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Most eukaryotes posses a certain amount of junk DNA in their cell nuclei. What is (are) the origin(s) of this junk DNA, And is it realy junk (superfluous)?

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  • $\begingroup$ There is nothing like junk DNA. Originally we thought this would make about 90% of our genome, but since then we learned a lot of functions for it: Regulatory, miRNA genes, etc. Carrying so much "junk" around would pose a massive evolutionary disadvantage. $\endgroup$ – Chris Jun 17 '16 at 10:45
  • $\begingroup$ You wrote that "all organisms...in their nuclei". Two of the three kingdoms of organisms do not have nuclei, so I have edited your question. I am also unsure whether all eukaryotes have junk DNA. I would advise you to think carefull before writeing "all" in relation to biology. $\endgroup$ – David Jun 17 '16 at 11:41
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    $\begingroup$ @chris - You're flat-out wrong. Many functions have been ascribed to regions once believed to be "junk", that's true. But if you add up all those now-functional regions, you're still left with about 90% of the genome being junk, because each of those new functions is only a tiny fraction of the genome. Don't read media reports, and don't even read the press releases from the teams who find functions -- go and actually do the math, and it still turns out that 90% of genomes are junk $\endgroup$ – iayork Jun 17 '16 at 13:56
  • $\begingroup$ @iayork Not junk - non-coding. That's a big difference. $\endgroup$ – Chris Jun 17 '16 at 14:46
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    $\begingroup$ Most scientists are virtually ignorant of the whole field of junk DNA. There are people who actually do study junk DNA, and they call it, yes, junk. The less people know about the field, the more absolutely confident they are in their claims about it; and that includes scientists in unrelated fields, who rarely other to read the literature of the specialists. $\endgroup$ – iayork Jun 17 '16 at 17:17
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"Junk DNA" is more aptly named noncoding DNA. This is defined as any DNA region that does not encode for a gene or more precisely is not within an open reading frame. In the human genome over 98% consists of noncoding DNA. However the more we learn about molecular biology the more we understand the biological function and importance of noncoding DNA. Examples for important functions are:

  1. Regulatory regions that control the expression of a gene
  2. Regions coding for regulatory RNA
  3. Regions where epigenetic regulation takes place

However, there are also regions which likely do not have beneficial biological function, which may rightfully be called junk:

  1. Transposons are genetic regions that can copy themselves (either by an enzymatically active RNA or by encoding for the protein transposase). They are believed to have evolved as "selfish genes" and several known defense mechanisms against rogue transposons exist (siRNA, RNAi). Transposons and the defense mechanisms have now become powerful tools in molecular biology research.
  2. Endogenous retrovirus sequences which are remainders of retroviruses which have inserted themselves into the germ line and become inactive through mutation.

However, even these "junk" regions are believed to have important evolutionary functions such as protection from mutation through retroviruses: Because there are large DNA regions where the precise order and function is not important, a retrovirus that inserts itself at random positions of the genome is less likely to cause permanent damage.

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    $\begingroup$ "Junk DNA" is more aptly named noncoding DNA. I don't agree with this. Much non-coding DNA is functional, and there is no reason in principle that non-functional DNA couldn't produce at least a (non-functional) transcript - as ENCODE showed directly. Trying to make "non-coding" synonymous with "junk" confuses the issue. $\endgroup$ – iayork Jun 17 '16 at 14:06
  • $\begingroup$ @iayork Did you read beyond the first sentence? I am saying exactly what you are saying. The reason I open with this particular sentence is that most people do use junk DNA and noncoding DNA synonymous. In fact, if you search google or wikipedia for junk DNA, the first hits you find are all about noncoding DNA. $\endgroup$ – Thawn Jun 17 '16 at 15:21
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    $\begingroup$ Since you agree that junk DNA is not non-coding DNA, why confuse the issue by saying the junk DNA is "more aptly called" non-coding DNA? The two are very different in concept and practice. $\endgroup$ – iayork Jun 17 '16 at 17:20
  • $\begingroup$ @iayork Sorry pal, but your definition of junk DNA is just different from how most people understand the term. Therefore this discussion will lead nowhere. I am just going to say that I will stick to using junk DNA and noncoding DNA synonymously since that is what most people do (as you can see if you look at the top 10 hits for "junk DNA" from google). $\endgroup$ – Thawn Jun 18 '16 at 7:01
  • $\begingroup$ @Thawn I liked your description , you can refer to this paper as an example nature.com/nrg/journal/v6/n12/full/nrg1756.html $\endgroup$ – Learner Jun 18 '16 at 8:59
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Briefly, we know of many mechanisms by which genomes can get larger. Tetrapods had at least two complete genome doublings in their history; transposons expand; retroviruses insert; partial duplications lead to pseudogenes. And these expansion mechanisms can be fast -- full genome duplications double size in a single generation.

But we know of very few mechanisms by which genomes can get smaller, and most of those are very slow, and very few are targeted.

From an mechanistic viewpoint, it's very difficult to imagine a targeted way to remove useless but harmless DNA quickly, and with 100% accuracy. If accuracy is not 100%, then the pathway would be more harmful than the DNA it seeks to remove.

The key is that if extra DNA is either harmless, or nearly harmless, there's no reason to eliminate it, and there are reasons (errors in removal) to not try to remove it.

So the short and simple answer is that genomes can accumulate useless DNA much more readily than they can get rid of it. It's just common sense, which matches 30 years of experimentation.

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    $\begingroup$ This is a good explanation why evolution tends to favour "bloated" over "streamlined" genomes. However, this is only true for higher, multicellular organsims, where fast replication is not key to survival (in multicellular organisms, most of the cells are not replicating throughout large portions of the organism's life). For single celled organisms this is definitely not true and they quickly loose genes unless there is selective pressure to keep them. $\endgroup$ – Thawn Jun 17 '16 at 16:46
  • $\begingroup$ @Thrawn Agreed that the genomic dynamics change in different groups. The theoretical arguments are the same, but the "cost" even of non-functional DNA becomes higher. A trivial cost for multicellular organisms, that's not sufficient to select for genome shrinkage, may be a significant evolutionary cost for others. $\endgroup$ – iayork Jun 17 '16 at 17:14
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    $\begingroup$ You know, for someone who so vociferously and adamantly claims to know what the "true scientists of junk DNA" are doing and saying, there is a rather obvious lack of citations in your answer. $\endgroup$ – MattDMo Jun 17 '16 at 22:07
  • $\begingroup$ @MattDMo which part don't you understand? Most of this is pretty basic stuff. As I say, it's just common sense. $\endgroup$ – iayork Jun 18 '16 at 23:22

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