A good metaphor describing gene-environment interactivity



P

Peter F.

Guest
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."
 
S

SeeBelow

Guest
"Peter F." wrote:
>
> 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

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

John H.

Guest
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 protected] wrote in message
news:<[email protected]>...
> "Peter F." wrote:
> >
> > 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
 
S

SeeBelow

Guest
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." wrote:
>
> 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 protected] wrote in message
> news:<[email protected]>...
> > "Peter F." wrote:
> > >
> > > 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

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

Malcolm

Guest
<[email protected]> wrote in message
>
> What I want to know is, is it known for certain that every
> gene fits > the
"If - Then" mode described by the OP.
>
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.
 
D

Dunk

Guest
On Wed, 17 Mar 2004 15:57:11 +0000 (UTC), [email protected] wrote:

>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 http://www.mansfield.ohio-
state.edu/~sabedon/biol1070.htm

http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/prokaryo-
/prokaryo2.htm

Dunk
 
P

Peter F.

Guest
"Malcolm" <[email protected]> wrote in message
news:[email protected]...
>
> <[email protected]> wrote in message
> >
> > What I want to know is, is it known for certain that
> > every gene fits >
the
> "If - Then" mode described by the OP.
> >
> 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.

If you (especially [email protected] ) 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