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“Junk DNA”: Seems Vital


I’m just posting this to give people an update on what researchers are finding. More and more, so-called “junk DNA” is proving to be essential for life. Here, transposons, considered, generally, to be the “junkiest” of the “junk”, is found to have a rather central role in the development of a pond critter. Here is the write-up on PhysOrg. com.

If you look at the first comment at the end of the article, a blogger named “flag” writes:

“The label junk DNA is a testament to junk science.

It is obvious to anyone who actually understands evolution that no organism can ever contain 90% of useless DNA. It is simply impossible. Unused DNA would be lost in a very short time frame as it’s maintenance incurs huge costs.”

So, once upon a time, we were told that transposons show that the genome couldn’t possibly be designed because it had all this wasteful DNA around. Now, per ‘flag’, “it’s obvious … that no organism can ever contain 90% of useless DNA.” Life as a Darwinist must be fun: you’re never wrong. You only have to reverse what you say every once in a while.

Of course larger deletion mutations have the potential to do that. They also have the potential to take out large sequences of useless DNA without affecting useful DNA. Do you deny this? If I am supposed to believe that millions of years of evolution can overcome the probability barriers to finding functional sequences, then why should I not believe that over the same time frame deletion mutations can weed out all useless DNA? This is a profound contradiction within evolutionary theory. What do you mean by "non-coding"? Non-coding DNA I take to be DNA that does not undergo any transcription. Non-coding RNA would not undergo translation. Either way, both ncDNA and ncRNA may have function and if they do are not "junk", and we already know of many examples of each having some other function. Just because that function sometimes does not depend on the sequence does not make it "useless baggage". Let me predict that the number will be far closer to 93% than to 6%. Let me further predict that it will be possible to reverse engineer, so to speak, "junk" DNA to find the original, designed function. tragic mishap
Mr Mishap, I know that deletions _can_ happen at all scales, the issue is if they _do_ happen, and do the resultant organisms survive to reproduce. At first, I thought that deletion size plotted against frequency would follow a Poisson distribution. But now I am not sure. If you look at the numbers on that Wiki page for diseases caused by different deletion events, you can see that some deletions, at least, recur frequently - much more frequently than a single base copying error! The difficulty is that these deletions cut across both coding and non-coding regions. Because of the pattern of interspersal of coding and non-coding regions on the chromosome, once deletions get above a certain size, they are almost sure to take out a gene. As a result, the cells of the organism aren't making all the proteins they need. This is usually fatal. The issue with prokaryotes is that they do not have "junk DNA" in the same way as eukaryotes. So a general theory explaining junk DNA has to explain the differences between eukaryotes and everythng else. The Wiki page on "Junk DNA" links to this recent article on the size of 'required' non-coding regions. The basic idea of the article is that eukaryote architecture solves a connectivity problem by using non-coding DNA to create non-coding RNA, and it is possible to calculate how much ncDNA is needed for this purpose. The answer for a human size genome is about 6% of ncDNA. So the ultimate answer on how much ncDNA is uesful to the organism, and how much is excess baggage, will probably fall simewhere between this number (6%) and the 93% quoted by PaulN from the ENCODE preliminary results. Nakashima
Nakashima, Why do you insist that we are only talking about "base by base" deletion? This is not what is meant by a deletion mutation. http://en.wikipedia.org/wiki/Deletion_mutation "Any number of nucleotides can be deleted, from a single base to an entire piece of chromosome." I see no reason why this is somehow restricted to prokaryotic cells either. There are single-celled, eukaryotic organisms as well, and I'm quite sure their mutation and replication rates are similar to prokaryotes. As for multicellular, complex eukaryotic organisms such as mammals, the difference is only one of scale. As you have said, "The answer would seem to be that some really is junk, and is therefore decaying away, while some other part is serving some function and being conserved." I don't think that any of it is junk. If it is decaying away, it is only doing so because natural selection was not strong enough to weed out mutant individuals, allowing non-functional mutants to propagate slowly throughout the population. You wouldn't call extinct species "junk" would you? Was the dodo "junk"? Were the dinosaurs "junk" species? Are all the animals on endangered species lists junk? I think they function just fine. If not, why try to save them? tragic mishap
Nakashima: "We can see how useful it would be to cull non-functional DNA from the genome, and reduce the energy budget of the cell. But if there is no source of variation that regularly deletes large swaths of non-coding DNA, it will never happen in nature." I never suggested it was a single mutation that did this. Multiple mutations deleting small swaths of useless DNA would add up. We are talking about DNA in general here, which has been in existence since the beginning of life on earth. There is plenty of time for multiple deletions to do the job. Perhaps not for recent organisms with slow mutation and reproductive rates, but the genetic material from whence they came would have already been established before then. tragic mishap
Tonsils, anyone? Appendix? "Junk" and "useless", when applied to something we ourselves did not have a hand in building, designing, creating, or otherwise bringing into being, are more likely to indicate a failure to understand on our part than a failure to design well on the builders part. music2myear
Mr Jerry, I agree, but base by base deletion is not going to eliminate 90% of the DNA in the genome. To accomplish the large efficiencies under discussion, you need some wholesale process. Just for a reference point, I looked at Allen Macneill's list of sources of variation to see if it included such a method. It did not. At least in eukaryotes, it looks like the best we can do is turn things off, but leave the code in place. Nakashima
Deletions are one way of changing a genome. Hence if useless DNA is deleted and this should happen often enough, then one would expect using efficiency arguments that this version would be preferred. jerry
Mr Mishap, Ok, going back over the OP. Mr PaV got the attribution slightly wrong. The comment is by someone posting as "superhuman". "Flag" is a link to report the comment as abuse or spam. In any case, the comment is, I think, incorrect. Selection can only act on the variations that are present. If there is no mechanism to create that variation, it can't be selected. We can see how useful it would be to cull non-functional DNA from the genome, and reduce the energy budget of the cell. But if there is no source of variation that regularly deletes large swaths of non-coding DNA, it will never happen in nature. Nakashima
What the author said was, "Unused DNA would be lost in a very short time frame as it’s maintenance incurs huge costs." This means that whether the protein itself is actually deleterious or not doesn't matter. If the protein doesn't do anything, the genome is likely to lose the gene for it in a short amount of time. It's very easy to imagine. Mutations can cut out entire genes quite often. If the organism doesn't need that gene, then there is no selective pressure to weed out the mutated organism. In fact, the organism is spending less energy than the wild type, so it may even provide a selective advantage to lose genes that don't do anything. This has happened in the lab with microorganisms. Grow E. coli on a particular medium for long enough, and it will lose the genes it uses for other food sources. Why? It doesn't need those genes because it's getting all it needs from one medium. tragic mishap
Mr Mishap, Ah, do you mean "how long can either gene stay in some mutated, non-functional state"? I think that the answer depends on selection pressure, or if the products of the mutating gene are actually deleterious. For example, a duplication of opsin genes might be responsible for some of our color vision. If the duplicated gene started making poison, not opsin, then its population share will drop fast. I don't know enough population genetics to give a better answer. Nakashima
Nakashima, The whole point of the gene duplication hypothesis is that one copy continues expressing a functioning protein while the other copy is allowed the freedom to mutate through several non-functional intermediates to a new functional protein. tragic mishap
Mr Mishap, But when it is duplicated, it still has the original function, still makes the original protein. Why would it get weeded out? Nakashima
Mr Jerry, That 93% number is the most optimistic figure in the ENCODE paper from 2007. out of three technologies used to detect transcription, even if only one of three saw the transcript, then it counted towards the 93%. Two of three dropped the number to about 74%, three of three to about 36%. It is going to take a lot more work to pin that number down. Nakashima
I was referring primarily to the gene duplication hypothesis, wherein a gene is duplicated and one copy is conserved and the other is not, supposedly evolving through several non-selectable mutations to a new selectable sequence. How long does such a gene have to evolve before it gets weeded out of the genome? Not long, and there is research to support this. tragic mishap
Another "bulk" function is to provide spacing between genes, and protective regions at the caps of chromosomes and at the centromere. Again, no special sequence necessary. Nakashima
Mr Mishap, The answer would seem to be that some really is junk, and is therefore decaying away, while some other part is serving some function and being conserved. It is also possible that some of the "function" does not depend on the sequence of the bases. Remeber the discussion recently about the lensing properties of the nuclear DNA in rod cells? That function relied on the bulk chemical properties of tightly wound vs loosely wound DNA, not the sequence of bases. As Woody Allen might have put it, just showing up was enough! Nakashima
I was just about to post on that magnan. If: "Unused DNA would be lost in a very short time frame as it’s maintenance incurs huge costs." Then where is the material for evolution to evolve towards new function? tragic mishap
What seems especially strange to me is that much of the formerly-called "junk" DNA is supposedly not conserved over evolution. Is this really true? If so, how could its nucleotide sequences be essential as information for growing the organism? magnan
I don’t know. But what percentage has been proven to be functional?
A good, reasonable answer, which I've noticed you generally provide. I would agree this is the right way to look at things. The problem is that this way was not in vogue even ten years ago. Back then, the "obvious fact" of junk DNA not only proved evolution, it killed God. Because, as we all know, God would certainly not create DNA with so much junk. It's such grotesque professions of certainty based on so little evidence that are so unacceptable. I would also agree that the percentage of functional DNA will increase, every year, as research occurs, thereby reducing the Darwin-of-the-gaps effect as it did with vestigial organs. In the case of junk DNA, ID is predicting correctly, Darwinism is not. That doesn't "prove" either, but it does suggest one over the other. The correct answer to the percentage question is 0%. Without complete information, a negative cannot be proven. Assuming non-function was a bad idea. SpitfireIXA
jerry in [3]: This pond critter I suppose might be a little unusual, but what the authors are reporting--and I can't quite follow because this article represents but a snippet of their work--is that the transposases, guided by an RNA template, reconfigure the "somatic" nucleus of this protozoa, reducing the genome by 95%. What this might suggest is that this very basic, and hence early, form of life already exhibits a mechanism for getting rid of unnecessary DNA. The additional DNA is shed 'after' the organims has gone through its developmental stage. Thus, two things: (1) 'nature' has the ability to get rid of unwanted/unnecessary DNA whenever it is needed, (2) more speculatively, that if any truly 'junk DNA' is found--which I suspect will be minimal--it might only represent the fact that it is much more 'cost effective' (both informationally and energetically) to 'keep' the junk-DNA rather than getting rid of it. Their research is intriguing in other respects as well, in the sense that one more clearly gets the sense that 'genes' are but raw material guided by higher informational systems. The whole new area of 'systems biology' reflects this growing appreciation that 'genes' are not really all so fundamental. The book, "What Genes Can't Do", makes this point quite powerfully. The author notes that after 40 years of cancer researchers looking for supposed 'cancer genes', that these same researchers are coming to the sad conclusion that they might have 'wasted' 40 years. You'll notice RNAi's are now in the limelight when it comes to cancer therapy and such. This pushes us in the direction, then, that ID has touted for so long: that genes are but a 'material list' for the assembling of life, and the overriding work of most DNA is that of directing the genes to do what they do. IOW the "junk DNA" (the 'non-coding' portion) is the MOST important part of DNA, not the genes. This paper just offers further proof of this position--contra the Darwinist position (as ever-changing as it may be). PaV
"What percentage of DNA sequences have been proven to be non-functional? 95%, 50%, 10%?" I don't know. But what percentage has been proven to be functional. So far not very much from what I understand. See my comment below. More will be coming but as of the moment, it is small. I would like to see the 93% functional DNA cites as mentioned by PaulN. From what I understand a large portion of the DNA has been transcribed but that does not mean it has function only that various RNA polymers have been transcribed. I suspect that many of them will have function but if you have anything on that, let me know the source. I made a similar observation a couple weeks ago and no one challenged it. Also before people start to be experts on junk DNA they should be knowledgeable on the C-value paradox http://en.wikipedia.org/wiki/C-value_enigma jerry
Gotta love how the consensus contorts to internal paradigm shifts. As long as they define the rules of the game and the conditions to win it, they will always win. SpitfireIXA, Even though something tells me your question might be rhetorical, I'll bite. The most up to date research from the ENCODE team discovered at the very least 93% to be functional, as well as discovering multiple overlapping functionality for the non-coding regions, alongside 95% of which shows no evidence for selection pressures in humans. =) PaulN
jerry: What percentage of DNA sequences have been proven to be non-functional? 95%, 50%, 10%? SpitfireIXA
So while we expect to find much use for what was called “junk” this does mean that we expect all of it to have function. It is unlikely either extreme is correct.
So, non-functional junk DNA proves evolution (as per what we have heard for the last three decades), unless it doesn't, in which case the opposite proves evolution. PaV is right, what fun to so easily cast off your previous "unadultered facts as confirmed as gravity." SpitfireIXA
I do not want to rain on the parade but this has been discussed recently. Apparently the term "junk" stuck for very obvious reasons but did not prevent it from being studied. And it seems that the processes that create additions to the genome often in fact have no use for this additional parts of the genome. Some very simple organisms have much larger genomes than humans and it is not thought that all or most of these genomes have functions for these simplistic creatures or plants. These additions to the genome are also thought to be the breeding ground for additional function in the future and is proposed that this is how organisms get more complicated and sophisticated over the eons. So while we expect to find much use for what was called "junk" this does mean that we expect all of it to have function. It is unlikely either extreme is correct. jerry
I wonder if the source of the transposons was a viral infection of the ciliate creature? There was a recent article on a similar case where wasp venom actively used viral DNA that might have landed in the wasp genome 100 million years ago! Nakashima
Here's the authors related article on the RNA role in these protozoa:Link PaV

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