4 ms·

While there might be some signal noise ratio, I highly doubt we have any junk dna. I imagine a good modern analogy here would be http://en.wikipedia.org/wiki/E

by MollyR 12y ago

While there might be some signal noise ratio, I highly doubt we have any junk dna. I imagine a good modern analogy here would be http://en.wikipedia.org/wiki/Evolvable_hardware http://en.wikipedia.org/wiki/Evolvable_hardware. http://www.damninteresting.com/on-the-origin-of-circuits/ http://www.damninteresting.com/on-the-origin-of-circuits/ in the two articles I mentioned,I think the way the "offspring" circuit worked in an extremely baffling(complex) way relying in physics in way beyond human design (aka the way the disconnected logic gates were still necessary for functionality) have insight into some of possible complex interactions of dna. They look like unnecessary garbage until you try to remove them and break a ton of stuff.

NathanKP 12y ago
According to the article: On average, each baby is born with roughly 100 new mutations. If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct. The point this article is making is that new techniques are finding that some portions of DNA assumed to be junk might have a use, and removing or changing them certainly does have an effect. But that doesn't mean we should jump ahead too far and say that none of the DNA is junk, because there are obviously some things that have no effect when changed.
- simcop2387 12y ago
  I wouldn't be surprised if some of it really has no effect and that's the whole point. As you mentioned if there's 100 new mutations per baby then if the coding is as dense as possible that means each mutation will cause some significant change. If it's got a lot of coding that doesn't do anything, by probabilities it'll likely not change anything important and cause no ill effects. Having that extra unused DNA could pose an evolutionary advantage in the face of an imperfect copying mechanism.
  - ajuc 12y ago
    Assuming mutation probabiity don't depend on the length of the copied DNA - copying 40 MB you will probably introduce 10 times more mutations than if you just copied 4 MB. only 10% of them will on average change the important code, so the end result is the same. So I don't see how NOP padding helps.
- kryptiskt 12y ago
  I don't get it, there's no choice between everything being essential and lots of the genome being junk. Redundancy mechanisms like multiple copies of genes, which we know is there, reduces the risk of harm from mutations. Why can't most of the stuff in the genome have the label "useful, but we have backups", rather than "essential" or "junk"?
- MollyR 12y ago
  I see. That's a good point, its difficult to say if DNA has no junk. So I'm going to avoid the categorical issue, of junk,non junk,essential,redundant(but useful in a replication failure). maybe My thoughts are this, DNA is not used just for an individual survival but also a mechanism to allow adaptation at some higher level. Like how some deep learning AI's learn how to play games by making random moves and getting feedback from the score changing. For DNA, we get random mutations/moves in the form of transcription,replications errors or Meiosis , and the feedback comes from successful reproduction(surviving to play the game again). So what we call junk DNA, might actually play a large role in this sort of "learning" mechanism. I hope I explained that decently. A lot of my thoughts come from this book http://en.wikipedia.org/wiki/The_Selfish_Gene http://en.wikipedia.org/wiki/The_Selfish_Gene
- sumitviii 12y ago
  What if we have wild mutations AND exceptionally good exception handling?
  - ajuc 12y ago
    We do. We have 2 mechanism for this. First mechanism - to go into production you have to pass unit tests (race to the egg). It's only 1 cell, so either it works or not, and if you were the fastest you probably didn't have most of the really bad mutations. Then after you are in production you run million copies of the code, and to be safe against mutations there's sth like erlang exception handling - if sth's wrong kill the process, start a new one. The problem is - sometimes the process gets so wrong it doesn't respond to kill signal.
    - sumitviii 12y ago
      >if you were the fastest you probably didn't have most of the really bad mutations How did they arrive at this conclusion?
      - ajuc 12y ago
        The mutations that makes your cell die will prevent you from being the first to the egg. The mutations that makes you immobile - the same. The mutation that mess up with your instincts, and reactions to chemical enzymes - same (you won't go the right way). And so on. It's a little like unit testing - it checks all the basic routines.
thaumasiotes 12y ago
> I highly doubt we have any junk dna Telomeres (the HLT HLT HLT HLT HLT... sequence at each end of a chromosome) are pretty well documented. They can be reasonably analogized to those 404 pages with a comment along the lines of  They're totally necessary if you don't want to quickly suffer a horrible death, but there's definitely also a sense in which they're junk.
- MollyR 12y ago
  I'm not sure of that analogy. Somehow telomeres are thought to connected to aging. http://www.progeriaresearch.org/cbs-monday-night.html http://www.progeriaresearch.org/cbs-monday-night.html Cancer cells can extend their telomeres, and are also immortal. I imagine them to be some sort of internal counter that other components of the system listen to. I guess I also have a hard time figuring out what people are trying to say when they call parts of the genome "junk". Perhaps what's "junk" is contextually dependent ? One human's trash is another human's treasure ?
  - thaumasiotes 12y ago
    > Somehow telomeres are thought to [be] connected to aging The mechanism here isn't a mystery. As I originally pointed out, you'll die when your telomeres are gone from loss of DNA. Every time a cell divides, a certain amount of DNA is lost from the ends of each chromosome. Imagine if every time you copied a file 4 kilobytes were lopped off the beginning and end of both copies. Telomeres are padding (again, they code HLT HLT HLT HLT HLT HLT HLT HLT HLT...) that can be lost without affecting the functioning of the cell.
    - MollyR 12y ago
      I do agree with you, that is the general scientific consensus. I made that statement vague because new data is emerging about the telomere network,so I'm not sure what is the current correct way to think about telomere's. Some new research papers are emerging that question the existing model we have about telomeres. http://journal.frontiersin.org/article/10.3389/fgene.2015.00082/full http://journal.frontiersin.org/article/10.3389/fgene.2015.00... Quote from that paper "summarizing recent research findings, Trusina (2014) conclude that recently obtained knowledge ‘shift the telomere paradigm from a simple clock counting cell divisions to a more complex process recording the history of stress exposure within a cell lineage.’ " So I find it reasonable to think that telomeres could be more than just padding, like a clock or history of stress exposure in a cell lineage.

by MollyR 12y ago

NathanKP 12y ago

According to the article: On average, each baby is born with roughly 100 new mutations. If every piece of the genome were essential, then many of those mutations would lead to significant birth defects, with the defects only multiplying over the course of generations; in less than a century, the species would become extinct. The point this article is making is that new techniques are finding that some portions of DNA assumed to be junk might have a use, and removing or changing them certainly does have an effect. But that doesn't mean we should jump ahead too far and say that none of the DNA is junk, because there are obviously some things that have no effect when changed.

simcop2387 12y ago
I wouldn't be surprised if some of it really has no effect and that's the whole point. As you mentioned if there's 100 new mutations per baby then if the coding is as dense as possible that means each mutation will cause some significant change. If it's got a lot of coding that doesn't do anything, by probabilities it'll likely not change anything important and cause no ill effects. Having that extra unused DNA could pose an evolutionary advantage in the face of an imperfect copying mechanism.
- ajuc 12y ago
  Assuming mutation probabiity don't depend on the length of the copied DNA - copying 40 MB you will probably introduce 10 times more mutations than if you just copied 4 MB. only 10% of them will on average change the important code, so the end result is the same. So I don't see how NOP padding helps.
kryptiskt 12y ago
I don't get it, there's no choice between everything being essential and lots of the genome being junk. Redundancy mechanisms like multiple copies of genes, which we know is there, reduces the risk of harm from mutations. Why can't most of the stuff in the genome have the label "useful, but we have backups", rather than "essential" or "junk"?
MollyR 12y ago
I see. That's a good point, its difficult to say if DNA has no junk. So I'm going to avoid the categorical issue, of junk,non junk,essential,redundant(but useful in a replication failure). maybe My thoughts are this, DNA is not used just for an individual survival but also a mechanism to allow adaptation at some higher level. Like how some deep learning AI's learn how to play games by making random moves and getting feedback from the score changing. For DNA, we get random mutations/moves in the form of transcription,replications errors or Meiosis , and the feedback comes from successful reproduction(surviving to play the game again). So what we call junk DNA, might actually play a large role in this sort of "learning" mechanism. I hope I explained that decently. A lot of my thoughts come from this book http://en.wikipedia.org/wiki/The_Selfish_Gene http://en.wikipedia.org/wiki/The_Selfish_Gene
sumitviii 12y ago
What if we have wild mutations AND exceptionally good exception handling?
- ajuc 12y ago
  We do. We have 2 mechanism for this. First mechanism - to go into production you have to pass unit tests (race to the egg). It's only 1 cell, so either it works or not, and if you were the fastest you probably didn't have most of the really bad mutations. Then after you are in production you run million copies of the code, and to be safe against mutations there's sth like erlang exception handling - if sth's wrong kill the process, start a new one. The problem is - sometimes the process gets so wrong it doesn't respond to kill signal.
  - sumitviii 12y ago
    >if you were the fastest you probably didn't have most of the really bad mutations How did they arrive at this conclusion?
    - ajuc 12y ago
      The mutations that makes your cell die will prevent you from being the first to the egg. The mutations that makes you immobile - the same. The mutation that mess up with your instincts, and reactions to chemical enzymes - same (you won't go the right way). And so on. It's a little like unit testing - it checks all the basic routines.

thaumasiotes 12y ago

> I highly doubt we have any junk dna Telomeres (the HLT HLT HLT HLT HLT... sequence at each end of a chromosome) are pretty well documented. They can be reasonably analogized to those 404 pages with a comment along the lines of  They're totally necessary if you don't want to quickly suffer a horrible death, but there's definitely also a sense in which they're junk.

MollyR 12y ago
I'm not sure of that analogy. Somehow telomeres are thought to connected to aging. http://www.progeriaresearch.org/cbs-monday-night.html http://www.progeriaresearch.org/cbs-monday-night.html Cancer cells can extend their telomeres, and are also immortal. I imagine them to be some sort of internal counter that other components of the system listen to. I guess I also have a hard time figuring out what people are trying to say when they call parts of the genome "junk". Perhaps what's "junk" is contextually dependent ? One human's trash is another human's treasure ?
- thaumasiotes 12y ago
  > Somehow telomeres are thought to [be] connected to aging The mechanism here isn't a mystery. As I originally pointed out, you'll die when your telomeres are gone from loss of DNA. Every time a cell divides, a certain amount of DNA is lost from the ends of each chromosome. Imagine if every time you copied a file 4 kilobytes were lopped off the beginning and end of both copies. Telomeres are padding (again, they code HLT HLT HLT HLT HLT HLT HLT HLT HLT...) that can be lost without affecting the functioning of the cell.
  - MollyR 12y ago
    I do agree with you, that is the general scientific consensus. I made that statement vague because new data is emerging about the telomere network,so I'm not sure what is the current correct way to think about telomere's. Some new research papers are emerging that question the existing model we have about telomeres. http://journal.frontiersin.org/article/10.3389/fgene.2015.00082/full http://journal.frontiersin.org/article/10.3389/fgene.2015.00... Quote from that paper "summarizing recent research findings, Trusina (2014) conclude that recently obtained knowledge ‘shift the telomere paradigm from a simple clock counting cell divisions to a more complex process recording the history of stress exposure within a cell lineage.’ " So I find it reasonable to think that telomeres could be more than just padding, like a clock or history of stress exposure in a cell lineage.