This link, which asks the question, "Is it possible to identify individual
dogs as members of a specific breed?"
is interesting with regard to the question of what is a species and what is
a variety within a species. I was thinking of all the different varieties
of Phal. equestris I have accumulated while I was reading it.

http://www.eurowaf.org/id.htm

I found it while I was searching for a bit of info I remembered about how
much of the variation in dog breeds comes from mutations that occurred in a
group of genes that switch on and off at different times during a puppy
fetus's growth. I think this is a sub group within the hox box gene group

While I was looking I also came across a link that better explained the idea
of neoteny in dogs. For what it's worth,
http://www.wolfology.com/id86.htm

I newver did find the puppy fetus thing and I forget why i was looking for
it...

Anyway, I guess these links are somewhat helpful to people like me seeking
to understand what is really going on in our genes... and the genes of our
orchids (keep it topical)... and what you guys can talk so intelligently
about. I remember reading someplace that the gene group which controls
early embryonic development in all animal species are exactly the same no
matter where they show up on a species chomosomes. From mice to men and
from chickens to fruit flies and worms, this gene group works so well to get
things started and causes things to go so terribly wrong if it mutates that
it is invariable across the whole spectrum of animal life on this planet.
When every animal on this planet gets started the same set of chemical
switches is thrown in the exact same order because the same genes do it. I
keep thinking this gene group is called the hox box, but that's wrong. The
hox box is like the next main group of gene switches tha tcomes into play
during early embryo development. Mutations to it are supposedly responsible
for what makes each life-form group unique from all the others life-form
groups in terms of body shape. "If this switch is not thrown at this exact
moment in the sequence you don't develop legs, arms, wings or fins and you
grow up to be a snake (or at least something without legs, arms, wings or
fins)..." All life has certain basic things in common. What makes us
different is not nearly as important as what makes us the same. As the
Aliens say, "you won't be sorry if you try to prove yourself unique and
apart because it will teach you what a great and important organism you are
a part of....." (They're so full of crap. They recently rejected my latest
attempt at "Hamlet Unaided" saying only "Your pencil is clearly not as sharp
as you want us to think it is.")

That was really interesting and coherent stuff, BTW. What you all wrote, I
mean... I hope there's more... I won't interrupt again.

And you know Rob: requarding the Alien's return to get me... It will be so
nice when they do. If for no other reason then it means they must have left
at some point....

Rob Halgren" wrote in message
...

How identical *is* species DNA anyway?



Is the genome like a template? If one could put the entire DNA strands
of a
species on an overhead projector acetate, could one overlay all the G-C
and
A-T base pairs on top of one another would they all line up? Could you
say
that any variation within that line-up would be something like 'different
colored eyes, and so same species' or 'different all together and so a
hybrid'? I mean, how can one isolate individual variation within a
species? And how would one know that the aberrant base pairs weren't
individual variation but the result of hybridization?



This _is_ actually my field, for once... And yes, the genome is a
template, if you aligned all of the DNA for all of the individuals in a
species, it would line up pretty darn well. The last estimate I heard
for the human genome was one SNP (single nucleotide polymorphism) for
every 1000 bases or so. Not every SNP (in fact very few) actually does
anything significant to a gene. We don't know enough now to read the
genome quite like a book. The main problem is that there are very few
single locus traits, most are multiple loci working in various degrees
of collaboration. It isn't easy to read a book when the sentences
bounce around between chapters and the grammar isn't entirely worked out.

How do you know the difference between individual variation and
hybridization? In a grossly oversimplified view: Most of the genes
for two closely related species will be very close in sequence. This is
as it should be, if they are derived from a common ancestor. But, if
you look at the right genes, there should be a consistent difference in
the sequence between two species. If you know that difference, then it
is easy to look and see if an organism has two copies of organism A's
gene, two copies of organism B's gene, or one of each. You need to
look at many different genes, usually. Actually, a variation of this is
exactly how a paternity test works (children are hybrids too).

Note that is only the closely related things that we have a problem
with... We can all tell that Paph. rothschildianum and Paph. armeniacum
are distinct species. We can get a pretty good idea that Paph.
Dollgoldii is a hybrid. We don't need DNA evidence for that...

Who is to say what species DNA is? Lord knows there's enough bickering
and
infighting amongst taxonomists who classify species according to set
international rules. Who would be the agency that would determine and
stamp
approve what 'species DNA' looks like? And how would they know? What if
they missed a few individuals? Like if a Greater Alien Space Race came
to
the Earth they'd think by preponderance of numbers that the human species
was Asian, and take that DNA as criteria of human-ness. The tiny Bushman
from the Kalihari Desert would be shit out of luck because they don't
look
Asian. What then? Would The Aliens be justified in eating Bushmen
because,
according to their definition of human-ness, they weren't human?



I actually have a talk about this worked up for orchids... The
answer is that there is no magic answer when you use DNA, any more than
there is when you use phenotypic markers for taxonomy. But, you can get
good estimates of how far apart things are. The boundaries are always a
mess, and always will be. DNA is just another tool. A powerful tool.
Somebody still needs to decide just how far apart is far enough to
qualify as a separate species.

What makes something a distinct species is genetic isolation and
time. Given enough of each, you don't fancy science to tell them
apart. It is those fuzzy edges that kick you in the head. When Al's
aliens come to pick him up, they will realize that his DNA is 99.9999%+
similar to both the Kalihari bushman and the Eskimo. It is
extraordinarily similar to that of a chimpanzee. It is remarkably
similar (in both sequence and the organization of the genes on the
chromosomes) to the DNA of a mouse. It is somewhat (disturbingly)
similar to the sequence and organization of the genes on the chromosome
of the zebra fish. The farther apart we get, the more difference there
is, but there is still remarkable conservation.

Besides, we all know that the aliens (or monsters) eat the cute,
mysteriously underdressed girls, who get separated from their group of
friends by strange plot twists. I learned that from the movies.

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

"K Barrett" wrote in message
news:h1WUb.108599$U%5.557761@attbi_s03...
Thanks for your response. It'll take me a while to assimilate it (I
know,
its futile...)

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.

Cheers,

Ted

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

--
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

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

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 wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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

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 wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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

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 wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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

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 wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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

Al wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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

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 wrote:

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? :-)



Effectively. Turns out that although chromosomes break and swap
pieces all the time (with their partner chromosome, remember, orchids
are nominally 2N - diploid), the breakage isn't random. Geneticists
thought it was random for the longest time, but it turns out there are
'hotspots' which tend to recombine more frequently than the rest of the
chromosome. So large pieces of DNA tends to move in 'chunks'. And
yes, we have to assume (because it works, among other things), that
function and sequence are inherited from common ancestors. These
sequences change with time, but the function must be conserved if the
gene is critical. If the gene isn't critical, it can diverge faster,
but will still be related to its ancestral sequence.

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?



Not as far as I know. I don't think we know enough about the
genomes of enough plants. We did a project here which looked at genes
which were 'specific to plants', but not flowering vs. non-flowering.
This has holes you can drive a truck through, for various technical
reasons, btw. If there is a group of 'flowering specific genes' I don't
know about them. Doesn't mean they don't exist, and I'll be happy to
take citations...

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?



Genes are found a) by similarity to known genes - we know a lot of
genes, b) by software that looks at the genome and tries to predict gene
structure - it is 'trained' on a reference set and let loose on your
genome, or c) by good old fashioned cloning - a scientist generates a
copy of a mRNA (the 'message RNA' that gets translated into a protein),
and we work backwards from there. No, we can't tell between angiosperms
and gymnosperms just by sequence. We could take a gene sequence from a
bunch of different organisms and run software that tells us what is
'most closely related' (quotes mine) to what. It might divide them into
those two classes, or not...

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'd bet good money that flowering (as we think of it) is a single
evolutionary event, with all of the flowering plants descended from a
single common ancestor.

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 guess so... That is not a wrong way of thinking about it, anyway.

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?



If we had enough information, probably. Somebody might be working
on it as we speak. There are a lot of questions out there. Your
questions are pretty good ones. I might steal a few for my own work, if
you don't mind... *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