What do we know about Junk DNA?

[baftan]

Let's start with a definition from Wikipedia under the title of "Noncoding DNA":

In genetics, noncoding DNA describes components of an organism's DNA sequences that do not encode for protein sequences. In many eukaryotes, a large percentage of an organism's total genome size is noncoding DNA, although the amount of noncoding DNA, and the proportion of coding versus noncoding DNA varies greatly between species.
Much of this DNA has no known biological function and is sometimes referred to as "junk DNA". However, many types of noncoding DNA sequences do have known biological functions, including the transcriptional and translational regulation of protein-coding sequences. Other noncoding sequences have likely but as-yet undetermined function, an inference from high levels of homology and conservation seen in sequences that do not encode proteins but appear to be under heavy selective pressure.

Everybody who has some ideas on this subject are welcomed. I can see from the definition that we don't have too much information, but if you have some new, explanatory or unheard knowledge to improve the issue please make your contribution.

My drive behind submitting this thread is mainly the thread called "Command Language of Thinking". Basically, I suspect from a sort of natural software -which itself has been evolving parallel to protein/neuron making DNA- going on behind neural activity. One of the expected question will be "where does this so-called software information registered?" This "noncoding DNA" somewhat looks like a good candidate. If this is the case, junk DNA must have a pattern (that will require a new type of code breaking efforts) of itself in order to execute protein making DNA as well as registering the necessary information for this execution.

I would like to know if there is any scientific knowledge for/against this possibility.

 

[madanthonywayne]

There is a somewhat new field known as epigenetics that deals, I think, with what you're talking about.

 

[baftan]

There is a somewhat new field known as epigenetics that deals, I think, with what you're talking about.

Not exactly, as far as I understood from the entry you referred, Epigenetics is about the ability of genes to reflect various environmental changes; and these changes rarely leaves hereditary marks to offspring (unless the changes are substantiated by critical mutations). Once I had watched a documentary about Epigenetics; it was about how stress level of one generation is passed to grandchildren, and they were suspecting partly from Junk DNA, that's right. However, at this level it is impossible to say that noncoding (junk) DNA is equal to Epigenetics:

The molecular basis of epigenetics is complex. It involves modifications of the activation of certain genes, but not the basic structure of DNA.

-Wikipedia-

Moreover, Epigenetics is nothing to do with patterns: What I find critical is that if there is any pattern behind ( or "within") Junk DNA. Because if there is, Junk DNA is not "junk" after all, but has important role even if there is not a protein equivalent. If we follow Wikipedia definition:

epigenetics is the study of inherited changes in phenotype (appearance) or gene expression caused by mechanisms other than changes in the underlying DNA sequence

If this "mechanism" has a correspondent junk DNA pattern, yes, in this case this is part of what I am looking for; because it will have other implications such as certain part(s) of noncoding DNA might be having influence over other mechanisms of the body (or maybe even of mind) system.

 

[pgsleep]

I always just figured that "junk DNA" was dormant genetic potential.. their application contingent on environmental changes..

 

[baftan]

I always just figured that "junk DNA" was dormant genetic potential.. their application contingent on environmental changes..

And I thought about it as some type of "left over" after useful DNA codes make their jobs. But our ideas are necessarily layman's predictions...

 

[madanthonywayne]

I spoke with a PhD in genetics the other day, and he said there really was no "junk" DNA. It's there for a reason, most likely something to do with gene expression. For instance, it might simply affect the way the DNA folds.

 

[baftan]

I spoke with a PhD in genetics the other day, and he said there really was no "junk" DNA. It's there for a reason, most likely something to do with gene expression. For instance, it might simply affect the way the DNA folds.

That's exactly what I suspect too, must be "a reason" or "a function", and imagine I don't even have a degree in biology. I found some papers on internet through Google search, and they basically say that parts of junk DNA is reflecting the useful DNA. This reminded me back-up/restore copies of a computer. A part of me expects to hear more substantial functional roles, that's why I am interested in patterns.

 

[Walter L. Wagner]

"junk" DNA is of many origins.

For example, the DNA that is required for tooth production is present in birds. However, it is not normally expressed, because other DNA has developed that prevents the hormone production for activation of tooth expression. If that hormone is artificially introduced to a bird, their beaks will grow teeth. However, since this DNA is not normally used, and is not expressed, it could be considered 'junk' DNA for birds.

The same types of situations exist for all species. As they evolve, different sections of DNA that might have evolved over eons becomes inactivated at a later time. Still later, it might be re-activated, or activated with mutation for other purposes. This is a huge area of interest in genetics for which a single term of 'junk' DNA is likely grossly inadequate to describ numerous stretches of DNA that are present for myriad reasons.

 

[Darwinian]

Amounts of non-coding DNA vary considerably.
Is there a tendancy for DNA to increase during the existance of a species?
Are there any mechanisms that tend to reduce it?
Does the amount of non-coding DNA relate to the age of the species or clade?
If it is not used then it forms a biological load on the cell and organism.
Do lifeforms with an easy niche (ie grass) have more than those with a tight niche (ie higher predators)?