"junk DNA" a useful term or not?

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"Junk DNA" is currently an active (albeit probably off-topic) discussion being held elsewhere. I tracked down the existance of this topic, to guide that discussion to, but discovered that this topic had gone bad (althought there is some good stuff on page 1).
So, I'm going to bump it, but also close it.

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A "new and improved" "Junk DNA" topic would probably be a good thing.

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Adminnemooseus

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Added by edit: There is also the "Junk DNA introns are actually fractals used as "building construction blueprints"?" topic, which is currently at only two messages. That may or may not be a good place for further "Junk" discussion.

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Added the quote box, and added link to mentioned topic - Adminnemooseus
Note - the above quoted is from the closed topic "Junk DNA", message 32 - Adminnemooseus------------------M:
For my part I find the term completely useless as there are many genes that have no known function (should they be called junk?), retroelements make up a huge part if not most of many genomes...why are they necessarily junk? Does it make sense at such an early stage of genomic science to call most of the genome junk without really knowing how the genome works?Let's see how long this thread stays on topic Moose [This message has been edited by Adminnemooseus, 07-16-2003]

In another thread, a creationist has used the argument that since a lot of "junk DNA" may be functional it is "evidence" of design. I have also heard the exact opposite argument that "junk DNA" is associated with the fall of man and our genome is degrading.If you take the first argument, then clearly some species of frog are more developed and "designed" than humans as they have larger genomes.If you take the second line of arguement then clearly zebrafish are a higher and better "designed" species than humans as they have a very compact genome for vertebrates....so..is it fish or frog

I am not sure why one would expect transposons etc. to be removed as long as they are selectively neutral or only mildy deleterious. It is not clear why some organisms have extremely high retrotransposon or intron copy number and others (even closely related) organisms do not...but that may have more to do with the activity of the elements as opposed to selection against them by the host...for example, mouse endogenous retroviruses are much more active than human HERVs (for most classes). Thus, some groups are greatly expanded in mice that are not in humans...but this usually has to do with the presence of intact open reading frames in muliple family members of the ERV.The only cases where there seems to be fairly rigid selection against huge accumulation of pseudogenes, retroelements, etc. are in organisms like bacteria which have very streamline genomes relative to multicellular organisms.

Another term that is not particularly useful and often mis used by creationists is "living fossil"But to get back on topic, the problem with the term "junk DNA" is not so much that it is mis-used by creationists..it is mis-used by scientists as well i.e. a large part of the genomics community in dismissing a huge component of most genomes as irrelevant before it has been shown to be so.As to the creationists getting their stories straight...LOL!

Hi Asgara,
Actually, non-coding does not work as a definition for "junk DNA" either..for example, IAP (intracisternal type A particles) are a type of endogenous retrovirus group (in mice) some members of which can produce viral particles i.e. the envelope gene protein product is produced. That is the again the problem with junk DNA as a term as it lumps a lot of classes of genetic material together that should not be.The average American however gets terms fed to them like "living fossil" or "junk DNA"...and it comes from either the science community itself via science reporting or by scientists trying to become famous by inventing a term that they can always associate their names with...it is not always useful and in some cases very inapporopriate.The problem in America is that there are not so many lay articles or so much tv programming dealing with science relative to some places. I also get the impression that it really depends on where you live in the US as to how much science exposure you get as a student. I am always amazed now that I live in Germany how many channels and hours of programming are dedicated to current topics in science which are usually pretty competently prepared....I guess it is an issue of interest and priority.
Cheers,
M

Hi Asgara,
I am sure you were clear...I have been debating Symansu in the Free for All and I get the impression my IQ drops 50 points any time I read his posts ...so I probably just mis-read what you wrote."junk DNA" is not only a problem for lay people..it is particularly bad for scientists as well and in that regard I find it one of the most objectionable terms to come out in a long time.I also went to school in the north (in a university town) and science was strongly emphasized...as a lot of us including myself had parents who taught at the university, we were often able to take class trips to the labs...or had guest lectures from some of the professors. I would say we got a fairly deep appreciation for science as a result of our access to scientists as opposed to just reading textbooks....my guess is such an experience would be exceedingly rare in large parts of the bible belt...or any community that does not have money/universities/etc.cheers,
M

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While we can be pretty sure that repetitive elements (30-40% of the human genome) and pseudogenes are genuinely junk, the position on introns is less clear.

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This may be too general a statement. There are HERVs that have known fucntion such as some of the the env genes of the HERV-W and HERV-FRD class HERVs (syncytin genes). There are hints that other HERVs have cellular functions i.e. shaping the developing immune system, but since it has not been intensively researched it would be premature to lump all repetitive DNA together as junk. SINES may be mostly junk and most LINEs as well...pseudogenes are also most likely totally functionless like mtDNA pseudogenes (Numts...unless you count totally messing up mtDNA phylogenies as a function). I think it is too early to really say what is junk and what is not..though some research on large scale deletions in mice suggest that large portions of the genome have no impact on fitness i.e. junk.