"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]

'Junk' DNA is mis-leading to say the least.I read a New Scientist article a few months back concerning
research that had found that a segment of 'junk' DNA was
actually used as a kind of place-holder for intermediate
products along the synthesis route.Just because we do not know what it's for doesn't make it
'junk'.

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 read that too.Not sure how that follows, since someone else (Mr Hambre I think)
suggested that one would expect an evolutionary process to elliminate
'junk' over time.Not sure I agree with either.The term IS mis-leading though.If we have a segment that exists between encoding regions that looks
like a part of a similar gene in another genome, but there's a
'stop' extra ... I'd call that residual rather than junk.If we have a segment that is just there and we don't know what
it's for we should be able to say so ... there's nothing wrong
with not knowing (try telling THAT to an 8 year-old!!)

In the spirit of the forum guidelines, and so as not to
avoid a direct question I'd go for fish.

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.

"Junk DNA", like "gill slits", seems to now have more of an "historical" ring to them than anything else. Sure, creationists use them as ammunition (we know how they love their dictionaries), and they are misleading, but I don't think they are going anywhere.So, I think that if the terms are used, we should be sure to use them in the proper context - i.e. with others who will know what you are talking about.Interesting about transposons and such - some creationists argue that functional pseudogenes is evidence against evolution, while others argue that they are bad news for the concept of post-Fall degenration.They should probably get their stories straight.

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 All,Coming from a background such as mine (science education only to high school, but definately more of a scientific worldview, coupled with a decidedly agnostic frame of mind), I understood the general concept of "junk DNA" to be "non-coding". Most of my aquaintances have hardly ever heard the term, but of those that had, most understood it to mean "useless".It seems to me that they are the "average" Americans. Neither well educated nor poorly educated. This is the audience that needs to have the term better defined. Bio-science scholars already have a better understanding of how the term is meant. Rabid creationists will always mis-use it as a point of attack, no matter what their educational level.The "average" American is the backbone that needs better lay-articles and a better high school science education. They are the ones that need to be targeted to keep creation out of our science curriculum.------------------
Asgara"An unexamined life is not worth living" Socrates via Plato

Well said...

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 Mammuthus,Thanks for replying. I understand "now" that non-coding is a misnomer also. I was referring to my understanding of the term prior to actually searching out information. I was trying to point out the differences in understanding between myself and friends of similar background. Sorry if I didn't make myself clear.I definately agree with you about the amount, and level of science programming and lay articles relative to area. I went to school in the northern mid-west and live here currently, but I did spend several years down south. While not wanting to disparage another region, I am glad that I and my children had a northern education. I believe that areas traditionally referred to as "the Bible belt" have a lower priority on the sciences in general.------------------
Asgara"An unexamined life is not worth living" Socrates via Plato

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

With bacteria is that likely becuase they have
more compact genomes to start with, so any disruption
has a higher probability of being unviable?

An attempt to repsond to Faiths questions in Message 96 On junk DNA: It's the same basic stuff as normal DNA (chains of adenine, thymine, cytosine and guanine, the four bases). IIRC pure DNA's a sort of white slime, although you need a lot to be visible. If it is really junk, than that's right, although a lot of sequences get labled as junk just because we don't know what they do do. Pseudogenes are the remains of genes that once did something useful, but don't any more. If a gene is no longer needed (because it codes for an emzyne that is no longer needed, for instance, or simply got duplicated and is a spare) it may mutate into somthing that looks like a gene, but is gibberish. Definatly junk... Introns act a bit like the spaces in a sentence: The really useful information is in the Exons (words), but if you shoved them all together in wouldn't be very readable. They may also have some functions in replicating/checking the rest of the code, but that's a bit deep for me... I hope you mean for Introns... Try this... I think most evo's would agree that for a lot of it, the function is just unknown. I think the Human Genome Project succesfully identified the code sequences for every protien in the body. It was the other 99% that was a problem.I await one of our resident biologists to tell me this is all completely wrong...