'Junk' DNA proves functional

In a paper published in Genome Research on Nov. 4, scientists at the Genome Institute of Singapore (GIS) report that what was previously believed to be "junk" DNA is one of the important ingredients distinguishing humans from other species.

More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution.

Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.

The GIS study also highlighted the functional importance of portions of the genome that are rich in repetitive sequences.

"Because a lot of the biomedical research use model organisms such as mice and primates, it is important to have a detailed understanding of the differences between these model organisms and humans in order to explain our findings," said Guillaume Bourque, Ph.D., GIS Senior Group Leader and lead author of the Genome Research paper.

"Our research findings imply that these surveys must also include repeats, as they are likely to be the source of important differences between model organisms and humans," added Dr. Bourque. "The better our understanding of the particularities of the human genome, the better our understanding will be of diseases and their treatments."

"The findings by Dr. Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade," said Raymond White, Ph.D., Rudi Schmid Distinguished Professor at the Department of Neurology at the University of California, San Francisco, and chair of the GIS Scientific Advisory Board.

"We have suspected for some time that one of the major ways species differ from one another – for instance, why rats differ from monkeys – is in the regulation of the expression of their genes: where are the genes expressed in the body, when during development, and how much do they respond to environmental stimuli," he added.

"What the researchers have demonstrated is that DNA segments carrying binding sites for regulatory proteins can, at times, be explosively distributed to new sites around the genome, possibly altering the activities of genes near where they locate. The means of distribution seem to be a class of genetic components called 'transposable elements' that are able to jump from one site to another at certain times in the history of the organism. The families of these transposable elements vary from species to species, as do the distributed DNA segments which bind the regulatory proteins."

Dr. White also added, "This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins."

Source: Agency for Science, Technology and Research (A*STAR), Singapore

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Nov 04, 2008
Quantum_Conundrum, I begin to despair. I am not sure you can be saved. Everybody knows that the devil has a great deal of influence here on Earth and that it was the devils work that changed the sacred texts NOT written by God himself.

We no longer accept "the devil made you do it" as a valid form of defense so you need to break free from the devil on your own.

The bible is just a book to scripture teaches that it is devils work to worship idols and the bible should not be worshiped as if it IS the word of GOD because it is Just a thing, an object.

Nov 04, 2008
Of course JUNK DNA is not all JUNK. DNA is just DNA. Yes the sequences to maketh the man. BUT, there is a lot of room for variation and that variation is not always evident. Some variations may appear to nothing at all for generations but that does not mean they will continue to do nothing at all.

All mammals may share 90% of their DNA and considering the variations present in all the mammals then that 10% difference does a lot.

Yes most creatures have evolved over time with merged interface of viruses. Some of our parasites are so good that they become part of us for ever. That does not mean that they do nothing for us along the way. Some of these viral modifications may well make us better at something that has survival potential and is therefore not JUNK.

Quite likely viral inserted strands of DNA at the least may well contribute to our disease fighting defenses and that is a lot more than nothing. Plus they could help stabilize parts of our DNA in the area where they have been inserted thus improving birth rate or reducing the amount of infertility this too is not nothing.

So you can see that an effect may be quite subtle but that does not mean it is not there.

Nov 04, 2008
Ha, I think that quantum_conundrum is silly trying to get his religious ideas accepted as fact on a SCIENCE website.

In response to Traveller, music and the arts actually have a huge evolutionary significance becasue they are important socially in human culture. Social interaction & language is one of the key components in the evolution of human intelligence.

Nov 04, 2008

My conclusion is based on having experimented with genetic algorithms (GA). It is a fact that, once you climb above a very low threshold of complexity, the exponential explosion that ensues kills any subsequent evolution in its track: it doesn't even start. The only way to have a successful evolution is for it to be highly constrained in such a way that only an extremely limited number of specific codes (compared to the overall complexity of the organism) are allowed to mutate randomly. This requires forethought and design. ID proponents call it front loading.

Anybody who speaks of complex species arising through random mutations is woefully ignorant of the true meaning of exponential explosion. In other words, he or she is mathematically and logically challenged. Whichever way you look at it, evolution was designed. Live with it.

As an aside, I am still waiting for Darwinists to explain why all human races are so obssessed with music and the arts, a behavior that has absolutely no evolutionary value. And don't give me any cockamamie story about it being a side effect of high intelligence; that is not science.

Excellent post.

One of the things I am interested in is attempting to model "random" changes to a self replicating information system.

This is very hard to implement without crashing a computer, as even the slightest change in the wrong area of code will cause a pointer or variable to become complete garbage.

The program needs to load itself to memory, then make a copy of itself and randomly modify one or more bits (random number of bits) in the copy at a random location in the file (signifying genetic mutation). Then the copy file is "called" symbolizing reproduction, and the process repeats (if possible).

I have not successfully created this program, though I came "relatively close" a while back with a machine level program.

unfortunately, I already know what the result of the experiment is going to be: The probability is very high that the "simulated organism", i.e. "the program" will go "extinct" after just one generation.

The probability of a random change doing anything other than creating a run time error (death of the organism) is very, very slim.

High level programing languages do not even allow this sort of code because of the danger of accidentally over writing or deleting key files of the computer or other similar glitches.

And ideal model would use operators in base 64, which is what DNA codons are(the 4 bases are base 4, obviously, but the codons are 4^3 = base 64), and every number from 0-63 would represent a different command or component object.

I've been thinking about this and it really is not that hard to program this in PHP using the "eval" script.

A data file represents a single cell organism.

a script inside the file, programmed to copy that file, represents DNA.

A script in the calling program inserts a random error in each "daughter" file. This error is biased so that it can be no change at all, or a truly random change, or more likely, a change that represents copying part of the file an extra time. Then the "daughters" are saved, and a loop continues, now calling each "daughter" function until the browser/server crash (probably immediately).

The problem with all of this is, we already know from "common sense" that the program will fail and "die" within a generation or two, even if it is mass reproducing with different combinations of errors.

Nov 05, 2008
@paulthebassguy wrote:

"In response to Traveller, music and the arts actually have a huge evolutionary significance becasue they are important socially in human culture. Social interaction & language is one of the key components in the evolution of human intelligence."

This is funny. Always some cockamamie answer that does not address the question posed. Let me rephrase. Language and interaction make sense as far as evolution is concerned because communication is beneficial to survival. Music and the arts, however, do not make sense because they are not beneficial to survival. In fact, they are detrimental because they require a large group of people to dedicate their lives in acquiring skills that are unnecessary to the survival of the group. How is playing music or acting in a play going to save a species from predators or famine? Where is the evolutionary advantage? Don't bother replying. You got no answer. I know.

Nov 05, 2008
The Bible is nothing but a series of stories that may or may not have been true in the first place, mistranslated, edited for content in the 4th century by people who wanted it to portray a certain image, and then blindly copied by a Gutenberg press as a test-subject for mass media publishing. It's full of hypocrisy, partial truths, bold face lies, and some interesting cultural observations of life in earlier times.

The only relevance this book should have, is a historical backdrop to what superstitious people used to believe. Church organizations are corporations fed by greed and vanity feeding on the population using propaganda and whatever they feel like making up.

While I am in support of love and support and charity and a number of other virtues that are, mostly implied, in the bible, I cannot take it at face value, or even as divinely inspired. Lets not even talk about the Mormon bible, which is wrong on every level. (Purports to be a followup to the bible, but if the bible was divinely inspired AND the Mormon bible was to be used, it would have mentioned something about it.)

Blind faith is toxic to humankind. It leads to every kind of strife and mental disconnection with reality. Think for yourself! Even if you believe in god, assume he gave you a brain for a reason!

Nov 05, 2008
Quantum_Condumdum's assertions about genetic mutations only make sense when artificially constraining the problem, allowing only point mutations to occur. In real life other processes to occur, including the making of additional copies of a gene. One copy by chance will not suffer a deleterious mutation and will retain the gene's original function, but the additional copies are free to mutate or not as they please or not, thus ending up doing nothing at all (except acting as a hidden backup copy), performing the original function, or mutating to the point where they perform a different function. Additional copies of genetic elements are the true driving force behind evolution and it is therefore not surprising that QC ignores them.

Nov 05, 2008
Anyway The bible is a sample of evolution itself up until the printing press, after which time the evolutionary principle in the bible has slowed down but not stopped.

You can compare bible texts sourced from different locations and find constant and numerous changes. Some of these will be a minor word meaning here and there or change in emphasis that may change the meaning of a phrase but maintains something close to the integrity of the whole.

But if you considered each paragraph as a living organism then you would have new species cropping up here and there throughout the bible, along with each viable variation.

As for self replicating examples in human society you don't have to go much further than riddles, jokes, stories and songs. These things are constantly evolving and the pace of evolution is directly proportional to the ability of these things to die or cease to exist. Once put into print media they can still evolve (more slowly), new copies and variations tend to be more deliberate than accidental but the accidental variation can still occur - just at a slower pace.

Nov 05, 2008
I wonder how many of the people commenting actually know what they are talking about. It is amusing to see half-truths and ignorance being spewed like nobody's business. Before you suggest that we correct your mistakes, pick up a book on genetics and molecular biology. There is no reason why posters on this site should take the time and argue with you over things that could be learned on your own time. Likewise, before you open your mouth to discredit a theory, please take the time and effort to learn exactly what the theory consists of, or you'll be wasting everyone's time.

Nov 05, 2008
@Traveler wrote:

This is funny. Always some cockamamie answer that does not address the question posed. Let me rephrase. Language and interaction make sense as far as evolution is concerned because communication is beneficial to survival. Music and the arts, however, do not make sense because they are not beneficial to survival. In fact, they are detrimental because they require a large group of people to dedicate their lives in acquiring skills that are unnecessary to the survival of the group. How is playing music or acting in a play going to save a species from predators or famine? Where is the evolutionary advantage? Don't bother replying. You got no answer. I know.

Right.. Because evolution is all about personal survival. Or is it? What about the survival of the species? Does reproduction ring a bell?

Nov 05, 2008
I know I may not be an authority on the subject with only one biology and zoology course under my belt, but I still say DUH!

I'm dumbfounded that much of the scientific community had accepted the idea of 'junk' DNA.

Over hundreds upon thousands of years of evolution, did they really believe we (human beings) had evolved to most dominant species on earth being as inefficient as having some 30% plus of useless DNA?

Wherever you turn in nature you see images of efficiency and adaptation that permit life to thrive in every environment on earth. Can you do that being inefficient, I'm guessing not.

I think this is a perfect example of people coming to realize we really don't know as much about our origins as we may think.

Nov 05, 2008
This is a very interesting article. I am glad that our understanding of DNA is being pushed further and further.

That said, the comments are far more interesting.

Why must Jesus be the One? What of Krishna? Of Buddha? What of the Hindu Gods and Goddesses? Or those of the Maya? Do they not also say that they are the only? The alphas and omegas? That all other religions are false?

What then is the difference?


One never sees a member of one of those faiths preaching mindlessly do a group of people who have expressed no desire to listen to their sermon. The Christian Faith's evangelical qualities and militant attitudes are unnatractive and unneccessary.

The few religious who read this article simple to profess their faith and condemn the few who read for knowledge share the same disrespect of the Crusaders, Fred Phelps, and Brother Micah.

Please, respect whatever beliefs someone may have. Please, do not try to save me unless I have asked you too. It is a journey that must be undertaken on ones own. I know your faith is there should i ever decide yours is the path to my salvation.

I do not ask you to renounce your faith, to change your god. I ask you respect the faiths of those around you, even if their faith is none.

The comments on linguistic evolution and the evolution of the bible i found particularly interesting.

As for music and arts, i believe that the complexities of human evolution are just beginning to be uncovered. The growth of human knowledge has been nearly exponential, and i believe there is a piece of evoltuion that few (if any) have chosen to research or explain.

With this exponential growth of knoledge came technology. Flint tools and fire first. Today, computers, cell phones, the internet. These tools have expanded the nature of humanity to include the environment it interacts with.

Music, arts, and culture, therefore, are the results of complex forms of evolution beyond the genetic definition.

So, please, provide your solutions to life to someone who has first asked a question. Though i do enjoy the discussion, i dont believe this is the place.

Continue the research! Perhaps one day the intricacies of DNA will be revealed entirely.

Nov 06, 2008
I would suggest that you guys that DO NOT believe in evolution to read the book "The selfish gene" by Dawkins. It is, unfortunately very offensive, actually his rhetorics is very much like most of the creationist. But he does have some very good points, especially about the survival of the individual versus the survival of the species. There is a balance a species must walk. For example the male mantis does not concern himself too much with his own survival, but the survival of his genes. That is why he sacrifices himself. There's many situations where cooperation is the best way to survive for an individual.
About song and dance, it has use for the survival of the species, it's a way of showing and it is also seen in other animals, birds for example. But at this point in time, we have so much spare time and so few threats that we can dedicate a life to art.

Nov 06, 2008
You suggest that man only affects his tools, and that his tools do not affect him. When one sits in a chair, is his back not more comfortable than if he should sit on the ground? Does sitting not cause every man to be at the same level as one another? Does it not allow for more leisure time? A better place to read?

So, your faith requires you to preach, to spread the message of salvation. That is fine. I will sit contentedly ignoring your words, or listening out of curiosity when i choose, until the day (should it come) that i would like to be saved by your message.

Yes, respect must be earned--in a sense. When you meet someone for the first time, do you not grant them respect simply because of your ignorance to their personality? I respect that for you, your religion is the one truth! You know that it is right! I know that your texts tell you to spread the word, and i have heard your word! Respect my decision to believe on my own anyway. You lose the respect of many when your militance continues. Perhaps try another approach?

If you choose to respect only those who serve your god, then most of this world does not deserve your respect. I pity that close minded view. If you find a man to be a close friend before you find he is jewish, do you renounce your friendship?

And yes, Buddhism does not say who to worship. However, it does say more than "nothing at all." The religion teaches morals and shows a path for one to live their life on, just as all religions do.

You say they would bow before any god you brought before them. Have you tried walking into a temple for any polytheistic religion and preaching your god? They will not bow before jesus because their gods are sacred to them. Do not assume that they will fall on their knees because you asks them to.

Back to the article. I wish i understood more of it, but on reading it a second time, i feel i grasp the concept more.

Nov 06, 2008
Only the idiots in the mainstream press refer to these elements as 'Junk DNA'. As far as I know, no actual scientist calls it by this name. They're called by various names, including 'repeats', 'transposons', 'transposable elements', and there are many different kinds, some of which derive from retroviruses, and some of which are just repetitive sequences that are prone to replication errors due to the way the DNA replication process works (look up microsatellites). There's one microsatellite in particular that's responsible for Huntington's disease, in particular, and the number of repeats present is an accurate predictor of when the patient starts showing symptoms. No molecular biologist worth his salt would actually call this 'junk dna', it's just that we don't know what most of it does.

And to all you creationists/armchair debaters - read a freakin' book already. Tired of reading your ridiculously outdated misinformation.

Nov 07, 2008
There is no junk DNA, some ignorant fool called it that long ago when the only role for DNA he could envision was to encode proteins. No sane biologist who understand evolution will use this term.

All DNA plays some role, besides proteins there are a lot of non-protein-coding RNAs, but the primary role for all the non-coding sequences in mammal DNA is structural. Bigger nucleus is beneficial for multicellular organism as it allows for a much more complex gene regulatory pattern.

Nov 07, 2008
As for the religious debate, its your IQ that defines the camp you are in so theres no converting really.

Nov 08, 2008
Complexity continues to grow and margin of error shrinks. The idea that blind naturalistic processes could create the stunning diversity of life becomes more and more of a fairytale. The idea that life was an engineered process grows immeasurably stronger.

Sadly, this horribly missed prediction by the Darwinists will be twisted around to where it's actually further proof of their dogma. Unfalsifiability at its worst.

I dream of the day when biology stops relying on 1850's pseudoscience and follows the modern evidence pointing towards Intelligent Design. I.D. is not only the best answer - it's the only answer.

Nov 09, 2008
I'm surprised to see how many religious-based thinkers there are on a science website.
Quantum_Conundrum seems to be the biggest manipulator of "fact" to prove a point. Manipulating the word "streak" and "steak" to make a point? Compelling argument. Except that DNA coding transcends language, where as using the words streak and steak to make a point would not hold any validation in, lets say, Spanish. DNA coding would be the same any language. It simply is.
And this theory of creative design is simply a compromised version of the creation theory after religious folks became tired of trying to defend the ridiculous idea that we all came from 2 people that were created by God.
However, history has repeatedly shown that people who accept the norm, whether it be in medicine, sociology or science, always feel threatened by those who try to discover new frontiers.
I watched a movie the other day called "What the Lord Made" about the first heart surgery done at John Hopkins University. There were so many doctors who simply accepted "the norm" that heart surgery could not be done safely, and ridiculed the doctor (Dr. Blalock) for even considering it. Where would we be today if those who dared to discover simply caved to those who do not have the courage to do so themselves?
Religious based thinkers, more times than not, seem to be at the heart of these situations. I think mainly because it threatens the foundation of everything they've been taught and have willfully accepted to be true without any qualms.
My thinking is that this "junk DNA" is simply remnants of the building blocks that simply tie us all back together at a similar point of origin, changing ever so slightly over time and making us a little bit more individualistic.
To my religious brethren, take a back seat on this one. If you're right in your beliefs, then you stand to lose nothing, and those sinners who choose to find their truth in science will live on as they always have throughout history, and it will have no effect on your lives otherwise.
To my brethren who choose to challenge the norm and traditional thinking, don't ever cave to the critics and nay sayers. They are simply envious of your courage to discover. A courage they didn't dare to have themselves and simply accepted what they were told.

Nov 09, 2008
I wish this thread had stayed on point and not strayed into a cause for Christians to take up the calling of converting free thinking people. Quantum_conundrum, your acceptance of Jesus wasn't a free choice as much as it was simply a choice influenced by where you live and your surrounding enviroment. Meaning, if you were born in China, your prophet would have been Budha, and you would have been none the wiser to the exhistance of Jesus. Your comments about the "evil atheists" and agnostics and their resistance to accept Jesus is the same as your resistance to accept Budha, Alla, or Shiva as yours. And you have had the same amount of personal and physical interaction with Jesus as you have had with Budha, which is none. And yet you willfully and blindly accept Jesus and denounce those that don't or have chosen another god.
Here's my last comment about Christianity. Keep in mind I am a Christian myself, but believe I was blessed with a great mind by God to think rather than just accept what I'm told or read out of a book written by men 2000 years ago who had limmited scientific knowledge.
Christians believe that if you do not accept Jesus as your savior, you are condemned to hell. They also believe that all humans are created in the likeness of God. So here is my challenge with these two beliefs that I have always had. If God created us all, then that means he even created people who are indiginous to areas that are deprived of modern knowledge. So lets take the medieval era. During these times the crusades were happening and wars were waged on behalf of "God". Meanwhile, across the Atlantic, there is evidence of thriving societies in Peru and Chile' during this same time. So, given Christian beliefs, were these people condemned to hell because they did not accept Jesus? If God created all people, why would he bother creating people (who he had to of known would never have the opportunity to know Christianity or be introduced to it) that were simply going to be fated to hell anyway?
It is my personal belief that if you look at the core beliefs of Christianity (The beatitudes, the commandments, etc.), Budhists actually behave more like Christians than actual Christians do. Christians would be better served if they lived lives of example rather than preach to everyone. As the saying goes..."Your actions are so loud, I can't even hear what you are saying."
I believe in evolution, not because I hold it as true, but because it is a forum what welcomes new ideas and open thought. Religion, especially Christianity, does not welcome new ideas. What's the point of having a brilliant mind if you're just going to accept old ideas?

Nov 09, 2008
god must be full of manure why else does he need so many rectums?

Nov 09, 2008
ZZZZZZZOD ok - I think you have it.

religion is an accident of geography and the DOES seem to hold true.

In fact I think there is very little difference between the religious fanaticism of Central North America and Central North Africa. They have chosen a different representative (long dead) as the basis of their viewpoint. Unfortunately they still feel that they have the right to do unto others whatever they want because the others do not agree with them.

It is unfortunate that this type of tribalism is bred in the genes through evolutionary pressures that strengthened gene pools within small tribal communities.

It is a survival trait in the right circumstances where you kill the stranger and interbreed within the community. But, The only cure for this narrow minded parochialism is to include in your "tribe" a larger community.

If you think of yourself as a world citizen instead of as a Christian Fundamentalist or an Islamic Fundamentalist then you will lose that hatred and aggression to those that are not like you.

Even in the small tribe there was room for people that did not always agree with each other. They did need some kind of cement that made a tribe a community. It could have been a shared custom of burial or respect. Not all tribes used the same technique to cement a community and we do not all have to be hateful to others that are not like ourselves.

Even Jesus thought he was worshiping a loving and kind forgiving god. Not the same god that rules the old testament at all. Did Jesus have a different god? I think so.

Just goes to shoe there could be room for more than one god.

Nov 10, 2008
to traveller and quantum whatever your name is-
dear religious folks.
while i can appreciate you have something to say and argue about, it is not on topic- (so called junk dna being found useful by some researcher)
while we are off topic i might ask somethings:

1) supposing everything in the universe was designed- i dont see how you would "prove" or even indicate such a thing as you would be attempting to posit something outside of all this here. but lets suppose this is so.

2) now lets suppose this is happening-
let me understand you correctly here:
you think the God spoken of in the pages of your religious text that hails from a council of Priests in Nice France about 1500 years ago (make that "bad translations of those texts")
basically a hodgepodge of texts stolen from Judaism and 4 books by buddies of the guy who was crucified and "came back to life and went up to heaven" and then some book at the end written by a crazy guy predicting the end of the world in full hellfire & brimstone glory...
anyway this text and the God described in this text- you think this being created all the world we live in and the entire universe and space and time and all that?

are you daft, arrogant, stupid or all 3?
maybe just gullible?

there is nothing scientific or inquisitive about any of your claptrap.

you think the talking snake is the bad guy and all our problems came from a lady eating an apple naked in the garden one day.

get a life. did you just fall off the turnip wagon yesterday?

but anyway, i digress, we should be discussing the research on so-called junk dna...
if this article was about new polymers then people like traveler would not be spouting their tall tales...

Nov 10, 2008
and quantum whatever you call yourself- i dont think you are qualified to deliver comparative religions 101 with your bias.
you actually think you believe the one true faith and all others are wrong...
amazing. where did you get your sacred "book"? a cereal box? maybe if you learned a little about where each piece came from before you open your arrogant mouth up and claim buddhism is "stolen"
half your "bible" (means BOOK mr.) is "stolen" from judaism. Additionally you still think everyone plays the same games in their religions as you guys with pathetic "worship" and fealty like some sick dog capable of adulation only due to fear of the stick. well some are less into worship and more into other aspects that you wouldn't understand unless you actually tried to.

well i guess i got a little carried away there but my point is that your bias has blinded you to the fact (i love using that word "fact" for any opinion etc... in conversation. works great. and thats a fact) that your literal interpretation of your religion- with zero respect for your context in a body on a planet etc...
you see, god forgot to tell you that this religion stuff involves lots of metaphor and symbolism. maybe even some nuance. something you would seem to be lacking.

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