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Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy

Non-biologist here. It would seem to reason that since non-coding DNA has a role in RNA manufacturing, it would be susceptible to resonance from specific energy signals that would invoke its expression, effectively appending new information to RNA. Once propagated that information made be difficult to subdue. Maybe an analogy is an unexpected object being written to a pubsub topic. Each consumer may have different side-effects based on that object depending on how well they validate the message. Some will properly ignore it or throw an error, but others may yield a proper side effect where one should be, or even a malformed side effect. In any case, once it’s in the log it’s really hard to get rid of, short of replaying the topic to a new stream that filters out that data. This is truly clueless conjecture. This noncoding DNA stuff is fascinating; a rare bit of unexplored territory in science that seems to be coming into focus. I think as scientific methods mature around system dynamics and emergence these types of complex behaviors are finally going to be better understood.

refurb 7y ago
resonance from specific energy signals Did you have something more specific in mind?
- reilly3000 7y ago
  Unfortunately no. The article and other literature I could find in my recent googling suggested that free radicals may have something to do with it, but more generally it seems that gene expression is often conditional. Some genetic markers go expressed in some but not in others. Some only express under conditions of chronic stress or specific toxins. The only thing you might be able to say is that merely having information in your genome doesn’t guarantee it will ever be used, but what causes it to be used varies per circumstances that may vary for each type.
  - reilly3000 7y ago
    I’ll also add that I mean “resonance from specific energy signals” in the most general sense possible, not ‘quantum woo woo’. Like a lock opening when a matching key is inserted and rotated. You want the lock to open with means motion; resonance is motion in response to specific energy, not general energy. It may be awkward to refer to the ridges of a key as energy, but it is in an abstract and absolute sense. My only formal training is in acoustics to that’s part of my lexicon.
astazangasta 7y ago
This is what my thesis is about (I titled it "Rehabilitating Junk DNA"). It isn't that complicated. Your resonance comment is gibberish, sorry. The DNA is a giant tape in base 4 (ATGC). There are programs written at random places on the tape that in a 64 bit encoding (i.e. triplets of quaternary bits). This is "coding sequence", about 1% of the genome (itself 3 gigabases, so 30 Mbases of coding sequence). A tape head (polymerase) comes and reads these out into RNA. The RNA is like a flash copy that is sent to a compiler (ribosome) that translates it into a working protein molecule (a sequence of 20 amino acids with the mapping encoded in base 64, see "genetic code"). There are control sequences proximal (~within 30k bases) to each program that tell the tape head when and how much to read each program into flash (i.e., transcribe RNA). These control sequences are in the 99% non-coding part of the genome. In my thesis i estimated about another 1% is actual control sequence. The rest may be random noise, we'll see.
- reilly3000 7y ago
  Fascinating, thanks for breaking it down into data structures.
- klmr 7y ago
  Nice explanation but you seem to be saying that at most 3% (being generous) of DNA would be functional (if the rest is “random noise”). This number is over twice as small as the lowest estimate (~ 8%) of even the most fervent critics of ENCODE’s number. I’d love to hear a brief break-down of your reasons, if possible.
  - mnw21cam 7y ago
    As an added complication, a decent proportion of DNA in the genome is meaningful at least in how long it is, because it separates two functional pieces of DNA that interact in 3D space due to the way the DNA wraps around other stuff. If you change the content of this DNA, it doesn't cause disease, but if you change the length, it does.
  - astazangasta 7y ago
    Eh, I graduated in 2008. ENCODE was only a pilot yet. We didn't know about lincRNAs. My estimate was based on multi-species sequence alignments so it is pretty conservative. At the time it was not, however; it was doubling the amount of functional sequence. To be honest i am not sure what the current best estimates are based on (i switched fields). 8% seems absurdly high to me, but there is a ton more evidence now than i had.
j7ake 7y ago
A simpler and perhaps more useful way of thinking of non coding DNA is to use analogy of a recipe. Coding DNA tells you the ingredients used, noncoding tells you when and how to use those ingredients. Both are essential to proper gene regulation, but one is much harder to study.

refurb 7y ago

resonance from specific energy signals Did you have something more specific in mind?

reilly3000 7y ago
Unfortunately no. The article and other literature I could find in my recent googling suggested that free radicals may have something to do with it, but more generally it seems that gene expression is often conditional. Some genetic markers go expressed in some but not in others. Some only express under conditions of chronic stress or specific toxins. The only thing you might be able to say is that merely having information in your genome doesn’t guarantee it will ever be used, but what causes it to be used varies per circumstances that may vary for each type.
- reilly3000 7y ago
  I’ll also add that I mean “resonance from specific energy signals” in the most general sense possible, not ‘quantum woo woo’. Like a lock opening when a matching key is inserted and rotated. You want the lock to open with means motion; resonance is motion in response to specific energy, not general energy. It may be awkward to refer to the ridges of a key as energy, but it is in an abstract and absolute sense. My only formal training is in acoustics to that’s part of my lexicon.

astazangasta 7y ago

This is what my thesis is about (I titled it "Rehabilitating Junk DNA"). It isn't that complicated. Your resonance comment is gibberish, sorry. The DNA is a giant tape in base 4 (ATGC). There are programs written at random places on the tape that in a 64 bit encoding (i.e. triplets of quaternary bits). This is "coding sequence", about 1% of the genome (itself 3 gigabases, so 30 Mbases of coding sequence). A tape head (polymerase) comes and reads these out into RNA. The RNA is like a flash copy that is sent to a compiler (ribosome) that translates it into a working protein molecule (a sequence of 20 amino acids with the mapping encoded in base 64, see "genetic code"). There are control sequences proximal (~within 30k bases) to each program that tell the tape head when and how much to read each program into flash (i.e., transcribe RNA). These control sequences are in the 99% non-coding part of the genome. In my thesis i estimated about another 1% is actual control sequence. The rest may be random noise, we'll see.

reilly3000 7y ago
Fascinating, thanks for breaking it down into data structures.
klmr 7y ago
Nice explanation but you seem to be saying that at most 3% (being generous) of DNA would be functional (if the rest is “random noise”). This number is over twice as small as the lowest estimate (~ 8%) of even the most fervent critics of ENCODE’s number. I’d love to hear a brief break-down of your reasons, if possible.
- mnw21cam 7y ago
  As an added complication, a decent proportion of DNA in the genome is meaningful at least in how long it is, because it separates two functional pieces of DNA that interact in 3D space due to the way the DNA wraps around other stuff. If you change the content of this DNA, it doesn't cause disease, but if you change the length, it does.
- astazangasta 7y ago
  Eh, I graduated in 2008. ENCODE was only a pilot yet. We didn't know about lincRNAs. My estimate was based on multi-species sequence alignments so it is pretty conservative. At the time it was not, however; it was doubling the amount of functional sequence. To be honest i am not sure what the current best estimates are based on (i switched fields). 8% seems absurdly high to me, but there is a ton more evidence now than i had.

j7ake 7y ago

A simpler and perhaps more useful way of thinking of non coding DNA is to use analogy of a recipe. Coding DNA tells you the ingredients used, noncoding tells you when and how to use those ingredients. Both are essential to proper gene regulation, but one is much harder to study.