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Junk DNA Strikes Again

This is like the junkiest of junk, and it turns out to be so critical:

From a PhysOrg article:

To find out what was going on, the researchers began testing the DNA of several families that showed a proclivity for harboring the disease. Some actually had it, while some did not. Comparing the two allowed the team to track down which differences in their genes might be accounting for the presence of the disease. Much to their surprise, they found it lay within gene SLC7A2, which is known to be used by the brain during its development stage. But what was most remarkable was the fact that it was a single letter change, from an A to a G, found inside an intron, which was in turn embedded in a LINE jumping gene, which was itself inside of a dead jumping gene called a SINE element, all three of which were up to now, considered junk genes. The researchers found that if a child got the G marker from just one parent, it was safe. One from each however, meant developing Ravine encephalopathy.

Junk-DNA indeed strikes the Darwinists again.

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18 Responses to Junk DNA Strikes Again

  1. If we look at the paper (or even the title and abstract, which are shown on PhysOrg) we see that we are not dealing with a challenge to the concept of junk DNA.

    Firstly, the sequence in question is a conserved sequence in primates – the title of the paper tells us this. This, of course, indicates that we are probably not dealing with junk. Junk DNA is predicted to evolve rapidly because it is not subject to purifying selection.

    Secondly, we are told in the abstract that the sequence codes an RNA that is expressed in the brain. Nothing at all about this says ‘junk’.

    Your errant assumption is that SINES and LINES are proposed to be all junk. This is not and has never been the case. Some are active, and others form parts of essential genes.

  2. @paulmc
    You’re focused on rebutting the author of this post, who mostly copy/pasted some excerpt and linked to an article linked to another article that both seem to disagree with you at some level. My question is why do you and these articles (notwithstanding PaV’s view) disagree on what clearly has been assumed to be junk? Perhaps, the perspectives are one is seeing where the mutation was nestled (i.e. within junk) versus what was nestled.

    Medical Express title:
    “Research team finds key to childhood brain disease lies in genetic junk”

    Discover magazine title:
    “Under three layers of junk, the secret to a fatal brain disease”

  3. My question is why do you and these articles (notwithstanding PaV’s view) disagree on what clearly has been assumed to be junk? Perhaps, the perspectives are one is seeing where the mutation was nestled (i.e. within junk) versus what was nestled.

    You’ll note that it is not the researchers who make the claim, but the journalists. Plus, you haven’t looked past the titles.

    In Ed Yong’s piece (Discover Magazine) he states:

    So, here was a mutation that caused a fatal brain disease, lying in the genetic equivalent of Russian nesting dolls. Clearly, these sequences aren’t junk. If they were, changing that A to a G would have no effect. So what are they doing?

    It turns out that the brain retains most of the discarded intron as a piece of “non-coding RNA”, which never goes on to produce a protein. It is, however, still important.

    IOW, Ed Yong and I are in complete agreement. The title of his piece refers to layers of junk, not to the sequence in question itself being junk.

    The other piece (which is the same as linked in the OP) states only that the researchers don’t know “why supposed junk genes appear to be serving a purpose” which is inconsistent with their paper in PNAS (and with Ed Yong’s excellent summary).

    What the articles are all essentially saying is correct – introns, LINEs and SINEs are more junk than not. So seeing them nested as they were makes for a nice, catchy story. But a direct claim that the sequence itself was junk DNA is without substance.

  4. “But a direct claim that the sequence itself was junk DNA is without substance.”

    If that is what you think PaV or the article said, you need to read more closely. Of course the sequence is not junk, because it served a purpose. That is why the article used words like “up to now.”

    The point is quite simple: there has long been a general presumption that most of these things are junk, which you also acknowledge. Finding a nested function in what would have been expected to be layers of junk is interesting.

    The Darwinian “explanation” for these used to be that essentially all of these are junk — the detritus of eons of evolution. Now the story is that “most” are junk (notwithstanding pervasive transcription). So the Darwinist says “Yes, yes, we know that some of these things aren’t junk,” and hopes everyone will forget what the earlier prediction was. Indeed more and more functions are being found all the time. Come back in a couple of years and we’ll be hearing “Yes, but some of these are still junk.” The Darwinian widespread “junk” expectation continues to retreat in the face of evidence.

    The junk DNA “explanation” is a specific claim of Darwinian thinking, regularly expressed, and widely trumpeted. We continue to see the expectations upended every time we look around. That is interesting. And instructive.

  5. paulmc:

    Eric, in #4, presents what my response to you would have been. LINEs are considered junk. SINEs are considered junk. Transposons are considered junk. Introns used to be considered junk.

    So, we learn more, and the Darwinist account changes. But you’ll notice that the ID has not had to change. Which position gives you more confidence?

  6. Eric:

    The point is quite simple: there has long been a general presumption that most of these things are junk, which you also acknowledge. Finding a nested function in what would have been expected to be layers of junk is interesting.
    The Darwinian “explanation” for these used to be that essentially all of these are junk — the detritus of eons of evolution. Now the story is that “most” are junk (notwithstanding pervasive transcription). So the Darwinist says “Yes, yes, we know that some of these things aren’t junk,” and hopes everyone will forget what the earlier prediction was.

    The point that is ‘quite simple’ is exactly the one I was addressing. You are wrong to say that the mainstream stance of molecular biologists was ever that LINEs, SINEs and introns are all junk. Since its conception in the 1970s, the concept of junk DNA has related to function and purifying selection. If we look at which sequenced are conserved by purifying selection and which are not, we see that introns and intergenic stretches – many containing broken copies of transposable elements – are the ones that are not conserved. We are led to the conclusion that most of them are junk because they are repetitive, long, variable, not consistently expressed, serve no structural role and relatively free to mutate.

    So, it does not follow that all introns, LINEs and SINEs are junk, nor that everything else is functional. It follows, though – as it always has – that the majority of the copies of transposable elements, meeting the criteria above, are junk. So while it’s quite nifty that an intron bearing a LINE inside a SINE is conserved and expressed in the brain, such a sequence would never qualify as junk simply because of its composition.

    Come back in a couple of years and we’ll be hearing “Yes, but some of these are still junk.” The Darwinian widespread “junk” expectation continues to retreat in the face of evidence.

    Whenever ID folk come out with a line like this it is always qualitative. The proportion of putative junk DNA has hardly changed in 40 years of investigation. So I seriously doubt it.

  7. PaV:

    So, we learn more, and the Darwinist account changes. But you’ll notice that the ID has not had to change. Which position gives you more confidence?

    Well, the figureheads of the ID movement claim that virtually no DNA should be junk. Although, they do so without providing the criteria for detecting which sequences are junk and which are not. So that’s vague.

    Others in the ID movement say that any amount of junk DNA is fine, and that the absence of junk DNA is not a prediction of ID.

    What about this vagueness and contradiction should give me confidence?

  8. Finding a nested function in what would have been expected to be layers of junk is interesting.

    Rather than a “nested function” I’d rather say that what was found was that changing a single letter in what would have been expected to be layers of junk could not be tolerated as early as during infancy.

    The assumption was that essentially all of these are junk — the detritus of eons of evolution. Now the story is that “most” are junk (notwithstanding pervasive transcription). Indeed more and more functions are being found all the time.

    Maybe now the story should rather be that at the very moment all the focus is brought to genetic diagnosis by whole exome capture, which roughly consists of 1% of the genome, this study and others prompt to aim at the conquest of this unknown part of our genome, which accounts for more than half of our genome.

  9. paulmc:

    I agree with you that the question of junk DNA will not resolve the question of whether DNA was designed or not. The design concept can certainly accommodate non-function (as we have been discussing the past couple of days on another thread). And traditional evolutionary theory can certainly accommodate function (although material processes have never been shown to produce complex specified information, I acknowledge that they are claimed to produce it, and, therefore, the theory can accommodate such information in DNA).

    So regardless of how much junk DNA there turns out to be, we will not ever be able to draw any definitive conclusions, on a deductive basis, about design. (It is quite a separate question whether functional DNA points to design, which ID proponents argue it does, but that is a separate, although certainly the primary, issue.)

    Thus the question with junk DNA is not so much one of particular percentages, but a consilience of evidence. Which way is the evidence pointing? Not in a logical, % cut-off, deductive sense, but in an inductive sense. What is the preponderence of the evidence suggesting; what are we learning; where are new discoveries pointing?

    As a result, your statement “The proportion of putative junk DNA has hardly changed in 40 years of investigation” is probably the most outrageous thing I’ve heard all day; possibly all week. Please don’t try to re-write history.

    There is no question that DNA, under the central dogma, was viewed as being functional only to the extent that it coded for proteins. There are numerous statements from prominent scientists over the decades dismissing essentially everything else as junk. As a result, by definition, virtually every new discovery over the past decades about function in DNA, of which there have been literally hundreds, has diminished the proportion of junk DNA. It has gotten to the point where some scientists are even hesitant to use the term anymore because it is questionable.

    So your attempt to re-write the Darwinian/evolutionary expectation is fabulously wrong on at least two fundamental levels:

    1- The proportion of junk DNA could not possibly have gone up from the early claims. It has only gone down. There is no reason, other than continuing to cling to our Darwinian mindset, to think the trend will not continue as we learn more.

    2- There is essentially almost no known junk DNA. (We could quibble about certain knock-out experiments, but most of those are inconclusive, and in any event, don’t amount to more than the tiniest fraction of DNA.) What there is instead is an unsupported assertion, which you and others continue to make, that there is a huge amount of junk DNA. That is an assumption. It is an assumption based on who knows what? Certainly not engineering analyses. Perhaps on a Darwinian/materialist creation myth? One thing is clear, it is an assumption that is having to retreat with each new discovery.

    So, yes, a particular % of junk DNA won’t answer the question of DNA being designed. But holding onto some idea of putatively vast amounts of junk DNA (particularly as ‘evidence’ for non-design) is a losing proposition. Such a person will clearly find themselves on the wrong side of the line when it comes to new discoveries and developments.

  10. As a result, your statement “The proportion of putative junk DNA has hardly changed in 40 years of investigation” is probably the most outrageous thing I’ve heard all day; possibly all week. Please don’t try to re-write history.

    OK, well, suspend your outrage for just a moment and consider what I am actually saying. I am not rewriting history at all. I realize that the framing of news stories always puts the ‘unexpected’ slant on discoveries of functional odds and ends in the genome, but this does not reflect the history of thought in molecular biology.

    Ohno proposed the concept of junk DNA in 1972. At that time, he suggested an upper limit of about 10% of mammal genomes that could be under purifying selection. This is before we had any detailed knowledge of mammal genomes. Far from being arbitrary, there are good reasons for this – first and foremost the cost of purifying selection, which relates to mutation rate (known with reasonable accuracy at the time). This has been since supported by studies of selective constraint on the genome. I’ve discussed these reasons elsewhere on UD, and of course Ohno explains his case well in the paper.

    Fast forward to 2012, the best quantification of the human genome gives us about 9% functional DNA (including all of the structural DNA and the non-coding but consistently expressed RNA). This leaves us with about 91% nonfunctional DNA, the vast majority of which is likely to be currently junk.

    Certainly, there are new genomic discoveries being made, they just need to be understood in perspective. Often we hear about a new 30-odd nt miRNA being discovered, for example. But you need to discover one million miRNAs to explain just 1% extra of the human genome. That would get us to about 10%. IOW, it does little to help us understand the broad structure of our genome.

    The other side is that if you have more functional sequence, you have to bear the selective pressure of maintaining it (i.e. through non-random death = selection). How many nucleotides in the human genome can be under purifying selection before the genetic load becomes unbearable? This is a quantitative problem that does not get addressed by critics of junk DNA. You can speculate about non-sequence-specific RNAs that could exist and could have function. But where is the evidence for these comprising a bulk of the genome and being largely cobbled together from all-but-endless transposon insertions?

    What there is instead is an unsupported assertion, which you and others continue to make, that there is a huge amount of junk DNA. That is an assumption. It is an assumption based on who knows what? Certainly not engineering analyses. Perhaps on a Darwinian/materialist creation myth?

    Sorry, but this is pure ignorance. The concept of junk DNA is not an assertion, it is not unsupported, and you would know what the assumptions are based on if you cared to know. I bet you’ve never read this paper.

  11. paulmc:

    Others in the ID movement say that any amount of junk DNA is fine, and that the absence of junk DNA is not a prediction of ID.

    Really? Who are they? Do you have any citations?

  12. paulmc:
    Others in the ID movement say that any amount of junk DNA is fine, and that the absence of junk DNA is not a prediction of ID.

    PaV:
    Really? Who are they? Do you have any citations?

    Why, in this very thread Eric Anderson @9 said:

    The design concept can certainly accommodate non-function…
    So regardless of how much junk DNA there turns out to be, we will not ever be able to draw any definitive conclusions, on a deductive basis, about design.

    Do you disagree with Eric?

    As for citations, I don’t know of any ID theorists producing peer-reviewed literature on the topic of junk DNA, although it turns up in some books. Most of the recent ID writing is extraordinary in its vagueness around the topic. Jonathan Wells, for example. He states that the human genome is “far from consisting of mainly junk”. For him, much less than half the genome must be junk, so he has a loosely defined upper limit for junk (how far is far?) – and that was in a book called The Myth of Junk DNA.

  13. paulmc:

    Most of the recent ID writing is extraordinary in its vagueness around the topic.

    What do you see as the trend? Don’t you see that what once was thought to be, no-questions-about-it, “junk,” is now found to have function? Isn’t it likely that as molecular biology becomes more and more sophisticated in its techniques that more and more function will be found?

    Now, does this trend move us in the direction of “random processes”, or in the direction of greater and greater complexity? Which side of the argument do you think this aids?

  14. I realise most of these are more-or-less rhetorical, but I’ll play along…

    What do you see as the trend?

    I’ve answered this already in this thread.

    The trend, over 40 years, has been no change in the broad proportion of the genome understood to be junk, despite our developing a much deeper understanding of the genome and its content.

    Don’t you see that what once was thought to be, no-questions-about-it, “junk,” is now found to have function?

    There’s no such thing as no-questions-about-it junk. But, you wouldn’t necessarily understand that as I don’t think you’ve followed the argument.

    Isn’t it likely that as molecular biology becomes more and more sophisticated in its techniques that more and more function will be found?

    Yes, most probably.

    Now, does this trend move us in the direction of “random processes”, or in the direction of greater and greater complexity?

    I don’t think there is a dichotomy between random processes and complexity.

    Which side of the argument do you think this aids?

    Whoever follows the evidence … wherever it may lead.

  15. paulmc:

    I bet you’ve never read this paper.

    I’ve read plenty of papers and am always happy to learn more. I hope, however, that you are not pulling a Matzke on us. Almost invariably when I read a paper cited as evidence by some evolutionary proponent, the paper doesn’t actually support what they claimed it was going to support. Hopefully this one will be different. Or perhaps it will assume lots of key questions up front, including the idea that there must be vast quantities of junk DNA?

    In any event, I’m happy to look at the paper if it isn’t behind a paywall, but if you would be so kind as to offer just a couple of sentences stating what you think the paper demonstrates, that would be helpful.

    —-

    . . . he suggested an upper limit of about 10% of mammal genomes that could be under purifying selection. This is before we had any detailed knowledge of mammal genomes. Far from being arbitrary, there are good reasons for this – first and foremost the cost of purifying selection . . .

    This is an interesting point, and one worth exploring. However, we need to acknowledge that it assumes purifying selection is the process that governs. In addition to the several assumptions built into purifying selection, we now know that there are in fact machines that actively repair DNA in vivo on a regular basis, so purifying selection is not the only mechanism that can operate to determine the amount of functional DNA.

    This should be a relatively simple hypothesis to test experimentally. Take mammalian DNA, say a dog’s or a chimp’s, remove the 90% “non-functional” DNA and insert the remaining 10% into an egg, then: (i) see if a normal, healthy adult develops, (ii) whether the adult is able to reproduce normally, and (iii) what changes, if any, occur in the DNA after a couple of generations.

    I would be extremely interested in this kind of empirical study if anyone is aware of such a thing.

    Otherwise, the claims of pervasive junk DNA are just that, claims. Yes, it could turn out that the vast majority of mammalian DNA is junk. But we should at least be honest enough to acknowledge that it is a claim and that just because we know for certain 9% of DNA has function we cannot conclude:

    “This leaves us with about 91% nonfunctional DNA, the vast majority of which is likely to be currently junk.”

  16. Hey Eric-

    I have suggested similar experiments to see if the “90% junk” measures up.

    But even with that there would still be issues- some designs come with features that are for future considerations, meaning they ain’t being used in the current config. Then there are redundant features- there for back-up, easily removed without affecting current functionality.

    But anyway, I agree, until someone does the knockout tests it is all just speculation.

  17. Almost invariably when I read a paper cited as evidence by some evolutionary proponent, the paper doesn’t actually support what they claimed it was going to support. Hopefully this one will be different. Or perhaps it will assume lots of key questions up front, including the idea that there must be vast quantities of junk DNA?

    I think that it is an excellent review paper that carefully goes through the evidence for the broad structures of eukaryotic genomes being the result of genetic drift in populations that are unable to remove slightly deleterious expansions.

    The authors do no assume that there must be vast quantities of junk DNA, they demonstrate that such accumulations stand as the best explanation for the observed genome structures. In particular, the comparison of animal and plant mitochondrial genomes is enlightening.

    If you don’t have access through the other link, the paper is also available here.

    This is an interesting point, and one worth exploring. However, we need to acknowledge that it assumes purifying selection is the process that governs. In addition to the several assumptions built into purifying selection, we now know that there are in fact machines that actively repair DNA in vivo on a regular basis, so purifying selection is not the only mechanism that can operate to determine the amount of functional DNA.

    There may be assumptions, as there always are in science, but they are well-founded. There are a number of reasons to believe that purifying selection governs the evolution of coding sequences.

    Coding sequences evolve slower than sequences without known function, implying that many mutations in these sequences have been removed from the population to preserve function by purifying selection. There is no reason to believe that DNA repair varies in quality across the genome, so it would be difficult to argue for a lower mutation rate through such a mechanism. In any case, there are two additional patterns that further support my case. They both relate to the number of synonymous and non-synonymous changes that occur in coding sequences.

    Synonymous changes produce the same amino acid, and are therefore likely to be subject to far less purifying selection than changes that alter the structure of the protein. Synonymous mutations occur at the same rate as non-synonymous mutations, but they accumulate much faster than non-synonymous changes in the population. A typical gene might have a ratio of 5:1 or 10:1, meaning 80 or 90% or the non-synonymous variation has been removed from the population.

    Also, this ratio changes when we look at comparisons between species and within species. When we look within species, we are looking at the polymorphisms sitting in the population rather than the ‘successful’ alleles that have spread through the population. We see that the ratio in this situation is much more even – many more of the non-synonymous mutations are still present. This indicates that the non-synonymous mutations are persisting for many generations before being purged by purifying selection. There is no other known mechanism that can account for these observations.

  18. paulmc,

    Thanks for the additional information and the link. I appreciate you taking time to explain your view and I will try to take a look at the paper sometime in the next week or so if I can.

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