possible, exhibits function” is not a falsifiable hypothesis, and Dembski is not such a fool as to offer it as one. Furthermore, if Mullings had not quote-mined, it would have been evident that Dembski was discussing the heuristic value of the design assumption in scientific exploration, not stating a falsifiable hypothesis. Here are the two sentences immediately preceding those the preacher felt moved to share with his congregation of “onlookers”:

    But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it.

  17. I respond respectfully to some ID arguments, but the notion that a designed store of information would be nearly full is abysmally stupid.

    My laptop computer came to me with about 90% of the hard disk store available for future use. More than a year later, 74% of the store is available. This wastage does not bother me in the least. The relative expense of the hard disk drive is very low. The relative value of potential uses of the available storage is high.

    I believe that a religious view — specifically, that Divine Design happened in the past, and will not occur in the future — keeps many IDers from considering that a wise designer anticipates system upgrades. When a resource like DNA storage is relatively inexpensive, it makes sense to allocate a lot of it for future use.

  18. Sal Gal:

    respond respectfully to some ID arguments, but the notion that a designed store of information would be nearly full is abysmally stupid.

    Not more so than the superstitious and primitive belief that life arose spontaneously from dirt.

    I believe that a religious view — specifically, that Divine Design happened in the past, and will not occur in the future — keeps many IDers from considering that a wise designer anticipates system upgrades. When a resource like DNA storage is relatively inexpensive, it makes sense to allocate a lot of it for future use.

    But that is precidely the ID perspective, in my opinion. At least, I think that this is the way IDers should see in general. For one, there’s the concept of front loading, which is a way of saying that the designer anticipated that a whole bunch of future environmental scenarios would affect the evolution of the species.

    As far as junk DNA is concerned, I personally suspect that a lot of its functionality has to do with error correction and robustness which, as most software designers know, require a lot of duplication of information. So it makes sense that the removal of a seemingly non-functional gene turns out to be harmless to an organism. However, I suspect that the harm may turn up several generations in the future as the organism becomes less and less adept at correcting deleterious mutations.

  19. 19

    Hi merlin,

    Brian Sykes claims that the y chromosome is deteriorating (might have been a reference to some research on the radio, but I do not remember who or where) which supports Sanford’s position

    Deterioration of the Y chromosome is expected under evolutionary theory, primarily because of the lack of recombination between X and Y . There is a rich cytogenetic literature on the evolution of sex chromosome systems, going back around 50 years or so. Here’s a recent example:

    Engelstädter J (2008). Muller’s Ratchet and the degeneration of Y chromosomes: a simulation study. Genetics 180(2): 957–967.

    From the introduction (my emphasis):

    MANY animal and plant species have sex determination systems that involve distinct X and Y chromosomes (BULL 1983; SOLARI 1993). It is generally believed that these sex chromosomes evolved from common autosomal ancestors. However, Y chromosomes often have lost many of their genes, are highly heterochromatic, and exhibit a high density of transposable elements (reviewed in GRAVES 2006). In humans, for example, the Y chromosome spans ~60 Mb and contains only a few dozen protein-coding genes in its nonrecombining region (SKALETSKY et al. 2003). Moreover, the Y is rich in repetitive DNA without apparent function, and a large proportion is heterochromatic. By contrast, the human X chromosome measures ~155 Mb and contains >1000 genes (ROSS et al. 2005).
    Several mechanisms have been proposed for why Y chromosomes erode, but their relative importance is not fully understood and may vary between species (reviewed in CHARLESWORTH and CHARLESWORTH 2000; BACHTROG 2006). It is clear, however, that the ultimate cause of erosion is the lack of recombination between X and Y chromosomes over most of their length. For example, this lack of recombination can lead to “hitchhiking effects” of deleterious mutations (MAYNARD SMITH and HAIGH 1974): if a beneficial mutation arises on a Y chromosome and spreads to fixation, it will drag along all mildly deleterious mutations at other loci on the Y chromosome (RICE 1987). Another mechanism that leads to accumulation of mildly deleterious alleles is a reduction in effective population size due to “background selection” against linked, strongly deleterious alleles that arise continually by mutation (B. CHARLESWORTH et al. 1993

    http://www.pubmedcentral.nih.g.....7394#bib43

  20. Mapou,

    For one, there’s the concept of front loading, which is a way of saying that the designer anticipated that a whole bunch of future environmental scenarios would affect the evolution of the species.

    Then again, a non-omniscient designer designs adaptivity into a system because he / she / it cannot anticipate the particulars of future environments in which it will operate.

  21. Sal Gal

    I’m not sure who your post about designed stores of information is aimed at, perhaps that’s why it doesn’t make sense to me.
    Your laptop was designed to have more memory than any normal user could ever need because the cost was low and the relative value high. But it doesn’t follow that having a memory store that is just the right size for the job is “abysmally stupid”, the relative value of extra memory could, given different design requirements, be zero.

    However, this all seems to be missing the point. Junk DNA can’t be compared to empty space waiting to be filled. A better analogy (whilst keeping to your hard disk theme) would be a large file on your hard disk. The file gets deleted, then a new, smaller file is copied over the original and this process is repeated until you are left with one small functional file followed by several fragments of files which have no function. For example, if we start with “reallylargefile” then overwrite “notsobigfile” then overwrite “mediumfile” then overwrite “tiny” then overwrite “ok”, we are left with the fragments “y mfile e le” which is junk.


    reallylargefile
    notsobigfile le
    mediumfile e le
    tiny mfile e le
    ok y mfile e le

    So as the contents of your hard disk evolve so too increases the amount of junk.
    However, when the contents of a memory store are carefully designed there is unlikely to be any junk at all. For an example of this consider a computer’s BIOS. This is the first program run when a computer starts, and resides on it’s own special memory. The BIOS contains code for interacting with all kinds of hardware (i.e. the BIOS will contain more code than most systems require) and it is possible to make configuration changes to the BIOS. Despite this there’s little advantage in this memory being bigger than it needs to be and, due to be being carefully designed, it’s highly unlikely that the BIOS would ever contain junk.

  22. #21
    This is also a good example of what would happen to “front loaded” genes–if the organism is not using front loaded genes, natural selection cannot operate to remove aberrant point mutations from the population, causing drift to fixate junk sequences.

  23. SalGal @20:

    Then again, a non-omniscient designer designs adaptivity into a system because he / she / it cannot anticipate the particulars of future environments in which it will operate..

    That’s my point exactly. Evolution was designed. However, adaptation does not mean blind chance. The only way to prevent genetic adaptation from getting mired in an exponential explosion of possibilities is to program the genome with a whole slew of constraints. This requires anticipation on the part of the designer. Exponential explosion is a complete show stopper. Ask anybody who has ever played with genetic algorithms.

    By the way, this is one Christian who does not believe in an omniscient designer.

  24. Mapou writes:

    Ask anybody who has ever played with genetic algorithms.

    Mapou,

    Sal Gal has, to the say the very least, “played” with genetic algorithms.

  25. Sal Gal:

    There is a kind of hostile edginess to your posts. It makes me think your not a “gal” at all.

    Be that as it may, the quotes that kairosfocus give in an earlier post effectively demolish your thesis that this kind of “use” for so-called junk-DNA was “expected”. You have not been around for the online debates that have taken place over the last five years, because if you had been then you would have been well aware that ID was mocked by Darwinists who loved to claim that most of our DNA was junk, since 97% is “non-coding”. ID withstood these challenge. So don’t think you can come around now and simply say it wasn’t so (OR, it isn’t so, since even now there are Darwinists who want to make this same argument). This would be no more than simple rationalization—a mechanism that Darwinist “believers” find indispensible.

    On a more substantive note, in my earlier thread on this same organism and subject, I wanted to add a comment, but didn’t see the enthusiasm there for a discussion, so I didn’t. But I do so now.

    As I reflect on the kind of ‘function’ that we see junk-DNA provide in this instance, it may be necessary for us to begin thinking about the “structural” function of DNA. What I mean is this: in the kinds of code that we’re familiar with, computer code in particular, the code is of an electronic nature, and thus is not very ‘localized’ in space. This is not the case with DNA: not only is it a code, it is a code that exists in time and space, AND, is a code that must replicate itself. (Humans are the one who supply the means of replication of language using paper and ink) In the cell, for example, the ‘physical’ reality of the genome means that during meiosis chromosomes are pulled apart, and, proportionately, with significant force. Therefore, is part of the ‘function’ of LINEs (Long Interspersed Nucleotide Elements), or even the transposons of this particular paper, ways in which essential genetic material is ‘protected’ from the damage that ‘meiotic forces’ might apply? As well, in terms of the forces applied to the genome, we can think of the forces imparted by histones as they re-structure parts of the chromosome in preparation for transcription. Again, is there some kind of ‘structural’ function that is played by LINEs and SINEs and transposons, or other “non-coding” DNA?

    I think very little thought has been given to these kinds of scenarios, and probably it represents an oversight on the part of UD thinkers. Perhaps it will be the very kinds of experiments now being reported that will bring this putative aspect of the genome into greater relief. The point here might be simply that we should not think of the genome strictly in terms of “front-loading”, but think of the genome’s needs as well, needs arising from the fact that this ‘coding system’ is not ‘ethereal’ reality, but physical one, and, as such, in need of physical restraints and constraints like all else that exists in time and space.

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