Thread: "Junk" DNA has a purpose

I've head mention that there is a lot of DNA that is Junk. Is this True and if so might it be that it is there as a buffer for random mutation. So that as mutations occur, if they happen in the "junk" DNA there wont be effects to the organism. If every bit of DNA did something then the rate of mutation would be higher. So it slows the rate of mutation. See what I mean. So what are your thoughts?

I think what they(how ever it was that siad this) meant was that every single eveloutionary variant that we took before we became the humans of today we still have that information in our DNA like if we used to have bony plates we still have the DNA that ssays hot to grow bony plates and the such that has bony plates the thing is it is dorment and if you make it active it is the equivelent of mutating yourself. i.e. you would start growing bony plates.

I see. So it's meaningful junk.

Some of at least is meaningful. Some of it probably is junk.

As to your original suggestion I believe it is faulty. Mutations are not limited to so many per cell, or so many per chromosome. They will occur at a rate per unit length of DNA. So, just as an example, if 0.01% of an organisms DNA suffers a mutation then 0.01% of its functional DNA mutates whether or not their is junk DNA present.

Ok thanks.

Originally Posted by Wildstar

I've head mention that there is a lot of DNA that is Junk. Is this True and if so might it be that it is there as a buffer for random mutation. So that as mutations occur, if they happen in the "junk" DNA there wont be effects to the organism. If every bit of DNA did something then the rate of mutation would be higher. So it slows the rate of mutation. See what I mean. So what are your thoughts?

This has been a popular idea for some time now, since less than 3% of our DNA codes for proteins. However, recent work has at least 79-93% of the "non-coding" regions identified as contributing to cell function, which leaves a lot less to act as this buffer that had previously been believed. Function has also been identified for many pseudo genes and inrons. It is likely that over time even more of the DNA once described as junk will turn out also to have function. It seems reasonable now to think that very little of DNA code is junk. It had been seen as strong confirmation that evolution proceeds by random genetic error and selection because such a process would necessarily produce a great deal of junk, with this hypothesis in the process of being disconfirmed, and numerous other serious issues with the idea, it seems timely to search for processes that better fit available evidence.

The junk DNA hypothesis seems destined for the dust bin.

Originally Posted by Wildstar

If every bit of DNA did something then the rate of mutation would be higher.

No. The rate of mutation is given as change per base pair (per generation). More base pairs, means more changes. The rate doesn't change amongst the useful DNA just because there is additional DNA.

Your line of thinking is like saying it would be best to have extra work, some of which is completely unecessary, because then if one makes a mistake and it happens during a job that is not necessary, it is not so bad.

The idea that junk DNA serves as a buffer against mutation is not new and dates back to the early to mid 1970's - it was known as the "Bodyguard Hypothesis".
The thinking is that large amounts of non-functional DNA would protect functional DNA from environmental damage - primarily UV, ionising radiation and chemical attack.

If you imagine a 500 million bp chromosome that only had three genes on it, then the thinking goes that any stray cosmic ray or chemical nasty is far more likely to result in damage to an area that is not essential to the organism.; hence the "buffer".

Unfortunately there has never been any good evidence in support of this hypothesis, And doubly unfortunately there appears to be too much contradictory evidence. For example: bigger genomes are more susceptible to radiation damage; organisms living in high UV regimes often have small genomes and vice versa; organisms exposed to high internal levels of reactive oxygen species often have small genomes; a selection of organisms picked from a particular environment can have wildly differing genome sizes - even amongst those that are closely related. It seems that the bodyguard hypothesis is taken more seriously by the armchair biologist these days than it is by the professional. However, it hasn't been ruled out completely - there's just no evidence to support it right now.

Cypress indicates that about 80 to 95% of DNA is useful. Whatever happened to the theory that the non-coding areas were "scratchpad" areas that held former coding areas, now partially overwritten, mutated, etc? To me, the presence of scratchpad areas (ie, "working space"), seems to be an evolutionary mechanism. That is, DNA is not a sleek, trim listing of only essential data (like compiled computer code).

Amongst greater eukaryotes, very little of the genome codes for protein. Whats in the remainder of the genome, or the scrap/junk deoxyribonucleic acid in Homosapiens, is figured to be virtually ninety seven percent of the genome?

Here is an interesting perspective on the role of introns.
http://singh101.com/role-of-introns

Originally Posted by jrmonroe

Cypress indicates that about 80 to 95% of DNA is useful. Whatever happened to the theory that the non-coding areas were "scratchpad" areas that held former coding areas, now partially overwritten, mutated, etc? .

The suggestion that upwards of 90% of the genome was actively transcribed and therefore carrying out some useful function comes, in part, from results produced by the ENCODE project. However, the result was a bit contentious - even at the time. It now appears that they were detecting "junk RNA" - low levels of aberrant transcripts or "transcriptional noise" as some call it. A recent study (PLOS Biology is down for maintenance at the moment so I can't provide the relevant link) used a more refined technique (RNA-Seq instead of tiling microarrays) that is not prone to pick up such noise. They found that most of the genome is not transcribed in to RNA. You can read a summary of this recent work in NatureNews: Existence of RNA 'dark matter' in doubt.

Still one of the best ideas of what junk DNA does, is that most of it is actually just junk. But junk that may come with function, since there appears to be an interesting correlation between genome size (and hence, junk DNA) and cell size.

An organism is capable of switching on or off a section of DNA as need calls.
We have a lot of vestigal organs, but their DNA is still in our genes. They are switched off, but don't just dissappear. That segment of DNA would be appearantly useless.
I don't know how much junk DNA this accounts for, (Do early organisms have less junk DNA?) there may also be other reasons.

i haven't heard anyone mention the possibility that one of the possible functions of junk DNA could be a way of quarantining retrovirus insertions ?

Retroviruses have a range of places they like to insert. Some insert within genes, some near promoters and some just about anywhere. For example, HIV tends to integrate in areas that are rich in actively transcribed genes; while the MLV tends to integrate near transcription initiation sites. There appears to be a complex interaction between the virus and the host cell in selecting an integration site, which is not entirely random.

The "quarantine of retrovirus" (if I follow your point correctly) would appear to be a variation on the previously mentioned bodyguard hypothesis. If it was true, which seems unlikely, I would think that a retrovirus would enjoy being quarantined, since the genome is littered (8%) with their fossils. Busted retroviruses make up a significant proportion of the junk DNA itself.

saw a presentation once where this guy had looked at highly conserved sequences outside coding regions and knocked them out.

Highly conserved should indicate important function.

the knockouts didn't produce any phenotypes.


Word of caution. Don't assume that we know a lot about how the genome actually workds, because we really don't. Junk DNA is really a meaningless concept since we are still learning.