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  1. #21
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    It's also important to note that much of our genome (90 odd %) consists of non-coding DNA (what's known as junk DNA). Some sections might be necessary... but the sequence of these are not. The amount of random mutation arising in these segments can also be used to track time.
    As a side note, figuring out what, if anything, "junk DNA" does is something being researched at the moment, since it otherwise seems strange that so much of DNA would not be being used. the amount of junk DNA also tends to increase with organism complexity, from what I've heard, while the amount of genes do not, which suggests ot a lot of people that it has some other important functuions that haven't been worked out yet, that do not involve proteins.

  2. #22
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    Quote Originally Posted by Zergling View Post
    As a side note, figuring out what, if anything, "junk DNA" does is something being researched at the moment, since it otherwise seems strange that so much of DNA would not be being used. the amount of junk DNA also tends to increase with organism complexity, from what I've heard, while the amount of genes do not, which suggests ot a lot of people that it has some other important functuions that haven't been worked out yet, that do not involve proteins.
    one theory has to do with evolution: that people/all creatures are essentially made of different insensate cells which got together, because it was beneficial for them. In time, as the whole organism evolved, some of these unnecessary cells lost their function (like the human appendix), but their genome still remains within, becoming 'junk DNA' (otherwise known as non-sense DNA).

    The other thing that is interesting is this: diseases which kill, tend to start from the ends of the cells. Also, all cells die natural programmed deaths: there is a time frame for life. The process is known as apoptosis: programmed cellular death. Enzymes known as telomerases are responsible for 'eating' up DNA sequences.

    It is because of this that we have death. Since on a micro-level, what is death but the loss of genes.

    Man seeks for immortality. But the only cells that are immortal are cancer cells. Their telomerases have stopped functioning. So cancer cells are the only ones that grow and grow, and live forever. (perhaps poetry has it right, intuitively: that death is the only immortal thing. Ironically, immortality is to be found in what brings death.)

    Which brings us back to junk DNA. Quite a large proportion of them are found at the end of the cells. So when the telomerases start eating up DNA, these go first. In essence, they become infantry soldiers who fall first in the line of fire, such that the important leaders (ie, the sense DNA) are still protected for a while.

    That's one postulated function.
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  3. #23
    ish red no longer *sad* nightning's Avatar
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    Quote Originally Posted by Zergling View Post
    As a side note, figuring out what, if anything, "junk DNA" does is something being researched at the moment, since it otherwise seems strange that so much of DNA would not be being used. the amount of junk DNA also tends to increase with organism complexity, from what I've heard, while the amount of genes do not, which suggests ot a lot of people that it has some other important functuions that haven't been worked out yet, that do not involve proteins.
    True... but there are also DNA elements within called transposons, or the jumping genes (not really genes at all ). They cut and paste themselves within the genome (can probably duplicate themselves as well). Scientists are not exactly sure whether transposons in the cell does anything useful. The common hypothesis is that these are parasitics DNA sequences that rides on the organism's genome. The cell evolved mechanisms to "tolerate" these parasites. When transposons manages to insert themselves into coding regions... the cell has enzymes that removes the offensives junk from the mRNA so that only proper proteins are expressed... Sometimes the transposons are "bad" and the cell fails to remove the junk... in that case you get diseases.

    That's the theory I prescribed to anyhow... It's interesting to note that the more complex the organism, the more of these transposons exists in the genome. Also that much of the non-coding regions consists of short sequences repeated over and over again. They might be spacers necessary for DNA histone folding (how DNA is packaged up into chromosomes)... but some of those can also be mutated transposons.

  4. #24

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    Quote Originally Posted by nightning View Post
    True... but there are also DNA elements within called transposons, or the jumping genes (not really genes at all ). They cut and paste themselves within the genome (can probably duplicate themselves as well). Scientists are not exactly sure whether transposons in the cell does anything useful. The common hypothesis is that these are parasitics DNA sequences that rides on the organism's genome. The cell evolved mechanisms to "tolerate" these parasites. When transposons manages to insert themselves into coding regions... the cell has enzymes that removes the offensives junk from the mRNA so that only proper proteins are expressed... Sometimes the transposons are "bad" and the cell fails to remove the junk... in that case you get diseases.

    That's the theory I prescribed to anyhow... It's interesting to note that the more complex the organism, the more of these transposons exists in the genome. Also that much of the non-coding regions consists of short sequences repeated over and over again. They might be spacers necessary for DNA histone folding (how DNA is packaged up into chromosomes)... but some of those can also be mutated transposons.
    Ar these pathological versions of Homeobox genes?

    From a computer geek's perspective... Self-modifying code can pack a lot more useful information than in the same amount of static code.

    Also, continuing with the analogy with the genetic algorithms, it was found that putting genes in the algorithm that modify other genes in our virtual chromosomes makes punctuated equilibrium in the population of solutions more likely (my theory is that the fitness landscape changes with these genes to have multiple plateaus).

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  5. #25
    ish red no longer *sad* nightning's Avatar
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    Quote Originally Posted by ygolo View Post
    Ar these pathological versions of Homeobox genes?

    From a computer geek's perspective... Self-modifying code can pack a lot more useful information than in the same amount of static code.

    Also, continuing with the analogy with the genetic algorithms, it was found that putting genes in the algorithm that modify other genes in our virtual chromosomes makes punctuated equilibrium in the population of solutions more likely (my theory is that the fitness landscape changes with these genes to have multiple plateaus).
    Hmmmm could be convergent evolution by these two sets of genes. I'm not sure. My guess is they share similarities but have arisen differently. Homeobox genes evolved to serve the cell, transposon evolved to serve itself.

    Self-modifying code... Hmmmm the question is how do you get it to modify the way you want it so that it will do what you want it to when placed under a changing environment in which you have no control over?

  6. #26

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    Quote Originally Posted by nightning View Post
    Hmmmm could be convergent evolution by these two sets of genes. I'm not sure. My guess is they share similarities but have arisen differently. Homeobox genes evolved to serve the cell, transposon evolved to serve itself.
    So what is your take on Richard Dawkins' notion of "selfish genes." Couldn't it be said that even the genes that don't harm the host organism are acting out of self-preservation. No?

    Quote Originally Posted by nightning View Post
    Self-modifying code... Hmmmm the question is how do you get it to modify the way you want it so that it will do what you want it to when placed under a changing environment in which you have no control over?
    That, in practice, turns out to not be too different from having static code do what is desired under environments where we have no control. Well-designed self-modifying code tends to be as robust as well-designed static code. However, the space savings can be immense. The usual place where I use it is in embedded systems for creating polymorphic interrupt behavior. Many hackers also use polymorphism of this sort to bypass security features and hide viruses. This unfortunately gives the technique a bad rep.

    (If you couldn't tell by now, I am fascinated with the links between biology and computing)

    Accept the past. Live for the present. Look forward to the future.
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    "[A] scientist looking at nonscientific problems is just as dumb as the next guy." Richard Feynman
    "[P]etabytes of [] data is not the same thing as understanding emergent mechanisms and structures." Jim Crutchfield

  7. #27
    ish red no longer *sad* nightning's Avatar
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    Quote Originally Posted by ygolo View Post
    So what is your take on Richard Dawkins' notion of "selfish genes." Couldn't it be said that even the genes that don't harm the host organism are acting out of self-preservation. No?
    I'm afraid I've been "brain washed" early in my scientific career on the selfish gene theory. (I can only blame my 1st year biology prof on it... crazy Rosie... a brilliant geneticist... but still crazy.) I prescribe fully to that line of thinking. The purpose in life for everything... even down to sequences of DNA is to survive... Obviously nothing last forever... it decays, decomposes, breaks down, whatever. So to keep on living forever, you make copies of yourself... from the "baby genes" to "mini mes". Inertia more or less applies to everything... even genes are "lazy". Why do more work than you have to? Forget about extra enzymes... The shorter your sequence... the faster you can replicate yourself... Being able to make 3 copies of yourself in the time your opponent can make 2 is so much better. Afterall resources are limited.

    Some genes (like the transposons and viruses) op for the parasite route... piggy back themselves on the suckers. Other genes rather prefer to cooperate to ensure their own survival. (Sure, your rate of replication will be slower, but at least you guarentee you survive to leave some copies.

    It's not much different than survival strategies of many animal species... a sort of gull for example. Some hunt their own fish, other steals it from the hunters. It's game theory played out in the biological world. I have more than a passing interest on this topic.


    That, in practice, turns out to not be too different from having static code do what is desired under environments where we have no control. Well-designed self-modifying code tends to be as robust as well-designed static code. However, the space savings can be immense. The usual place where I use it is in embedded systems for creating polymorphic interrupt behavior. Many hackers also use polymorphism of this sort to bypass security features and hide viruses. This unfortunately gives the technique a bad rep.

    (If you couldn't tell by now, I am fascinated with the links between biology and computing)
    Ah! Object oriented programming... I've always been meaning to learn more about it. But never gotten the time and energy to do so. Yes... I see what you mean now.

    Biological systems and computing, if I know more about computing perhaps I would be too. I like dynamic system interactions. ^^

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