While I was working out in the greenhouse i may have answered one of my own
questions/assumptions:

Because the gene group responsible for 'making flowers' is a gene group that
has been in the 'gene pool' for millions of years and copied itself into may
various organisms, it has moved around and changed alot. The various gene
components have separated from each other, crossed onto different
chromosomes, developed mutations, etc. So the group may still work to 'make
flowers' in all the species that make flowers. However, comparing the
templates of, say, an oak tree and a petunia even the discerning viewer
would not recognize a common gene structure that was responsible for this
task? The genes to 'make flowers' are still there but they don't look the
same from template to template? I think one big mystery is that they
continue to do the same thing even though they have changed so much. Is
this right? Or is too simple?

Still there has to be something to the idea that the gene group responsible
for making flowers in all species that makes flowers has common features
across the spectrum of species templates?

I've got a headache.

"Al" wrote in message
om...
When you are looking a gene map, you are looking at a template for
making an individual that has been copied, (added to and slightly
rearranged and altered) from every individual ancestor from which it
has descended? So it seems that across species, genera and families
of organisms, the groups of genes that do something which helps the
individual pass those genes would have a common look and function
across the broad spectrum of creatures they create? These are
questions? :-)

Have a group of genes been found in plants that are only found in
plants which produce flowers? Have a group of genes been found in
orchids that are not found in any other flowering plants? Wouldn't
such a finding indicate that the gene group is responsible for
something that happens in flowering plants but not in other plants, or
in orchids but not in other flowering plants?

How do they find genes? Is it possible (yet) for a trained
botanist/geneticist to look at a bunch of genes and tell if it is a
gymnosperm or an angiosperm? That identifying structure he/she is
looking for being a thing common to all angiosperms but that is not
present in gymnosperms?

Did the flowering organ in plants develop in many different unrelated
species of non-flowering plants, and therefore maybe be relatively
uneasy to compare and identify in other flowering plant's genes?

I am sure gene groups that do the same thing in different animals are
moved all over the place in the various species they construct and may
not even stay together on the same chromosome even if they perform the
same function, so it follows that the relatedness of species and
individuals has something to do with where known gene groups are
located in the templates when compared to each other?

I would guess that the genes of plants would travel through time and
species the same way they travel through the genes of the animal
kingdom. A group of genes that performs a specific function in any
organism descended from a previous ancestor would be found in some
form in all species that, like the hox box gene that determines the
development of appendages in fetus. Can genes that 'make a flower' or
"make a fused reproductive organ called a column" be located by
comparing and contrasting genes from many species?

I think there is a common question in all of these questions. There
certainly seems to be a set of assumptions which I do not even know to
be correct.

I am genetically incapable of writing tight concise short sentences.
The same gene responsible for this behavioral trait is what makes
my... well, never mind...

Al






Rob Halgren wrote in message
...


Take your time to assimilate. We'll still be here and happy to help.
But
please don't slander yourself again like that. It is NOT futile. Way
back,
many many years ago, when I was teaching, I would rebuke any student
who
made such a remark, encouraging them to have more confidence. You can
learn
and understand anything you wish, if you are honestly trying. If, in
such a
circumstance, you don't understand something I have said, the fault is
mine;
not yours.



That is my philosophy too. Glad to see there are other people who
actually care about teaching out there. If you didn't understand me, it
was because I didn't use the right words. There are exceptions for
people who just don't listen, but you can't teach them anything they
don't already know anyway.

Rob

While I was working out in the greenhouse i may have answered one of my own
questions/assumptions:

Because the gene group responsible for 'making flowers' is a gene group that
has been in the 'gene pool' for millions of years and copied itself into may
various organisms, it has moved around and changed alot. The various gene
components have separated from each other, crossed onto different
chromosomes, developed mutations, etc. So the group may still work to 'make
flowers' in all the species that make flowers. However, comparing the
templates of, say, an oak tree and a petunia even the discerning viewer
would not recognize a common gene structure that was responsible for this
task? The genes to 'make flowers' are still there but they don't look the
same from template to template? I think one big mystery is that they
continue to do the same thing even though they have changed so much. Is
this right? Or is too simple?

Still there has to be something to the idea that the gene group responsible
for making flowers in all species that makes flowers has common features
across the spectrum of species templates?

I've got a headache.

"Al" wrote in message
om...
When you are looking a gene map, you are looking at a template for
making an individual that has been copied, (added to and slightly
rearranged and altered) from every individual ancestor from which it
has descended? So it seems that across species, genera and families
of organisms, the groups of genes that do something which helps the
individual pass those genes would have a common look and function
across the broad spectrum of creatures they create? These are
questions? :-)

Have a group of genes been found in plants that are only found in
plants which produce flowers? Have a group of genes been found in
orchids that are not found in any other flowering plants? Wouldn't
such a finding indicate that the gene group is responsible for
something that happens in flowering plants but not in other plants, or
in orchids but not in other flowering plants?

How do they find genes? Is it possible (yet) for a trained
botanist/geneticist to look at a bunch of genes and tell if it is a
gymnosperm or an angiosperm? That identifying structure he/she is
looking for being a thing common to all angiosperms but that is not
present in gymnosperms?

Did the flowering organ in plants develop in many different unrelated
species of non-flowering plants, and therefore maybe be relatively
uneasy to compare and identify in other flowering plant's genes?

I am sure gene groups that do the same thing in different animals are
moved all over the place in the various species they construct and may
not even stay together on the same chromosome even if they perform the
same function, so it follows that the relatedness of species and
individuals has something to do with where known gene groups are
located in the templates when compared to each other?

I would guess that the genes of plants would travel through time and
species the same way they travel through the genes of the animal
kingdom. A group of genes that performs a specific function in any
organism descended from a previous ancestor would be found in some
form in all species that, like the hox box gene that determines the
development of appendages in fetus. Can genes that 'make a flower' or
"make a fused reproductive organ called a column" be located by
comparing and contrasting genes from many species?

I think there is a common question in all of these questions. There
certainly seems to be a set of assumptions which I do not even know to
be correct.

I am genetically incapable of writing tight concise short sentences.
The same gene responsible for this behavioral trait is what makes
my... well, never mind...

Al






Rob Halgren wrote in message
...


Take your time to assimilate. We'll still be here and happy to help.
But
please don't slander yourself again like that. It is NOT futile. Way
back,
many many years ago, when I was teaching, I would rebuke any student
who
made such a remark, encouraging them to have more confidence. You can
learn
and understand anything you wish, if you are honestly trying. If, in
such a
circumstance, you don't understand something I have said, the fault is
mine;
not yours.



That is my philosophy too. Glad to see there are other people who
actually care about teaching out there. If you didn't understand me, it
was because I didn't use the right words. There are exceptions for
people who just don't listen, but you can't teach them anything they
don't already know anyway.

Rob

The January issue of Scientific American had an article about mRNA or other
genetic material and its influence on things like schzophrenia etc. i got
the issue in audio format, so I can listen in the GH, however I find it
difficult to concentrate on something so minute while orchiding. It will
have to wait for a long car trip when I can listen in peace without engaging
my mind... like while driving, *G*

K Barrett
(apropos of nothing)

"Al" wrote in message
...
While I was working out in the greenhouse i may have answered one of my
own
questions/assumptions:

Because the gene group responsible for 'making flowers' is a gene group
that
has been in the 'gene pool' for millions of years and copied itself into
may
various organisms, it has moved around and changed alot. The various
gene
components have separated from each other, crossed onto different
chromosomes, developed mutations, etc. So the group may still work to
'make
flowers' in all the species that make flowers. However, comparing the
templates of, say, an oak tree and a petunia even the discerning viewer
would not recognize a common gene structure that was responsible for this
task? The genes to 'make flowers' are still there but they don't look the
same from template to template? I think one big mystery is that they
continue to do the same thing even though they have changed so much. Is
this right? Or is too simple?

Still there has to be something to the idea that the gene group
responsible
for making flowers in all species that makes flowers has common features
across the spectrum of species templates?

I've got a headache.

"Al" wrote in message
om...
When you are looking a gene map, you are looking at a template for
making an individual that has been copied, (added to and slightly
rearranged and altered) from every individual ancestor from which it
has descended? So it seems that across species, genera and families
of organisms, the groups of genes that do something which helps the
individual pass those genes would have a common look and function
across the broad spectrum of creatures they create? These are
questions? :-)

Have a group of genes been found in plants that are only found in
plants which produce flowers? Have a group of genes been found in
orchids that are not found in any other flowering plants? Wouldn't
such a finding indicate that the gene group is responsible for
something that happens in flowering plants but not in other plants, or
in orchids but not in other flowering plants?

How do they find genes? Is it possible (yet) for a trained
botanist/geneticist to look at a bunch of genes and tell if it is a
gymnosperm or an angiosperm? That identifying structure he/she is
looking for being a thing common to all angiosperms but that is not
present in gymnosperms?

Did the flowering organ in plants develop in many different unrelated
species of non-flowering plants, and therefore maybe be relatively
uneasy to compare and identify in other flowering plant's genes?

I am sure gene groups that do the same thing in different animals are
moved all over the place in the various species they construct and may
not even stay together on the same chromosome even if they perform the
same function, so it follows that the relatedness of species and
individuals has something to do with where known gene groups are
located in the templates when compared to each other?

I would guess that the genes of plants would travel through time and
species the same way they travel through the genes of the animal
kingdom. A group of genes that performs a specific function in any
organism descended from a previous ancestor would be found in some
form in all species that, like the hox box gene that determines the
development of appendages in fetus. Can genes that 'make a flower' or
"make a fused reproductive organ called a column" be located by
comparing and contrasting genes from many species?

I think there is a common question in all of these questions. There
certainly seems to be a set of assumptions which I do not even know to
be correct.

I am genetically incapable of writing tight concise short sentences.
The same gene responsible for this behavioral trait is what makes
my... well, never mind...

Al






Rob Halgren wrote in message
...


Take your time to assimilate. We'll still be here and happy to help.
But
please don't slander yourself again like that. It is NOT futile.
Way
back,
many many years ago, when I was teaching, I would rebuke any student
who
made such a remark, encouraging them to have more confidence. You
can
learn
and understand anything you wish, if you are honestly trying. If, in
such a
circumstance, you don't understand something I have said, the fault
is
mine;
not yours.



That is my philosophy too. Glad to see there are other people who
actually care about teaching out there. If you didn't understand me,
it
was because I didn't use the right words. There are exceptions for
people who just don't listen, but you can't teach them anything they
don't already know anyway.

Rob

Al, I hope the head ache is a little better and this does not make it much
worst. If this does, just remember I'm a farmer who is out of date (while
writing this I am referring to a book coauthered by Watson) and has
forgotten most of what I learned about this sort of stuff.

That being said, I think you are thinking on much to simple of terms. I
think it is a mistake to think in terms of flower templates just as I would
not call a complex computer program a template. The making of a flower is
more a process with genes being turned on and off at different times and the
various proteins produced interacting with each other.

A gene is a template for a protein. There is DNA transcription to RNA which
is translated into a protein or an enzyme (which is itself a proteins). At
the underclass level each gene is a template for a unique protein. If there
is a protein that is in all flowers and only in flower tissue, we could find
the gene associated with this protein and all flowering plants would have
this gene in their DNA. Problem is a non flowering plant could also have
this gene, but never turn it on.

A flower is probably composed of 100's of proteins (50 to 1000 is a good
guess, I do not know if counts have been made). To make a flower these
proteins must be made at the right time, in the right mix, and at the right
place. I do not think anyone really has a grasp on how this is all
controlled, but I think people have played with gene precursors to affect
the number of petals produced on a flower.

When you are working in the lab with a piece of undifferentiated tissue, one
hormone will cause it to grow into a plant while another will cause it to
grow into a flower. I think this fits into this discussion, but I am not
sure how or why.


Pat B

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part of a
gene and thus only a small percent is used in the coding for protein. If you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .

One of the things science has been doing is gene mapping, finding which
chromosome and where on the chromosome a gene is located. But, the largest
percent DNA material will fall into the trash category.

About ten years ago (I am very out of date) I attended a seminar discussing
this "trash" DNA. (If they can not explain it, it must be trash --ha) One
theory was tied to evolution where some of the trash contained coding used
by ancient ancestors and no longer used. The same theory speculated that
coding that will be used in some future evolved generation is sitting in the
trash waiting to be turned on. Thus if a flowering plant evolved into a non
flowering plant, the non flowering plant could still carry the coding for a
protein required in a flower.

I do not think it is very likely some non flowering species is going to
evolve into an orchid. In an evolutionary time scale, I expect new orchid
species will result from current orchid species adapting to new niches and
global changes.

Pat


"J Fortuna" wrote in message
...
Pat,

Thanks for this info. I have been following this thread closely, though I
only understand some of it, but I wish I understood all!nna,

One thought occurred to me after reading your statement:
If there is a protein that is in all flowers and only in flower tissue,
we
could find
the gene associated with this protein and all flowering plants would
have
this gene in their DNA. Problem is a non flowering plant could also
have
this gene, but never turn it on.
So does this mean that there could be a plant somewhere out there that is
currently a non-flowering, purely-leafy plant, but if a descendent of this
plant turned on the flowering gene it might actually flower, and we might
get a completely new orchid species? I think I read somewhere that orchids
are mainly or only identifiable as orchids because of the flowers, and so
I
am thinking that there could be a plant species out there that would be an
orchid if only it did flower but it never does.

Does this make sense, or should I just go back to open-mouthed lurker
status
on the continuation of this fascinating thread?

Thanks,
Joanna

"Pat Brennan" wrote in message
...
Al, I hope the head ache is a little better and this does not make it
much
worst. If this does, just remember I'm a farmer who is out of date
(while
writing this I am referring to a book coauthered by Watson) and has
forgotten most of what I learned about this sort of stuff.

That being said, I think you are thinking on much to simple of terms. I
think it is a mistake to think in terms of flower templates just as I
would
not call a complex computer program a template. The making of a flower
is
more a process with genes being turned on and off at different times and
the
various proteins produced interacting with each other.

A gene is a template for a protein. There is DNA transcription to RNA
which
is translated into a protein or an enzyme (which is itself a proteins).
At
the underclass level each gene is a template for a unique protein. If
there
is a protein that is in all flowers and only in flower tissue, we could
find
the gene associated with this protein and all flowering plants would
have
this gene in their DNA. Problem is a non flowering plant could also
have
this gene, but never turn it on.

A flower is probably composed of 100's of proteins (50 to 1000 is a good
guess, I do not know if counts have been made). To make a flower these
proteins must be made at the right time, in the right mix, and at the
right
place. I do not think anyone really has a grasp on how this is all
controlled, but I think people have played with gene precursors to
affect
the number of petals produced on a flower.

When you are working in the lab with a piece of undifferentiated tissue,
one
hormone will cause it to grow into a plant while another will cause it
to
grow into a flower. I think this fits into this discussion, but I am
not
sure how or why.


Pat B

"Rob Halgren" wrote in message
...
Pat Brennan wrote:

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part
of a
gene and thus only a small percent is used in the coding for protein. If
you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .



Actually, in plants it looks more like this:
"trash".precursor.part1ofgene.junk.part2ofgene.jun k.part3ofgene.junk".
There is a whole lot of nothin' that breaks up the actual coding parts
of a lot of genes. Those are called introns, and I don't know that
anybody knows what they are for, either. Bacteria don't have them and
they get along just fine.

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?" or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene? or "How is the correct sequence of
introns in the gene stored and later recovered for use?" or "Does all this
happen in the nucleus?" or "How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?" or "Do the proteins within a chromosome have a role in any of
this, and if so, what?" Do you know if any progress has been made in
addressing any of these questions?

Cheers,

Ted

"Rob Halgren" wrote in message
...
Pat Brennan wrote:

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part
of a
gene and thus only a small percent is used in the coding for protein. If
you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .



Actually, in plants it looks more like this:
"trash".precursor.part1ofgene.junk.part2ofgene.jun k.part3ofgene.junk".
There is a whole lot of nothin' that breaks up the actual coding parts
of a lot of genes. Those are called introns, and I don't know that
anybody knows what they are for, either. Bacteria don't have them and
they get along just fine.

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?" or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene? or "How is the correct sequence of
introns in the gene stored and later recovered for use?" or "Does all this
happen in the nucleus?" or "How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?" or "Do the proteins within a chromosome have a role in any of
this, and if so, what?" Do you know if any progress has been made in
addressing any of these questions?

Cheers,

Ted

"Rob Halgren" wrote in message
...
Pat Brennan wrote:

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part
of a
gene and thus only a small percent is used in the coding for protein. If
you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .



Actually, in plants it looks more like this:
"trash".precursor.part1ofgene.junk.part2ofgene.jun k.part3ofgene.junk".
There is a whole lot of nothin' that breaks up the actual coding parts
of a lot of genes. Those are called introns, and I don't know that
anybody knows what they are for, either. Bacteria don't have them and
they get along just fine.

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?" or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene? or "How is the correct sequence of
introns in the gene stored and later recovered for use?" or "Does all this
happen in the nucleus?" or "How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?" or "Do the proteins within a chromosome have a role in any of
this, and if so, what?" Do you know if any progress has been made in
addressing any of these questions?

Cheers,

Ted

"Rob Halgren" wrote in message
...
Pat Brennan wrote:

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part
of a
gene and thus only a small percent is used in the coding for protein. If
you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .



Actually, in plants it looks more like this:
"trash".precursor.part1ofgene.junk.part2ofgene.jun k.part3ofgene.junk".
There is a whole lot of nothin' that breaks up the actual coding parts
of a lot of genes. Those are called introns, and I don't know that
anybody knows what they are for, either. Bacteria don't have them and
they get along just fine.

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?" or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene? or "How is the correct sequence of
introns in the gene stored and later recovered for use?" or "Does all this
happen in the nucleus?" or "How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?" or "Do the proteins within a chromosome have a role in any of
this, and if so, what?" Do you know if any progress has been made in
addressing any of these questions?

Cheers,

Ted

"Rob Halgren" wrote in message
...
Pat Brennan wrote:

Hi Joanna,

If you look at a plant's DNA only a small percent will actually be part
of a
gene and thus only a small percent is used in the coding for protein. If
you
look at a chromosome (a DNA strand) it looks something like:

. . . "tr a s h" . precursor . gene . " t r a s h" . precursor .
gene. . . .



Actually, in plants it looks more like this:
"trash".precursor.part1ofgene.junk.part2ofgene.jun k.part3ofgene.junk".
There is a whole lot of nothin' that breaks up the actual coding parts
of a lot of genes. Those are called introns, and I don't know that
anybody knows what they are for, either. Bacteria don't have them and
they get along just fine.

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?" or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene? or "How is the correct sequence of
introns in the gene stored and later recovered for use?" or "Does all this
happen in the nucleus?" or "How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?" or "Do the proteins within a chromosome have a role in any of
this, and if so, what?" Do you know if any progress has been made in
addressing any of these questions?

Cheers,

Ted

Ted Byers wrote:

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?"

There is a set of proteins (and some neat RNA molecules) in place
that takes care of splicing in your cells. That is what happens, the
full length message RNA is created from the DNA, exons (the coding bits)
and introns (the non-coding bits) both. It is rapidly processed by the
splicing machinery, which deletes the introns from the message, which is
then used as the template to create a protein. I haven't heard about
the age thing, but it is true that there can be many different messages
made from one template. This is called alternate splicing. Different
forms of a protein can be made by adding or removing exons from the
list, although I think they stay in order. So you can get protein ABCD,
BCD, ACD, etc. (where the letters represent an exon). Some of those
splice forms may be functional, some maybe not. The specifics of how
splicing occurs are pretty well worked out (it is complicated, of
course). The specifics of how the cell controls which splice form to
make are a little less clear, I think, although that isn't my area of
expertise.

or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene?

I don't think this is a frequent occurance. There are 'chimeric'
proteins, I know of a few involved in cancer, but I think those are
usually created by recombination of the genomic DNA, not the message. I
have heard of something called 'trans-splicing', which would seem to be
what you suggest, although I know absolutely nothing about it.

or "How is the correct sequence of
introns in the gene stored and later recovered for use?"

The correct sequence is stored in the genomic DNA. This isn't at
all affected by splicing. Message is created from the DNA template,
that RNA (message RNA, or mRNA) is then spliced. So you don't have to
worry about destroying the information. There is something called
recombination, which is particularly prevalent in creation of
antibodies, where the actual DNA of the antibody producing cell is
changed for the immunoglobulin genes. This is what allows you to make
such a large variety of antibodies (the number of possible combinations
is staggering). Or at least that is what I learned several years
ago... It is a special case though, and those rearrangements don't
carry over to your offspring.

or "Does all this
happen in the nucleus?" or

Pretty much.

"How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?"

This isn't my specialty either, but if this does happen, it is
probably a function of telomere length. The telomeres are repetitive
sequence at the end of each chromosome. Due to the way DNA replication
works, you lose a little bit of telomere with every cell division. So,
the sorter the telomeres, the older the organism. Neat... I think this
is one of the more prevalent hypotheses about how the aging function
works. There is probably also a contribution from DNA damage, your DNA
accumulates various mutations and damage over time, and there are
proteins which sense this. Next you are going to ask me how everything
gets reset to 'normal' in the next generation... I don't really want to
go there.

You learn all sorts of things from an orchid newsgroup... *grin*

Rob

--
Rob's Rules: http://www.msu.edu/~halgren
1) There is always room for one more orchid
2) There is always room for two more orchids
2a. See rule 1
3) When one has insufficient credit to purchase
more orchids, obtain more credit

Ted Byers wrote:

It has been more than ten years since I last discussed this with a
specialist in the genetics of animal development. At that time at least, it
was believed that the suite of introns used to form a gene varies through
development, so, for example, the actual composition of your hemoglobin
right now is different from what it was when you were a kid, and will be
different again when you're an ol' fossil like me. So, according to what
she told me, what counts as an intron or exon (what some refer to as junk)
will depend on age as well as the gene in question. Alas, she didn't have
answers for many of my questions, like "How exactly does the selection of
introns vs exons happen?" or "How is the gene constructed from the introns
once the introns have been made?"

There is a set of proteins (and some neat RNA molecules) in place
that takes care of splicing in your cells. That is what happens, the
full length message RNA is created from the DNA, exons (the coding bits)
and introns (the non-coding bits) both. It is rapidly processed by the
splicing machinery, which deletes the introns from the message, which is
then used as the template to create a protein. I haven't heard about
the age thing, but it is true that there can be many different messages
made from one template. This is called alternate splicing. Different
forms of a protein can be made by adding or removing exons from the
list, although I think they stay in order. So you can get protein ABCD,
BCD, ACD, etc. (where the letters represent an exon). Some of those
splice forms may be functional, some maybe not. The specifics of how
splicing occurs are pretty well worked out (it is complicated, of
course). The specifics of how the cell controls which splice form to
make are a little less clear, I think, although that isn't my area of
expertise.

or "Is there any intermingling of introns
from different genes (e.g. is it possible to have an intron from one gene in
between the introns of some other gene); if so, how does the cell know which
introns are part of a given gene?

I don't think this is a frequent occurance. There are 'chimeric'
proteins, I know of a few involved in cancer, but I think those are
usually created by recombination of the genomic DNA, not the message. I
have heard of something called 'trans-splicing', which would seem to be
what you suggest, although I know absolutely nothing about it.

or "How is the correct sequence of
introns in the gene stored and later recovered for use?"

The correct sequence is stored in the genomic DNA. This isn't at
all affected by splicing. Message is created from the DNA template,
that RNA (message RNA, or mRNA) is then spliced. So you don't have to
worry about destroying the information. There is something called
recombination, which is particularly prevalent in creation of
antibodies, where the actual DNA of the antibody producing cell is
changed for the immunoglobulin genes. This is what allows you to make
such a large variety of antibodies (the number of possible combinations
is staggering). Or at least that is what I learned several years
ago... It is a special case though, and those rearrangements don't
carry over to your offspring.

or "Does all this
happen in the nucleus?" or

Pretty much.

"How does the mechanism in a given nucleus know
what the age of the organism is in order to know which introns to use at any
given time?"

This isn't my specialty either, but if this does happen, it is
probably a function of telomere length. The telomeres are repetitive
sequence at the end of each chromosome. Due to the way DNA replication
works, you lose a little bit of telomere with every cell division. So,
the sorter the telomeres, the older the organism. Neat... I think this
is one of the more prevalent hypotheses about how the aging function
works. There is probably also a contribution from DNA damage, your DNA
accumulates various mutations and damage over time, and there are
proteins which sense this. Next you are going to ask me how everything
gets reset to 'normal' in the next generation... I don't really want to
go there.

You learn all sorts of things from an orchid newsgroup... *grin*

Rob

--
Rob's Rules: http://www.msu.edu/~halgren
1) There is always room for one more orchid
2) There is always room for two more orchids
2a. See rule 1
3) When one has insufficient credit to purchase
more orchids, obtain more credit

Thanks for bringing me up to date Rob.


"Rob Halgren" wrote in message
...
Ted Byers wrote:

It has been more than ten years since I last discussed this with a
[snip]
proteins which sense this. Next you are going to ask me how everything
gets reset to 'normal' in the next generation... I don't really want to
go there.

Yup. You're right.

But will you go there if we beg; perhaps offering a bribe of a sundae with a
cherry on top?

;-)

Thanks

Ted

Thanks for bringing me up to date Rob.


"Rob Halgren" wrote in message
...
Ted Byers wrote:

It has been more than ten years since I last discussed this with a
[snip]
proteins which sense this. Next you are going to ask me how everything
gets reset to 'normal' in the next generation... I don't really want to
go there.

Yup. You're right.

But will you go there if we beg; perhaps offering a bribe of a sundae with a
cherry on top?

;-)

Thanks

Ted

Thanks for bringing me up to date Rob.


"Rob Halgren" wrote in message
...
Ted Byers wrote:

It has been more than ten years since I last discussed this with a
[snip]
proteins which sense this. Next you are going to ask me how everything
gets reset to 'normal' in the next generation... I don't really want to
go there.

Yup. You're right.

But will you go there if we beg; perhaps offering a bribe of a sundae with a
cherry on top?

;-)

Thanks

Ted