More to junk DNA?

[Esoteric]

7 May 2004
In a world first, scientists from The University of Queensland's Institute for Molecular Bioscience (IMB) have uncovered a new class of genetic elements with the potential to radically alter our notions of how the genome "comes to life" to form humans.

http://www.imb.uq.edu.au/index.html?page=18382

 

[Buckaroo Banzai]

Other two links in the subject. A bit more detailed, but also there's a lot of redundance in reading all of them.

http://www.hhmi.org/news/haussler.html

http://www.eurekalert.org/pub_releases/2004-05/uoc--sr050404.php

 

[eddymrsci]

Yeah good topic, I am actually reading an article in SCIENTIFIC AMERICAN about the junk DNA.

 

[Eflex tha Vybe Scientist]

Junk DNA is a misnomer.

In ten years, we will have a greater understanding of the code and we will no longer refer to any parts of DNA as "junk"

 

[kriminal99]

..............................................

 

[Buckaroo Banzai]

I don't understant much about, but I guess that junk DNA is really junk, at least at the level of the individual, despite a possible evolutionary importance.
I think that the genome is more or less like a program with excessive, meaningless, dumb "loops", but at the same time necessary because if you simply break the "loop", you break the whole "program".

let's supose a program "phenotype" is showing "12345" in the computer screen.
The most obvous, functional, program in Basic to that would be:

1 print "12345"
2 end
or, let's supose that can exist only one number per each "print" command, it would be

1 print "1";
2 print "2";
3 print "3";
4 print "4";
5 print "5";
6 end

But evolution, instead of knowing what is the better code for the phenotype, selects a somewhat random code, as since it have the proper phenotype for the environment, making to a phenotype "12345", a program like:

12 goto 15 (1)
13 goto 700
15 goto 360 (2)
21 goto 39
25 goto 58 (4)
58 goto 460 (5)
39 end (15)
65 cls
80 print "1"
97 print "54";
360 goto 25 (3)
460 print "1"; (6)
461 goto 945 (7)
700 print "5"; (13)
727 goto 39 (14)
811 print "2"; (8)
813 print "3"; (9)
906 goto 1034 (10)
912 cls
945 goto 811 (8)
950 goto 970
970 goto 950
1034 print "4"; (11)
1035 goto 700 (12)

The program gets so messy because it's generated and selected in a way like shown in this page (the weasel), but rather than simply characters changing randomly in a phrase or word, there would be characters or functional commands changing randomly and then being selected by it's phenotype.

So, the numbers between paranthesis at the end of the some lines are not part of the code, I put them there only to show easily what is the functional part of the program, altough the most part of that is dumbly unuseful. The green lines are the only true genetic sequences, all the other lines are non-coding sequences, althought they're necessary due to it's position and the actual mess to the coding of the really coding lines...

At least, that's how I guess that it's like... but I'm not sure, if there's someone's who understands about this, and disagrees with the analogy, I'd like to know what's wrong..... remembering that of course it's a weak analogy, because genes are not like "commands", and etc...

 

[BigBlueHead]

When they refer to coding regions, I believe they leave out things like activation sites, telomeres, and other recognized genetic constructs. So, these sections are referred to as "Junk DNA", even though we know what they do.

WCF claimed not long ago that part of the "junk DNA" was probably ribosomal RNA (I think... can't find the link).

In any case, the term "junk DNA" is misleading, because it refers to
1) regions that don't code directly for proteins, but we still know what they do
2) regions that code for proteins but are not on in most people (6th finger code &c)
3) regions whose content and possible use is unknown.

Don't call it junk DNA, call it non-coding (1), inactive (2), or unmapped (3) DNA.

 

[kriminal99]

some of it could be genetic memory of things the unconsious mind has seen to be true 100% of the time.

 

[BigBlueHead]

Maybe... if you rewrote your DNA every time you experienced something. But probably not.

 

[wrmgrl]

This whole "junk DNA" thing has gotten a little old. Why do people assume that just because scientists don't know exactly what something does right at this minute it must be junk. What about epigenetics, what about imprinting, what about non-coding RNAs and the RNAi pathway? Just accept the fact that there probably are some regions that are not critical in and of themselves, but there place in the whole of the genome has been conserved for a reason. I know there was a long thread about this before so I won't go into it again.

 

[paulsamuel]

This whole "junk DNA" thing has gotten a little old. Why do people assume that just because scientists don't know exactly what something does right at this minute it must be junk.

You are absolutely correct, however either extreme is wrong. Obviously there are non-coding portions of the genome both important and necessary, but it doesn't follow then that the other extreme is correct, i.e.

In ten years, we will have a greater understanding of the code and we will no longer refer to any parts of DNA as "junk."

 

[Eflex tha Vybe Scientist]

You are absolutely correct, however either extreme is wrong. Obviously there are non-coding portions of the genome both important and necessary, but it doesn't follow then that the other extreme is correct, i.e.

I guess we will have to wait and see.

But I remember not too long ago that most "expert" geneticists we saying that 90% of the genome is "junk"


In fact, our view of DNA has changed dramatically since the 1950's.

now we have revelations that over the last 50 years, many discoveries, both small and large have challenged the original Central Dogma and the fixed, deterministic view of DNA. They reveal that the Central Dogma it is an over-simplistic model. Gene expression is subject to a regulatory network of a complexity that it only just being realised.

ex:
Genes that do not code for proteins but for ncRNA can be located in non-coding stretches of DNA. Such stretches of non-coding DNA have previously been dismissed in genome sequencing programmes as "junk DNA"

However, it is becoming clear that this so-called “junk DNA” is not junk but probably a vital part of the gene regulatory network. Many questions regarding these ncRNAs remain and will be the subject of ongoing research into the controls of gene expression: “How many RNA genes are there? How important are they? What function does a cell delegate to RNA instead of to protein, and why?"

And until we can answer these and many more questions, I think its safe to say that we cannot discount any part of the genome as "junk"

 

[paulsamuel]

And until we can answer these and many more questions, I think its safe to say that we cannot discount any part of the genome as "junk"

What about pseudogenes? Pseudogenes were once coding genes, obviously used to make necessary protein products, but are now not coding for anything and just sitting there. They may have been co-opted for some function since, but there is some period of time between the start of non-coding and the beginning of some potential non-coding function in the genome, where this pseudogene is junk.

Also, wasn't there a paper where they showed that the genome is pared down sometimes during phylogenetic history. If that's the case, then the parts of the genome that were paired down were not necessary.

 

[Eflex tha Vybe Scientist]

ps,

I really dont like the term "pseudogenes".
I think thats is alot like the term "planetary nebulae" (sounds cool, but doesn't reflect the real science underlying the objects importance)

I think that its impossible to rule out protein expression based solely on sequence information, since DNA coding can be altered by editing the transcribed RNA, or by skipping over parts of the master sequence, or by spontaneous mutation. Moreover, the inability to code for a protein useful to an organism hardly exhausts other possible functions "pseudogenes" may have.

with our present knowledge, we just cannot say with 100% certainty.
Some of the recently predicted pseudogenes such as tRNA-like pseudogenes may still be functional and without experimental characterization, we are just making educated guesses.

 

[My Sexy Blue Feet]

As we are still only in the very early stages of research of genetics, there are theories that are going to have to be learnt then unlearnt. Most of what we know is guesswork. We're learning a language totally new to us by poking the letters to see what they will do. Junk DNA is essencial, cause if we take it out, nothing works. BUT it doesn't explain what doesn't work. There's a plant with 4000 times more dna than humans, yet because of the junk dna, alot of it is unknown. What makes this plant so special?

 

[Buckaroo Banzai]

I had not read yet the "evolving inventions" article in SCIAM, by John R. Koza, but I've read another article with reference to it. It compared human designed inventions with inventions evolved by natural selection algorithms. Basically, the evolutive process produces excessive complexity, so there will be "vestigial organs", in the words that were said in the text I've read. But I think that it's best refers to the non-coding sequences. Althought these parts are necessary, they're at the same time junk, in the sense that if it was intelligently designed, would not need these parts. That's more or less what I tried to say with my analogy. I only can figure a code with any junk in it, if it were intellingently designed, not evolved. And even if it were designed, as things grow some junk is made. If that were not true, there wouldn't be that lot of people complaining about Microsoft all the time.

A exemple (in fact, a question) more on the genetics subjetct. A recently duplicated gene would not be junk, at least for some time? Unless it automatically gains a function in the moment it's duplicated....

 

[paulsamuel]

cause if we take it out, nothing works.

that's not true. there are many instances of insertions/deletions in non-coding parts of the DNA and there are no fitness effects. For your statement to be true, one would need to take out all 'junk DNA,' and of course, we are likely to be wrong about some portion of it. Also there are instances of the 'paring down' of the genome during phylogenetic history, and obviously the organisms were able to continue.

 

[ElectricFetus]

Junk DNA has been long know not to be junk. Though it does not code for protein producing genes it does code for RNA-only genes, inhibitor/activator sites that are needed to control the rate gene is expressed and at the very least structural purposes like telomeres, centromeres and DNA sections simple to align the chromosomes up in meiosis and crossing over.

 

[Hercules Rockefeller]

Also there are instances of the 'paring down' of the genome during phylogenetic history, and obviously the organisms were able to continue.

I would like to read more about this. Do you have a journal reference? Are you referring to the Fugu genome, per chance?

 

[paulsamuel]

Junk DNA has been long know not to be junk. Though it does not code for protein producing genes it does code for RNA-only genes, inhibitor/activator sites that are needed to control the rate gene is expressed and at the very least structural purposes like telomeres, centromeres and DNA sections simple to align the chromosomes up in meiosis and crossing over.

some of it, not all of it