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A good metaphor describing gene-environment interactivity

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General fitness, health and nutrition
Published
15 March 2004
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20 March 2004
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Peter F.
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  1. Sample of a meaty metaphor found at
    www.edge.org/3rd_culture/marcus03/marcus_index.html "A gene
    is really not a dictator, but an opportunity, because each
    gene actually has two parts. Everybody knows a gene
    constructs a protein, but not everybody realizes that the
    other half of every gene is essentially what's called a
    regulatory region. It's essentially like an "if" in a
    computer program. Each gene is really like an if/then
    statement. There's a "then" that says, build this particular
    protein. It could be insulin in the pancreas, it could be
    hemoglobin in precursors to red blood cells, or it could be
    a particular protein for building a neuron in the brain. But
    when it does that, it is controlled by the "if" part of each
    gene. So there's an "if" and a "then."

    This seemingly very simple idea, a tiny little twist on the
    usual idea of thinking of a gene as coding for a particular
    protein, means that every gene has some kind of way it can
    respond to the environment, either inside the cell or
    outside the cell. So the "if" that controls whether a gene
    is turned on or not is responsive to chemical signals that
    are around a particular cell, and those chemical signals can
    be used for things like telling the cell where it is in the
    growing body so if it moves around it can adopt a new plan
    according to its new location. It also means that the
    external environment can, in principle, modify gene
    expression. Each gene becomes like a switch."

  2. Peter F. said:


    Sample of a meaty metaphor found at
    www.edge.org/3rd_culture/marcus03/marcus_index.html "A
    gene is really not a dictator, but an opportunity,
    because each gene actually has two parts. Everybody knows
    a gene constructs a protein, but not everybody realizes
    that the other half of every gene is essentially what's
    called a regulatory region. It's essentially like an "if"
    in a computer program. Each gene is really like an
    if/then statement. There's a "then" that says, build this
    particular protein. It could be insulin in the pancreas,
    it could be hemoglobin in precursors to red blood cells,
    or it could be a particular protein for building a neuron
    in the brain. But when it does that, it is controlled by
    the "if" part of each gene. So there's an "if" and a
    "then."

    This seemingly very simple idea, a tiny little twist on
    the usual idea of thinking of a gene as coding for a
    particular protein, means that every gene has some kind of
    way it can respond to the environment, either inside the
    cell or outside the cell. So the "if" that controls
    whether a gene is turned on or not is responsive to
    chemical signals that are around a particular cell, and
    those chemical signals can be used for things like telling
    the cell where it is in the growing body so if it moves
    around it can adopt a new plan according to its new
    location. It also means that the external environment can,
    in principle, modify gene expression. Each gene becomes
    like a switch."

    This sounds very reasonable to me, but I would like to know
    if it has been confirmed as fact, or is it a hypothesis?

    m

    --
    "Many are stubborn in pursuit of the path they have chosen,
    few in pursuit of the goal." - Friedrich Nietzsche

    annevolve.sourceforge.netannevolve.sourceforge.net is what I'm into
    nowadays. Humans may write to me at this address: zenguy
    at shaw dot ca

  3. Yes, only last week a news item relating to the idea that
    genes are not the sole determinant of protein expression,
    which has always been rather obvious given downstream
    processes. Thus, even if a gene or genes is\are being
    actively transcribed that does not mean that the protein
    generated is an inevitable consequence, all sorts of
    processes can change the final product.

    For an obvious example, consider that of the mutual
    antagonism between GR and NFkb. Sustained GR occupation will
    inhibit NFkb transcription, thereby preventing various
    transcription activities initiated by NFkb, amongst these
    being AP 1 protective gene responses, which in part explains
    why protracted expression of cortisol leads to all sorts of
    deleterious consequences.

    John H.

    [email hidden] wrote in message
    news:<[email hidden]>...

    Quoted message said:
    Peter F. said:


    Sample of a meaty metaphor found at
    www.edge.org/3rd_culture/marcus03/marcus_index.html "A
    gene is really not a dictator, but an opportunity,
    because each gene actually has two parts. Everybody
    knows a gene constructs a protein, but not everybody
    realizes that the other half of every gene is
    essentially what's called a regulatory region. It's
    essentially like an "if" in a computer program. Each
    gene is really like an if/then statement. There's a
    "then" that says, build this particular protein. It
    could be insulin in the pancreas, it could be
    hemoglobin in precursors to red blood cells, or it
    could be a particular protein for building a neuron in
    the brain. But when it does that, it is controlled by
    the "if" part of each gene. So there's an "if" and a
    "then."

    This seemingly very simple idea, a tiny little twist on
    the usual idea of thinking of a gene as coding for a
    particular protein, means that every gene has some kind
    of way it can respond to the environment, either inside
    the cell or outside the cell. So the "if" that controls
    whether a gene is turned on or not is responsive to
    chemical signals that are around a particular cell, and
    those chemical signals can be used for things like
    telling the cell where it is in the growing body so if
    it moves around it can adopt a new plan according to its
    new location. It also means that the external
    environment can, in principle, modify gene expression.
    Each gene becomes like a switch."

    This sounds very reasonable to me, but I would like to
    know if it has been confirmed as fact, or is it a
    hypothesis?

    m

  4. What I want to know is, is it known for certain that every
    gene fits the "If - Then" mode described by the OP.

    Mitchell Timin

    John H. said:


    Yes, only last week a news item relating to the idea that
    genes are not the sole determinant of protein expression,
    which has always been rather obvious given downstream
    processes. Thus, even if a gene or genes is\are being
    actively transcribed that does not mean that the protein
    generated is an inevitable consequence, all sorts of
    processes can change the final product.

    For an obvious example, consider that of the mutual
    antagonism between GR and NFkb. Sustained GR occupation
    will inhibit NFkb transcription, thereby preventing
    various transcription activities initiated by NFkb,
    amongst these being AP 1 protective gene responses, which
    in part explains why protracted expression of cortisol
    leads to all sorts of deleterious consequences.

    John H.

    [email hidden] wrote in message
    news:<[email hidden]>...

    Quoted message said:
    Peter F. said:


    Sample of a meaty metaphor found at
    www.edge.org/3rd_culture/marcus03/marcus_index.html
    "A gene is really not a dictator, but an opportunity,
    because each gene actually has two parts. Everybody
    knows a gene constructs a protein, but not everybody
    realizes that the other half of every gene is
    essentially what's called a regulatory region. It's
    essentially like an "if" in a computer program. Each
    gene is really like an if/then statement. There's a
    "then" that says, build this particular protein. It
    could be insulin in the pancreas, it could be
    hemoglobin in precursors to red blood cells, or it
    could be a particular protein for building a neuron
    in the brain. But when it does that, it is controlled
    by the "if" part of each gene. So there's an "if" and
    a "then."

    This seemingly very simple idea, a tiny little twist
    on the usual idea of thinking of a gene as coding for
    a particular protein, means that every gene has some
    kind of way it can respond to the environment, either
    inside the cell or outside the cell. So the "if" that
    controls whether a gene is turned on or not is
    responsive to chemical signals that are around a
    particular cell, and those chemical signals can be
    used for things like telling the cell where it is in
    the growing body so if it moves around it can adopt a
    new plan according to its new location. It also means
    that the external environment can, in principle,
    modify gene expression. Each gene becomes like a
    switch."

    This sounds very reasonable to me, but I would like to
    know if it has been confirmed as fact, or is it a
    hypothesis?

    m

    --
    "Many are stubborn in pursuit of the path they have chosen,
    few in pursuit of the goal." - Friedrich Nietzsche

    annevolve.sourceforge.netannevolve.sourceforge.net is what I'm into
    nowadays. Humans may write to me at this address: zenguy
    at shaw dot ca

  5. <[email hidden]> wrote in message

    Quoted message said:


    What I want to know is, is it known for certain that every
    gene fits > the


    "If - Then" mode described by the OP.

    Quoted message said:


    We know that regulation is extremely complex, and it is not
    well understood. The "lac" operon in E coli, for example, is
    induced by lactose. However its discovery didn't lead to a
    flood of anolgous systems in other species for other sugars.
    The upstream portion of the gene certainly plays a role in
    transcription control. However in genetically engineered
    organisms the easiest way to down-regulate protein
    expression is to add genes for antisense RNA. Homeobox genes
    are arranged in a linear order which matches the part of the
    body in which they are expressed, which must have something
    to do with the control system, though no-one has solved the
    puzzle. So yes, it is right to say that control is just as
    important as the sequence of the protein coded for. However
    it is too early to be sure what mechanisms are used.

  6. Quoted message said:

    What I want to know is, is it known for certain that every
    gene fits the "If - Then" mode described by the OP.

    Mitchell Timin

    A good metaphor, although

    Gene regulation is old news. Evolution of regulation is
    important in evolution, as you would expect. Some proteins
    are made essentially all the time, (constitutive expression)
    but clearly there are many others that you wouldn't want to
    make except at special times, such as when the substrate
    they act on is present.

    Other instances: Consider fetal hemoglobin. The gene for it
    is in your cells all your life, but it is only made while
    you are a fetus.

    Differential gene expression makes the difference between a
    liver cell and neuron.

    links mansfield.ohio-mansfield.ohio-
    state.edu/~sabedon/biol1070.htm

    ndsu.nodak.eduprokaryo
    /prokaryo2.htm

    Dunk

  7. "Malcolm" <[email hidden]> wrote in message
    "]news:[email hidden]...

    Quoted message said:


    <[email hidden]> wrote in message

    Quoted message said:


    What I want to know is, is it known for certain that
    every gene fits >


    the

    Quoted message said:

    "If - Then" mode described by the OP.

    Quoted message said:


    We know that regulation is extremely complex, and it is
    not well


    understood.

    Quoted message said:

    The "lac" operon in E coli, for example, is induced by
    lactose. However


    its

    Quoted message said:

    discovery didn't lead to a flood of anolgous systems in
    other species for other sugars. The upstream portion of
    the gene certainly plays a role in transcription control.
    However in genetically engineered organisms the easiest
    way to down-regulate protein expression is to add genes
    for antisense RNA.


    Homeobox

    Quoted message said:

    genes are arranged in a linear order which matches the
    part of the body in which they are expressed, which must
    have something to do with the control system, though no-
    one has solved the puzzle. So yes, it is right to say that
    control is just as important as the


    sequence

    Quoted message said:

    of the protein coded for. However it is too early to be
    sure what


    mechanisms

    Quoted message said:

    are used.

    If you (especially [email hidden] ) have a chance,
    read the article on p. 42 in the March 6, 04, issue of New
    Scientist, titled Genomes Don't Play Dice. Blurb copied from
    from the NS website: "Genetic mutations may be the bread and
    butter of evolution, but genomes know better than to leave
    those fateful changes to chance alone".

    This great article will give you a feel for the awesomeness
    of what is is going!

    P

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