Junk DNA

[Mercedes Benzene]

DNA is still incredibly mysterious despite the many advances made in the past half-century. Now we know that only 2% of DNA codes for proteins and results in gene expression. The other 98% is consequently termed "junk DNA". Scientists think that junk DNA is most likely very important, but its function is still unknown.

I just wanted to get some opinions as to what you think the purpose of Junk DNA is.

Or maybe it does not have one?

Ideas?

[Biochemist]

I just wanted to get some opinions as to what you think the purpose of Junk DNA is....Ideas?

Goodness, MB. This is a prety big topic.

 

I think that opinions fall into two camps:

 

1) Most of this really is junk

2) Most of this really is not junk

 

I think more people are in the second camp, but I don't want to discredit the first group (I hope someone there chimes in here).

 

There are biological services broadly available in higher species (certainly mammals) that do not appear to have anything to do with gene expression. The embryological development of mammals (for example) is fascinating in that physical location of cells in the embryo tends to lead to differentiation as the embryo matures. In mammals, the embryo matures into three embryonic plates (or germ layers) and cells begin the process to differentiate not only by layer (internal organs versus skin) but also by location (hand versus foot).

 

All cells have the same genes, and the same "junk". Many folks presume that the junk DNA has a significant role in cell differentiation. There is simplistic circumstantial evidence for this (higher animals with more differentiation have more junk) and there is the recognition that biological systems generally do not store useless trash. In fact biological systems are so efficient at eradicating trash (there are nearly no unused proteins in the cell, for instance) that existence of an item usually leads biochemists to presume it is used for something. In this frame of reference "junk" is logically very unlikely.

 

But, as Dennis Miller says, "just my opinion, I could be wrong".

[HydrogenBond]

The primary purpose of the so-called "junk DNA", is for packing the DNA. The DNA-packing protein composites defines a different hydrogen bonding potential than the actively transcribed DNA. In that respect, it plays a very important role in cell differeniation by creating fixed configurational potentials within the DNA.

 

The packed junk genes set up a potential within the nucleus for genes to repack. The cells interacts with the environment and creates a feedforward response that will unpack some of the DNA against this counter potential that want to pack the DNA. The centromere region is the most reliable packing anchor and will only unpack during the duplication of the DNA.

[hallenrm]

The primary purpose of the so-called "junk DNA", is for packing the DNA. The DNA-packing protein composites defines a different hydrogen bonding potential than the actively transcribed DNA. In that respect, it plays a very important role in cell differeniation by creating fixed configurational potentials within the DNA.

 

The packed junk genes set up a potential within the nucleus for genes to repack. The cells interacts with the environment and creates a feedforward response that will unpack some of the DNA against this counter potential that want to pack the DNA. The centromere region is the most reliable packing anchor and will only unpack during the duplication of the DNA.

 

Any evidence to that effect Hydrogenbond?:hihi: I have a vague feeling that this is a kind of explanation that is often offered just to push uncomfortable phenomena under the mat!

 

My hunch is that, junk DNA is that part of DNA that has not been probably explored much, may be due to the shortage of resources. Perhaps one day when biochemists and molecular biologists will have sufficient gumption to explore it (without any bias ofcourse) we will learn that junk DNA is responsible for many traits of a biological organism, which we even hesistate to call traits!:)

[HydrogenBond]

The junk DNA is not used so it is packed away. The packing involves histone proteins which neutralize the negative charges along the DNA's phosphate backbone. As such, open genes have exposed negative charge, while packed genes don't. There is a potential there.

 

The histone or DNA packing proteins are made only very late in cell cycles. These genes stayed packed alongside the junk, until the last minute, when the DNA is being duplicated. If they were placed higher up closer to the active genes, more of the DNA would remain packed with the junk.

 

The junk genes may also define innate human potential both regressive and progressive. For example, if we take a three carbon alcohol, there are two places to put the -OH group, to get propanol or iso-propyl. The number and types of atoms has not changed, but the order can make a lot of difference with respect to properties. The same is true of the DNA. The orderring of the genes playing a very important role alongside the specific genes in the DNA. The junk genes is part of that orderring variable.

[Eclogite]

I do wish you wouldn't make such absolute statements about such controversial areas, especially without providing citations to support your contentions. It turns me off, for one, from what may valuable conjectures. However, conjectures dressed as established theory are too easily branded pseudoscience, don't you think?

[hallenrm]

However, conjectures dressed as established theory are too easily branded pseudoscience, don't you think?

 

But conjectures are essential for the progress of science! Don't you agree?

 

What is established, and what would be, only time will tell!!!;) :) :)

[Eclogite]

But conjectures are essential for the progress of science! Don't you agree?

 

What is established, and what would be, only time will tell!!!:shade: :) :)

A conjecture is a conjecture. It is not established fact. It may be truth, it may be remote from the truth, but it is not established. It may become established, but at this stage it is not.

 

A lengthy process of data gathering, analysis, interpretation, formulation of hypotheses, scrutiny by peers, adaptation, further observation, etc, is required to convert conjecture to theory.

 

Conjectures are welcome, for, as you say, they are essential to the progress of science. But presenting a conjecture as a fact or an established theory is detrimental to the progress of science. It is pseudoscience. Such practices should be eschewed.

[hallenrm]

But presenting a conjecture as a fact or an established theory is detrimental to the progress of science. It is pseudoscience. Such practices should be eschewed.

 

True, agree cent percent, a conjecture is a conjecture! One must be honest, that's the least requirement of good scientific temper!!!:shade: :)

[HydrogenBond]

I am using logic associated with basic chemisty. Why waste all those resources doing something one can do in their head. That is one of the problems with the life sciences. One is required to put aside common sense and waste resources so other don't have to use their brain either.

 

Logic and common sense should not play second fiddle to procedure. Under those conditions if one does not like a theory, merely prevent access to resources, and things don't have to change.

[HydrogenBond]

In another post, their is more to DNA, I attempted to better explain the basis of hydrogen potential. When DNA packs with packing proteins, not only is the negative charge of phosphate neutralized, which slightly increases the hydrogen bonding potential along the base pairs, and within the extra unbonded hydrogen bonding hydrogen within the base pairs, but the packing proteins are full of unbonded hydrogen bonded hydrogen. The result is that packed DNA has a higher electrophilic potential than unpacked DNA.

 

There may be axial conduction of this potential via the unbonded hydrogen bonded hydrogen along the DNA double helix. They appear able to share vertically or axially. But more importantly is the conduction of the electrophilic potential gradients, between packed and unpacked DNA, via the nucleus water.

[Eclogite]

I am using logic associated with basic chemisty. Why waste all those resources doing something one can do in their head. That is one of the problems with the life sciences. One is required to put aside common sense and waste resources so other don't have to use their brain either.

 

Logic and common sense should not play second fiddle to procedure. Under those conditions if one does not like a theory, merely prevent access to resources, and things don't have to change.

I have absolutely no idea what you are trying to say here. You make a series of statements that appear to me to be unconnected. I take it to be a response to my earlier observations, which you may have perceived as negative. Or perhaps it is something else. Either way, what are you talking about?

[HydrogenBond]

Sorry about the confusion I was in a rush when I wrote that and didn't take time to proof it.

 

I think what I was trying to say is that if one takes a new angle on established thinking, there is often no direct data yet in existence. If one uses indirect data, this will only work for a sympathetic audience. Such data is too easy to dismiss if one does not agree, even if it is reasonable. One never knows if logic or politics is talking. If one is placed in a catch-22situation of needing hard data before being given the resources to generate hard data, the resourceless alternative is to create a line of reasoning using basic principles of science. This is not hard data, but if others can see the line of reasoning it means the path is something more than imaginary.

 

Under the constraint of no resources I was like a miner prospecting for gold without access to all the hi-tech gadgetry. The gadgetry would make life a lot easier since hard data is easier for everyone to accept even of one can not explain the data (strange). All I had was an educated hunch, inspired by scientists from 40-50 years ago and the pick-axe and shovel of reason and established principles of chemistry. It is easy to discount the old miner. But what I learned is that it does not take a lot of equipment if one finds a rich vien of gold.

 

Hydrogen bonding is the basis for the living state. If one took the hydrogen bonding away all cellular structure would return to the sludge of life. Yet, so many are content to discount its importance.

[Kriminal99]

I think when a question like "What is junk dna for?" is asked, a rundown of its physical (or chemical whichever) interaction with its enviornment does not answer the question. At best you might claim that it makes it less likely that it has other purposes. But then you might ask yourself if there is any other way the same thing could be accomplished. If so why was this way chosen?

 

I heard that some parts junk dna of a given species matches its ancestor species to a given point. If so I would wonder if there isn't some form of genetic memory going on.

[HydrogenBond]

If we look at an enzyme, it has an active site where it does its catalytic stuff. One may say the rest of the enzyme is junk protein. But this is not the case at all. If one took nano scissors and cut out the active site it does not work the same without the rest of the junk protein. The rest provides a potential matrix for the active site. The DNA is the same, with the junk genes creating a matrix for the rest of the DNA that is active.

 

One good experiement that could prove this, is to take one of the chromosomes and cut out the junk genes. According to existing theory this should have no impact on functionality since all the active genes will be retained. Using hydrogen bonding theory I predict that the smaller DNA won't work the same since the structure of the DNA will be alterred.

[CraigD]

If we look at an enzyme, it has an active site where it does its catalytic stuff. One may say the rest of the enzyme is junk protein. But this is not the case at all. If one took nano scissors and cut out the active site it does not work the same without the rest of the junk protein. The rest provides a potential matrix for the active site.

Quite true. In general, if one changes the structure of a protein, one risks changing how it interacts with other substances, particularly other proteins.

The DNA is the same, with the junk genes creating a matrix for the rest of the DNA that is active.

I don’t think this analogy is correct.

 

If the correct expression of active (coding) segments depends critically on the presence of non-coding segments, how is it that coding segments transplanted into completely different genomes (eg: human insulin-producing genes in E.coli, as is used in the manufacture of Humulin pharmacutical insulin) continue to express the same proteins? ;)

[gribbon]

There are many hypothesis’, none conclusively established, for how junk DNA arose and why it persists in the genome. I find the one about how it orders the genes particularly interesting, though I can't say much about this field.

 

This material could be what remians of pseudogenes, (genes that have lost their protein-coding ability, and, presumably, their biological function). After these genes stop, they will usually acquire something called “genetic noise” in the form of random mutations. Other theroists point to how 8% of human junk DNA is formed by retrotransposons of Human Endogenous Retroviruses, though some would say that it is actually 25% or more, and seeing as two plants have been proven to have their genoime size drmaatically affected by the same phenomenon, this is some good theory.

 

It may provide a reservoir of material from which potentially advantageous genes could emerge, and there are nearly 500 ultraconserved elements, which are shared at extraordinarily high similarity among the available vertebrate genomes, in what was supposed to be junk DNA, and although this is still under research (not sure by who though) they probably play a regulatory role in vertebrate development from embryo to adult.

 

“Chromosonal crossovers” events can often lead to damage and mutations, but a high proportion of non-functional genetic material could make it less likely for this to happen, possibly making a species more resistant to this mechanism of genetic recombination, and furthermore, junk DNA may stand as intentially re-ordered or "unplugged" sequences.

 

It could just be that it allows enzyme shapes to form around functional elements more easily. This would give it some use, even if it didn’t code for anything. Yet another possibility (and for all we know), these could act as “master genes” (such as in the Fruit fly) which control the expression of all other genes. I think there are also a few scientists who think that it may, when put under unusual circumastances, provide a re-programming function. Even more so, you have to remember that approximately 5% of the human genome has been selected as the result of a constant stripping away of usueless genes, and so there may be more "junk" DNA in the human genome than there is known functional sequence.

 

I can remember I few studies on this topic such as a 2002 one from the University of Michigan showed that segments of junk DNA called LINE-1 elements, once thought to be "leftovers from the distant evolutionary past" now "deserve more respect" because they are capable of repairing broken strands of DNA, and a 2004 study from the Cell Press suggests that "more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity." The National Institutes of Health found that social behavior in rodents was altered by parts of the genetic code that were meant to be junk, and in 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs. These all seem quite palusible theories and findings to me….

 

I also remember hearing that researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which evolved from junk DNA. Ona completely different note, there was also a mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had a use.

 

There were also a great number of “findings” from Purdue University in 2005, and the McKusick-Nathans Institute of Genetic Medicine, along with those from Tel Aviv university, but I can remember them being so trashy that they’re really not worth repeating.

 

My little theory is that they could be the result of escaped “selfish genes” (probabaly Transposons) which copy themselves to different loci inside the genome. These elements constitute a large fraction of eukaryotic genome sizes, and I remember that about 45% of the human genome is composed of transposons and their defunct remnants. Supernumerary B chromosomes are nonessential chromosomes that are transmitted in higher-than-expected frequencies, which leads to their accumulation in progenies, which could lead to a constant accumulation.

 

Although we are all still asuming that the Junk DNA *must* have some function, there are some reasons I cantell you about why the DNA might not get stripped away with time: The energy required to replicate even large amounts of useless DNA is pretty small, so it isn’t strictly speaking necessary, and beyond this, Retrotransposon insertions of junk sequences can occur faster than evolution can eliminate them.

 

Trouble is though, is that an experiment to prove any of this would have to run over millions of years. :)