[yor_on (OP)]

What I'm thinking is that it must have, and so the definition of it as 'junk' can't be true. Also that all junk then must have some purpose, at some time.

But I may be wrong

[CliffordK]

Does the FBI's use of "Junk DNA" count?

[yor_on (OP)]

It's about if what we have in our genes all are needed or not, from a evolutionary point of view. Also about if there is a 'planning' involved somehow in what we have, as per the probability of the DNA we have being the best for taking care of us in a changing future? I'm betting on that mother nature indeed planned for that.

[schneebfloob]

This is a bit tricky. It depends on what you consider to be 'junk', and what you consider to be a purpose or role to play. There's loads of stuff in our genome that doesn't code for protein, but is still very important. Things like promoters, operators, enhancers and so forth. These things help regulate gene expression. Then in genes themselves you can have non-protein-coding regions called introns. Their functionality is not well understood, but it is thought that they may play some role in the regulation of gene expression.

Then you have the SINEs and LINEs (Short/Long Interspersed Nuclear Elements). They make up a frighteningly large proportion of our genome, and don't really do much. SINEs don't code for protein, yet the Alu repeat SINE is one of the most common features in our genome (and is found in many other primates). For a long time they were considered junk, but some research points towards some SINEs and LINEs doing things for us. The more we learn about things the less junky they become, I suppose.

[CliffordK]

Identification of people, of course, could have important evolutionary consequences in the future.

But...  as far as "Mother Nature".
I think there is some evidence that gene-to-gene spacing may benefit from longer gaps between certain heavily used genes. 

How are genes lost?

Is it possible that a gene would essentially get permanently deactivated.  But, otherwise largely remain intact in the genome.  Then eventually pick up numerous mutations as "junk DNA".  This might be part of the evolution and dynamic changes.

It may also be important to for re-purposing genes, and essentially creation of new genes de-novo.

Bacteria can gain DNA by picking up plasmids, and even sampling environmental DNA.  Higher organisms may require more stability by slowing down the picking up random environmental genes.  But, still need a method to get new genes de-novo.  Perhaps junk DNA is also part of that mechanism.

[yor_on (OP)]

interesting

Thnx schneebfloob and clifford.

My totally noob thought is that life seems a game of probability, ( and individually also a game of trust btw evolutionarily. And so you need a game theory that can plan for the unplanned, and that I believe to become more possible the more combinations existing. But it might be so that not all combinations are needed at a given moment and so becomes dormant. Is there any evidence for that?
==

Think I need to add something, as always Maybe a algorithm describing it (genes etc 'interacting' or dormant) should be one that is written in the shortest 'sentences' possible, whilst at the same presenting the greatest probability of outcomes. Is anyone looking at genes from that possibility?

A fractal containing other fractals sorts of...

[CliffordK]

It likely could be thought of as just "random".

Perhaps the hypervariable regions of DNA could be thought of the "normal" mutation rate.  But, in the case of one's genes, the mutations that are damaging to the organism are soon lost from the gene pool, while the mutations just build up in the the hypervariable regions.

[yor_on (OP)]

We have a direction it seems for living material? What will random mean if you find a behavior that produces life and intelligence? A truly random behavior shouldn't have any preferred traits, philosophically that is. But life has, and that should point to something? A principle, a algorithm, something has to be there.
==

There's a divider between statistics and deducting as I think. For statistics which is the best way I know to describe 'reality' you deduct over histories, the more the better (merrier:). But pure deducting is not limited to that, if it was intuition should make no sense, and a lot of good science seems based on some intuition, at its beginning.

[BioChemSFC]

The current thinking is that introns function as a part of alternative splicing. This means one gene codes for multiple proteins. There are more proteins expressed in a eukaryote than the number of genes. They must have a role but the actual sequence must not be as important since conservation of the sequences is lower than that of exons. They do play an important role but they may not code for any peptides. Think of them as buffer regions between exons that code for polypeptides. They may have signaling roles or may just be there to separate exons. Certain regions of introns are conserved meaning they must serve for some signaling or recognition of location in a gene. I believe there is little to no evolutionary pressure to remove excess DNA whereas overly aggressive removal of segments could be favored negatively since it may accidently remove coding regions and the results would be catastrophic to a dividing cell. Biochem 101.

[CliffordK]

The evolutionary advantage of getting rid of non-coding regions is that there would be less DNA required to be produced for every cell division, and thus less energy required for every cell division.

But, a mechanism to recognize a non-coding region, and splice it out (or splice something else in) would be extremely complex.

[BioChemSFC]

The evolutionary advantage of getting rid of non-coding regions is that there would be less DNA required to be produced for every cell division, and thus less energy required for every cell division.

But, a mechanism to recognize a non-coding region, and splice it out (or splice something else in) would be extremely complex.

Funny that there are quad and terta ploid animals and plants (like wheat) that are extremely prevalent. Thats not just a little extra DNA but a whole extra copy of their genome. So extra DNA obviously doesn't disadvantage the organism that much because of the prevalence of polyploid organisms in evolution.  And a mechanism for splicing and alternative splicing may be complex but it is proven fact that it happens. So Clifford your theories are interesting but the facts are on the table: non-coding DNA exists in huge amounts and alternative splicing is what accounts for there being more protein sequences than genes. These are undisputed facts of genetics. So Clifford I'm wondering who you are trying to convince? The existing DNA sequences show the best adaptations after millions of years of evolution. And they DO have extra DNA and perform complex alternative splicing. If the things you say would be an advantage why does nature do differently? Because there was an advantage to these things. Yes there are many examples of more conserved genomes but let's talk about primates for example. Part of the reason that it was an advantage is that these things allow for faster adaptation to pressures during evolution. How can you say we made it through millions of years of evolution but it wasn't the best way? Obviously it was very successful. So it may sound complex and inefficient but thats not the case. It is that complex and also works quite well.

[schneebfloob]

Yikes, settle down! He was just making a (valid) point.

Not all organisms achieve the same objective the same way. Some organisms may well be polyploid, whilst others aren't. There are evidently advantages and downsides to both. Bacteria tend not to have many introns, if any at all. This is quite possibly for the reason that CliffordK pointed out -- there's simply no need to process more genetic information than is strictly necessary. If there's an advantage to be gained that outweighs the downside of wasting energy and time replicating extra material then that's going to take priority.

[yor_on (OP)]

So that might mean two alternative approaches? Where the more complex solution is the one where we find duplicates??  How do nature use those more 'filled up' DNA? Intuitively it sounds like a 'hive mind' relative a 'individual' solution to me, remembering the way some discussing some type of 'intelligence' for bacterias, that is if I now remember right? And this BioC "So extra DNA obviously doesn't disadvantage the organism that much because of the prevalence of polyploid organisms in evolution."..

Would you mind explaining a little further on your thoughts there?
==

And maybe, one more thing? Can we see where those duplicates first comes into existing evolutionary (as well as environmentally)? And is there a importance of them coming into being at a certain point if so, what changes? And yes, this is me assuming a progression from 'simple to the complex', which might be a too simple idea? Is there any evidence for those approaches developing in parallel?

[evan_au]

From http://en.wikipedia.org/wiki/Genome_size#Variation_in_genome_size_and_gene_content

Genome size correlates with a range of features at the cell and organism levels, including cell size, cell division rate, and, depending on the taxon, body size, metabolic rate, developmental rate...

Speculation: A larger organism is less likely to become prey, so there is some advantage in getting bigger (provided there is ample food, etc). It is potentially lethal to modify the vital building blocks of a cell (the genes, control regions & other conserved regions), but there is less damage caused by increasing the non-vital regions.

On the other hand, if resources are scarce, animals tend to shrink (eg island dwarfism). It is less damaging to lose non-vital sections of the genome.

So perhaps the wildly varying ratio of "junk" DNA between species modulates some byproduct like organism size, food consumption or life cycle? (Also see http://en.wikipedia.org/wiki/C-value#Variation_among_species)

[BioChemSFC]

Yikes, settle down! He was just making a (valid) point.

Not all organisms achieve the same objective the same way. Some organisms may well be polyploid, whilst others aren't. There are evidently advantages and downsides to both. Bacteria tend not to have many introns, if any at all. This is quite possibly for the reason that CliffordK pointed out -- there's simply no need to process more genetic information than is strictly necessary. If there's an advantage to be gained that outweighs the downside of wasting energy and time replicating extra material then that's going to take priority.

Okay to add to my posts:
I am not trying to say there is only one answer. I am not trying to sound emotional or evoke emotions. I just like discussion. Yes there are just as many counterpoints as I have thoughts. Not trying to make anyone anrgry. I like to hear what others think. Clifford is right that less DNA can have advantages. In fact organisms with the need for compact DNA like viruses have very little "extra" DNA so this factor is crucial.  The qustion was does junk DNA have a purpose. For many higher organisms the answer is a resounding yes. I just wanted to give an example of where it is useful because I find it interesting. There is also an astounding amount of silent viral DNA that has been inserted into our genome. This probably serves no purpose. I am sure there are examples that span the whole spectrum. I am not right, nor am I wrong. I love the fact that the answer is not simple. That's why I am a biologist. 

[yor_on (OP)]

 'Silent viral DNA', would that be a byproduct of viruses? And would that be why you expect it to be of little concern BioC? So, why do viruses exist? And are they only harmful, or can we get benefits from them too?

[schneebfloob]

Some viruses, particularly retroviruses like HIV, incorporate their genetic code into the genome of the host cell. This means that every time the cell divides the viral genome is also being replicated. When external conditions are favourable for the virus to re-emerge it will produce all the proteins needed for new viral particles and kill the host.
To do this they need an enzyme called reverse transcriptase. The DNA in your cells is being transcribed into mRNA, which is then in turn translated to produce proteins. As its name implies, reverse transcriptase does the opposite, so RNA is converted into DNA which can then be incorporated into the genome of the host.

There are strange 'things' (I can't think of another word to describe them) called retrotransposons, of which the LINEs and SINEs I mentioned earlier are a type, and they are basically DNA that moves. Some of these are very similar to retroviruses (some even being referred to as endogenous retroviruses), in that they use reverse transcriptase to copy themselves and re-incorporate elsewhere. They aren't especially harmful, they don't produce viruses or anything, but they can cause damage if they re-incorporate into any crucial genes. They do make up a staggering amount of our genome as well: I'm not sure of the exact figure, but we're talking double digit % of our genome rather than single digit. It is possible that retrotransposons may have played a role in fuelling evolution, as they help generate genetic variation.

Viruses by their very nature are obligate parasites. They lack any way of replicating without a host. In that sense, they are only harmful. However, they can be used to our advantage too. Bacteriophage viruses infect bacteria with extreme specificity. In the Soviet Union they were utilised in place of antibiotics, and with the number of antibiotic resistant infections about they are being looked at again.

[yor_on (OP)]

retrotransposons? very interesting schneebfloob, if I get you right here they can create mutations, or is that too simplified? If that is possible, can they be a way of nature to introduce new combinations genetically?