Rethinking junk DNA

The article is from last year, and referenced in a previous post. In the context of a term coined in 1972 it's hardly stale.

Do you have more recent data?
Ever tried to actually read the posts about junk DNA in this thread? You will be surprised how quick science progresses in 2 years with regards to genomics, transcriptomics, proteomics, metabolomics etc. You really should not tell others they need to learn to read english you know.


What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?
Hey, you make assertions, you support them with references.

Oh yes, and how many DNA related articles have appeared since 1972?

and.

How many DNA related articles appeared between 1972 & 1987?
Pubmed is your friend, it won't bite.

BTW, haven't you got the memo? Here:
Junk DNA does not imply that junk DNA is actually functionless junk. It may turn out to be functionless, it may turn out to have a function.

The question now is: How do you scientifically determine function and confirm non-function.
 
Do you have more recent data?
Ever tried to actually read the posts about junk DNA in this thread? You will be surprised how quick science progresses in 2 years with regards to genomics, transcriptomics, proteomics, metabolomics etc. You really should not tell others they need to learn to read english you know.

A glorified argument from incredulity. I take it the answer is no.

What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?
Hey, you make assertions, you support them with references.

I did. You responded (as above) with an argument from incredulity.

how many DNA related articles have appeared since 1972?

and.

How many DNA related articles appeared between 1972 & 1987?
Pubmed is your friend, it won't bite.

I note, you still refuse to answer.

BTW, haven't you got the memo? Here:
Junk DNA does not imply that junk DNA is actually functionless junk. It may turn out to be functionless, it may turn out to have a function.

The question now is: How do you scientifically determine function and confirm non-function.

Fortunately the rest of us are under no obligation to accept your definitions. (indeed this brings on an eerie sense of deja vu)

However in the interests of forwarding the debate this article on Pseudogenes may prove useful.
 
alloytoo, for a fellar like you that knows so much about biology and evolution and other stuffs, I am sure you will appreciate a bit of talk about selection.

I think you would agree to the following statements.
A) If adaptation X is a beneficial with regards to fitness it is more likely to remain in a gene pool than being removed.
B) If adaptation X is neutral with regards to fitness it is unlikely that the chance of its removal from the gene pool will be greater than the chance that it remains in the gene pool and visa versa.
C) If adaptation X has a negative influence on an organism with regards to fitness it is more likely to be removed from the gene pool than being kept.

Now for a person with your wealth of knowledge with regards to biology and biochemistry, you know that copying and maintaining DNA information requires energy in the form of ATP (among other forms). ATP is needed to drive the molecular machines during replication and keep it in tact during periods of stress. If there is not enough energy for these machines, it won't work and the cell's fitness is compromised. If an organism's fitness is compromised, it is less likely to reproduce and produce offspring.

If you can get one thing out of this (you can probably add a little maybe, forgive me if I left anything out) you would know that the more DNA an organism has, the more energy will be needed to efficiently maintain its DNA integrity and replicate. From here I am sure you would like to point out to me that DNA with no function at all will have a negative influence on the fitness of an organism because it uses precious energy resources without contributing to fitness at all. And because of this wasteful energy usage without contributing to fitness, these sequences are thus more likely to be removed than maintained in the gene pool.

Now let's look at junk DNA. As you know, junk DNA does not imply that junk DNA is actually functionless junk. It may turn out to be functionless, it may turn out to have a function. It is just currently unknown.

Looking at the statements from above, it is more likely than not that these sequences fall under A or B (see above) because if these sequences have a negative influence on an organism with regards to fitness, it is more likely to be removed from the gene pool than being kept intact by the intracellular biomolecular machinery because of the energy needed to do so.

I am also sure that you will agree that sequences that are neutral with regards to fitness does not imply that they are functionless. Because, as you know after reading through this thread, junk DNA may not contribute to the fitness of an organism, but play a vital role in the evolution of a species. Without this junk DNA, organisms may be evolutionary less fit and face eventual extinction.

Just to highlight again recent advances in our understanding of genomics and transcriptomics (I am sure you are aware of it though).
'Junk' DNA Has Important Role, Researchers Find
Saved By Junk DNA: Vital Role In The Evolution Of Human Genome
Junk DNA may have handed us a gripping future
Shaking up the theory of evolution
RNAs Taking Center Stage
Spare Gene Is Fodder For Fishes' Evolution
Transposons, or Jumping Genes: Not Junk DNA?
And with your wealth of knowledge with regards to pseudogenes, I am sure you can add even more information to the above that you already knew about.

Now I am not sure about one thing and hope you can help me with this:
How does one scientifically determine function and confirm non-function.

I await your valued and insightful reply :).
 
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If you can get one thing out of this (you can probably add a little maybe, forgive me if I left anything out) you would know that the more DNA an organism has, the more energy will be needed to efficiently maintain its DNA integrity and replicate. From here I am sure you would like to point out to me that DNA with no function at all will have a negative influence on the fitness of an organism because it uses precious energy resources without contributing to fitness at all. And because of this wasteful energy usage without contributing to fitness, these sequences are thus more likely to be removed than maintained in the gene pool.

Probably not a very great "negative" influence, and there would be many, many "fitness factors", so to say.

Of course, this argument does rather blow out of the water your "pre-adaptations", would you not agree? All that genetic "stuff" awaiting its cue to enter centre-stage would take energy to maintain.
 
Probably not a very great "negative" influence, and there would be many, many "fitness factors", so to say.
Do elaborate please. Don't leave us in the dark here wondering. Provide us with some light and insight.

Of course, this argument does rather blow out of the water your "pre-adaptations", would you not agree? All that genetic "stuff" awaiting its cue to enter centre-stage would take energy to maintain.
I am not exactly sure what you mean here. Am I right in saying preadaptations are just features that had a function but where co-opted into a function that is unrelated to its old function?
 
Do elaborate please. Don't leave us in the dark here wondering. Provide us with some light and insight.


I am not exactly sure what you mean here. Am I right in saying preadaptations are just features that had a function but where co-opted into a function that is unrelated to its old function?

I am sure you can work out the first bit.

Would you say that no "dormant" genetic material ever gets resurrected in a new function? Is there "dormant" material or is every itty bit of DNA always in play in an organism in some way? If not, how did the first simple cells contain all necessary to make a human, as you ID boys seem to claim?
 
I am sure you can work out the first bit.
No, you are leaving us in the dark here. Please elaborate a bit.
1) "Probably not a very great "negative" influence"
2) "there would be many, many "fitness factors", so to say."

Thanks. I hope to learn from this.


Would you say that no "dormant" genetic material ever gets resurrected in a new function? Is there "dormant" material or is every itty bit of DNA always in play in an organism in some way? If not, how did the first simple cells contain all necessary to make a human, as you ID boys seem to claim?
I don't quite get what you mean by "dormant". Could you please put it in more scientific terms like you usually do. Forgive my ignorance. I am also unsure about this claim "ID boys" are making. I am fascinated by this. Could you perhaps lay out this claim in a clear manner so that I can understand it? Thanks man.

Oh, I don't know if I was right about preadaptations. Could you help me there a bit please. Is it right to say preadaptations are just features that had a function but where co-opted into a function that is unrelated to its old function?
 
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Do these "dormant stuffs" you are refering to fall under A, B or C in post #184? Please put it in your usual scientific terms if you don't mind. Thanks.
 
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ATP is needed to drive the molecular machines during replication and keep it in tact during periods of stress. If there is not enough energy for these machines, it won't work and the cell's fitness is compromised. If an organism's fitness is compromised, it is less likely to reproduce and produce offspring.

If you can get one thing out of this (you can probably add a little maybe, forgive me if I left anything out) you would know that the more DNA an organism has, the more energy will be needed to efficiently maintain its DNA integrity and replicate. From here I am sure you would like to point out to me that DNA with no function at all will have a negative influence on the fitness of an organism because it uses precious energy resources without contributing to fitness at all. And because of this wasteful energy usage without contributing to fitness, these sequences are thus more likely to be removed than maintained in the gene pool.

It's an valid hypothesis, but the questions have to be asked (again a strange sense of Deja Vu).

What is the actual cost of the retain non-coding DNA in relation to the organism 'hosting' it?

What it the cost of removing the the non-coding DNA?

To use a simple analogy:

Many buildings around the world have held multiple generations of furniture, and multiply generations of data network wiring.

Old furniture, which no longer has a function is removed from a building and replaced with the new. The cost of retaining the old non functioning furniture greater than the cost of removing it. Conversly many buildings contain multiple generations of data cabling simple because the cost of removing the cable is significant, while the cost of retaining it is negligible.

Here's an article which examines the issue.

And with your wealth of knowledge with regards to pseudogenes, I am sure you can add even more information to the above that you already knew about.

Now I am not sure about one thing and hope you can help me with this:
How does one scientifically determine function and confirm non-function.

The answer is rather simple, one looks for Non-Coding DNA then one Labels it Junk DNA.

There were some interesting experiments conducted in 2004 (IMS) whereby some non-coding DNA was deleted in a population of mice, which had no decernable effect on subsequent generations, turns out the Junk DNA in question was just that, Junk.

ETA: almost forgot:

How many DNA related articles have appeared since 1972?

How many DNA related articles appeared between 1972 & 1987?

What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?
 
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It's an valid hypothesis, but the questions have to be asked (again a strange sense of Deja Vu).

What is the actual cost of the retain non-coding DNA in relation to the organism 'hosting' it?

What it the cost of removing the the non-coding DNA?

To use a simple analogy:

Many buildings around the world have held multiple generations of furniture, and multiply generations of data network wiring.

Old furniture, which no longer has a function is removed from a building and replaced with the new. The cost of retaining the old non functioning furniture greater than the cost of removing it. Conversly many buildings contain multiple generations of data cabling simple because the cost of removing the cable is significant, while the cost of retaining it is negligible.
I think you know that a buildings and a cells are not comparable. The people moving and removing things from the building have minds. But, if you wish to take this analogy serious, the old furniture definately still had a function. Removing of functional elements and replacing them with other increasingly functional elements might have a negative effect on fitness. Random degradation and removal of functionless elements does not require energy, therefore that would be the most efficient "method" for removal of functionless elements.

That article just looked at non-coding genomic elements. As you probably know, non-coding does not imply non-functional.



The answer is rather simple, one looks for Non-Coding DNA then one Labels it Junk DNA.
As you know by now, neither "non-coding DNA" nor "junk DNA" implies the sequences do not have a function.

There were some interesting experiments conducted in 2004 (IMS) whereby some non-coding DNA was deleted in a population of mice, which had no decernable effect on subsequent generations, turns out the Junk DNA in question was just that, Junk.
Does this confirm that the sequence does not have, never had and never might have a function?
Did they test for all parameters? The details of the study would be interesting though. Would you care to share it? A lot of these studies just look at a few fitness parameters and it is not possible to test for all. Claiming it is non-functional would be pre-mature. As you know (Saved By Junk DNA: Vital Role In The Evolution Of Human Genome) it might have a positive effect on adaptability to strange, unforseen conditions. How would you test that? Scientists have already discovered this to be the case, thus it is pre-mature and silly to claim a sequence of code to be functionless without testing for all the parameters.

A simple analogy should demonstrate this. Computer codes have many lines of code that just accumulate and looks like junk. After a few rounds of testing you might find the code is useless and delete it and the system works just fine. Only to discover that after a while and using a few more exotic functions that the code actually had a function.


ETA: almost forgot:

How many DNA related articles have appeared since 1972?

How many DNA related articles appeared between 1972 & 1987?

What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?
No you did not forget silly... you never used pubmed or is not interested in doing so. Why you continually flout this ignorance while maintaining such high academic standards is a bit of a mystery. If you are really interested, which you seem to be, you can use pubmed as it really is a brilliant resource. You will really have to do the legwork if you want an exact number though. Nobody knows, and as I have told you before, it is more than a few million, a lot, and research is ongoing (premature to make any claims). Fascinating isn't it.

I am still fascinated by your use of reductionism for detecting something. How is it going there btw? Published anything yet?
 
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An example of a function for non-coding DNA:

MicroRNA Drives Cells' Adaptation To Low-oxygen Living

ScienceDaily (Oct. 6, 2009) — Researchers have fresh insight into an evolutionarily ancient way that cells cope when oxygen levels decline, according to a new study in the October 7th issue of Cell Metabolism, a Cell Press publication. In studies of cells taken from the lining of human pulmonary arteries, they show that a microRNA – a tiny bit of RNA that regulates the activity of particular genes and thus the availability of certain proteins – allows cells to shift their metabolic gears, in a process known as the Pasteur effect.

While the discovery is a fundamental one, the researchers say it could point to new ways to tackle diseases, including cancer and cardiovascular disease.

"The Pasteur effect is really best defined as the way by which cells adapt to low oxygen concentrations," said Joseph Loscalzo of Brigham and Women's Hospital and Harvard Medical School. Cells do that by switching from mitochondrial metabolism to glycolysis.

Normally, cells produce high-energy molecules such as ATP through components known as mitochondria, he explained. Loscalzo likens mitochondria to little factories that churn out ATP under normal oxygen conditions. If mitochondria continue to operate when oxygen becomes limited, they do so inefficiently, he said, spewing out toxic derivatives of oxygen (including superoxide and hydrogen peroxide) in the process.

"When cells encounter that situation, they need to direct their energy program from one with mitochondria to one that uses less oxygen," Loscalzo continued. That secondary program, called glycolysis, doesn't produce as much cellular fuel, but it does so without toxic byproducts.

In the new study, the researchers first went in search of microRNA that rise when cells become hypoxic, meaning that they are deprived of sufficient oxygen. That screen done in many types of cells landed them miR-210 as a key player. Using several methods, they were able to predict that miR-210 would influence activity of iron-sulfur cluster assembly proteins (ISCU1/2). Those proteins act as scaffolds that assist in the assembly of iron-sulfur clusters, important ingredients for mitochondria to function.

The team shows that miR-210 does in fact directly target ISCU1/2, which disrupts the integrity of iron-sulfur clusters. As a result, mitochondrial respiration and associated functions get shut down.

The basic findings may have clinical implications, Loscalzo said, noting that scientists have devised increasingly interesting ways to selectively inhibit microRNAs. For instance, cancer cells typically operate under Pasteur effect conditions (a phenomenon known as the Warburg effect.) The ability allows tumors to grow even when they outstrip their blood supplies and prevents the generation of toxic oxygen derivatives within them.

You could imagine that treatments designed to block miR-210 might hobble tumors by manipulating their usual metabolic profile, Loscalzo said. In other settings, you may want to increase miR-210, he added. Such a therapy may have potential in patients with blocked coronary arteries, for instance.

"The transition of heart muscle to miR-210-dependent glycolysis might be enhanced by administering [the miRNA]," he said. By helping that transition along, physicians might be able to help minimize the production of toxic byproducts by mitochondria in their patients, and ultimately preserve more heart tissue, Loscalzo adds.

The researchers include Stephen Y. Chan, Massachusetts General Hospital, Boston, MA, Harvard Medical School, Boston, MA; Ying-Yi Zhang, Brigham and Women's Hospital, Boston, MA, Harvard Medical School, Boston, MA; Craig Hemann, Ohio State University, Columbus, OH; Christopher E. Mahoney, Brigham and Women's Hospital, Boston, MA, Harvard Medical School, Boston, MA; Jay L. Zweier, Ohio State University, Columbus, OH; and Joseph Loscalzo, Brigham and Women's Hospital, Boston, MA, Harvard Medical School, Boston, MA.
 
I think you know that a buildings and a cells are not comparable.

This is why we call it an analogy, specifically a 'simple' analogy.

The people moving and removing things from the building have minds. But, if you wish to take this analogy serious,

the old furniture definately still had a function.

But no function in the place it's in.

Removing of functional elements and replacing them with other increasingly functional elements might have a negative effect on fitness.

Or it may have no effect on fitness, or improve fitness.

Random degradation and removal of functionless elements does not require energy,

Assumption.

therefore that would be the most efficient "method" for removal of functionless elements.

Conclusion built on assumption.

That article just looked at non-coding genomic elements. As you probably know, non-coding does not imply non-functional.

Non-coding elements may well have no function.

As you know by now, neither "non-coding DNA" nor "junk DNA" implies the sequences do not have a function.

Junk DNA refers to Non-coding DNA, it's a very specific reference. Some of it may well have NO function.

Does this confirm that the sequence does not have, never had and never might have a function?

Stupid question.

It confirms the sequence has no effect on current fitness.

It says nothing about the historical significance of the sequence (Bit of a strawman, since I never implied or suggested a lack of previous function.)

It cannot prophesise as to a possible future function.


Did they test for all parameters? The details of the study would be interesting though. Would you care to share it? A lot of these studies just look at a few fitness parameters and it is not possible to test for all.

http://www.sciencedaily.com/releases/2004/10/041021085247.htm



Claiming it is non-functional would be pre-mature. As you know (Saved By Junk DNA: Vital Role In The Evolution Of Human Genome) it might have a positive effect on adaptability to strange, unforseen conditions. How would you test that?

It's called natural selection.

Scientists have already discovered this to be the case, thus it is pre-mature and silly to claim a sequence of code to be functionless without testing for all the parameters.

So basically your argument boils down to:

We dare not label DNA which is non-functional today "non-functional" because it "may" acquire a future function. Then again, it "may" not.




A simple analogy should demonstrate this. Computer codes have many lines of code that just accumulate and looks like junk. After a few rounds of testing you might find the code is useless and delete it and the system works just fine. Only to discover that after a while and using a few more exotic functions that the code actually had a function.

I do recall a conversation I had with a real programmer who gleefully noted that a 'bug' which he had noted in some of his commercial programming (Which had no effect to the fitness of the software), had survived 10 years and scores of generations of the programme. It would have cost too much to remove when he did the coding, and clearly each subsequent programming team thought likewise.

It's an interesting analogy because:

1. While the bug does something,
2. It does nothing useful
3. It's removal would not effect the function of the software in the least.
4. The cost of removal was, for at least a decade, deemed too high.

Lest we forget the outstanding questions:

How many DNA related articles have appeared since 1972?

How many DNA related articles appeared between 1972 & 1987?

What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?

Disclaimer: Yes, I know they serve no useful function now and that their removal would have little effect on the fitness of this post, but I remain ever hopeful that they will become useful in the future.
 
Random degradation and removal of functionless elements does not require energy, therefore that would be the most efficient "method" for removal of functionless elements.

Don't tell me you are finally realising that random sh|t happens???

;)
 
So basically your argument boils down to:

We dare not label DNA which is non-functional today "non-functional" because it "may" acquire a future function. Then again, it "may" not.
No, you may call it "non-functional" at leisure, you my even dare to... However, the people doing the research noted that:


I do recall a conversation I had with a real programmer who gleefully noted that a 'bug' which he had noted in some of his commercial programming (Which had no effect to the fitness of the software), had survived 10 years and scores of generations of the programme. It would have cost too much to remove when he did the coding, and clearly each subsequent programming team thought likewise.

It's an interesting analogy because:

1. While the bug does something,
2. It does nothing useful
3. It's removal would not effect the function of the software in the least.
4. The cost of removal was, for at least a decade, deemed too high.
Strange, the bug does something but removal would have no effect on fitness? Ok, looks like the programmers were happy with their design and did not want to do too much to change since "removal would not effect the function of the software in the least."
Interesting analogy indeed.
 
No, you may call it "non-functional" at leisure, you my even dare to... However, the people doing the research noted that:

Through molecular techniques, a total of 2.3 million letters of DNA code from the 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic cells were genetically engineered to contain the newly compact mouse genome. Mice were subsequently generated from these stem cells. The research team then compared the resulting mice with the abridged genome to mice with the full-length version. A variety of features were analyzed, ranging from viability, growth, and longevity to numerous other biochemical and molecular features. Despite the researchers' efforts to detect differences in the mice with the abridged genome, none were found. "By and large, these deletions were tolerated and didn't result in any noticeable changes," said Nóbrega.
"An important caveat, however, is that no matter how detailed our analyses, our ability to test for a particular characteristic in mice is limited. All we know is that, in the time frame examined, there were no detectable changes in the specific features that we studied."

I wouldn't go so far as to call that a quotemine, but it certain comes a little close.

Strange, the bug does something but removal would have no effect on fitness? Ok, looks like the programmers were happy with their design and did not want to do too much to change since "removal would not effect the function of the software in the least."
Interesting analogy indeed.

Oh do you know many programmers who used to work for Delrina?

Lest we forget:

How many DNA related articles have appeared since 1972?

How many DNA related articles appeared between 1972 & 1987?

What percentage of the human genome is believed to be functional? Is it now more than 5%, more than 20%?

Disclaimer: Yes, I know they serve no useful function now and that their removal would have little effect on the fitness of this post, but I remain ever hopeful that they will become useful in the future.
 
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