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Genomics and biological evolution
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RonO
Feb 28, 2015, 1:15:00 PM2/28/15
to
I just got back from a week at the Gordon Conference on Quantitative
Genetics and Genomics and a lot of things are coming together to make it
much easier for anyone to make evolutionary inferences for just about
any taxonomic branch that you can imagine. The avian diversification
was just addressed in recent papers that I put up on TO and things like
where turtles fit in the evolution of terrestrial vertebrates has been
resolved. We aren't supposed to discuss the science of the meetings
outside the meetings because of the unpublished data presented, but
basically what has already been presented on this newsgroup is
accelerating. Just the rapidity with which new genomes can be sequenced
and assembled is mind boggling to me. In the late 1990's I submitted a
grant proposal to sequence 10 mitochondrial genomes (only around 170,000
base-pairs of DNA sequence) for over $250,000, about 5 years later I
sequenced 9 mitochondrial genomes for around $25,000 once our department
had it's own automated (Sanger type) DNA sequencers. Now with the next
generation DNA sequence technology. The new series of next generation
sequencing units is supposed to drop the cost of sequencing a human
genome (around a 3 gigabase genome) to much less than $1,000 for
reagents (the claim is less than 400 dollars) and since you can assemble
and do batch analysis of a bunch of human genomes at one time the cost
of sequencing and assembly of a human genome is less than $1,000.
We are dealing with terabases of DNA sequence instead of just a few
thousand base-pairs and it is more data than we can analyze at this
time. The avian example took over 400 years of processor time to
generate the bird phylogeny from whole genome sequence. This is only
possible using the massively parallel processor super computers. The
great thing about the technology is that we will identify the most
useful bits of the genome to make evolutionary inferences from and we
can deal with a few thousand genes instead of whole genomes in order to
answer the questions that we are asking. We will have the luxury to do
the analysis the most accurate way instead of the most economical or
practical.
Researchers are sequencing and assembling new genomes in months instead
of years. Soon just about any evolutionary issue will be able to be
addressed in detail. We have the 10,000 vertebrate genome project that
is on track. The avian papers that I put up on TO were just the latest
update on that project. They are sequencing a bunch of invertebrate
animals and pretty soon we will have a detailed description of the
evolution of vertebrates and the other major multicellular animal
lineages. Vertebrates are just one of the branches of the Cambrian
explosion. If we sequence the other phyla to the same extent we will
likely have enough sequence to start doing a top down type of analysis
that will allow us to map out the details both taxonomic and temporal
for the Cambrian diversification of animals.
Top down is just the type of analysis that Eddie put up for the steroid
receptor evolution where they were able to sequence a lot of steroid
receptor genes from a lot of different multicellular animals. In that
study they were able to do a backwards analysis to determine what
mutations occurred in what lineages and determine the order of the
mutations. They were able to determine that two mutations were
essential for the divergence of the two main steroid receptor families
that became major players in making the Cambrian explosion possible.
Once you have enough sequence from enough different branch points in the
phylogeny you can backtrack through the sequences and generate a ton of
inferences. This will be done for thousands of genes and not just two
receptor families. Even though the "explosion" occurred over just a few
million years details of events and what happened will be able to be
determined. Like the steroid receptor example, we will be able to
determine what event preceded the Cambrian diversification and the order
of such events, and we have a good chance of determining just what was
happening during the Cambrian diversification event. The steroid
receptor evolution was just one of the events that predated the Cambrian
explosion that had to happen in the common ancestor of multicellular
animals.
It is pretty definite that all extant vertebrates are descended from a
common ancestor that became a new species by duplicating it's genome
(tetraploid) or by two different species mating and a doubling of the
genome (amphidiploid tetraploid) to make a fertile individual. Like a
lot of plant examples where doubling the genome to make a tetraploid
individual facilitates speciation, doubling of the genome happened in
our vertebrate tetraploid ancestor. The vertebrate lineage has done a
lot with the extra genes provided by the doubling of the genome. Many
of the duplicate genes were lost, but many of the duplicated genes
evolved new uses for the animals, and that will all be mapped out.
The level of detail should become undeniable, but you just have to look
at IDiots like Eddie and Kalk to know that denial is all they already
have. It all isn't going to be roses. There are accuracy issues in
assembling new genomes. Even existing genome assemblies have issues
with the next generation technology. Things like duplicated sequences
(gene duplications) have been found to be much more prevalent than we
expected and they mess up assemblies and can do things like inflate
diversity measures if they are not accounted for. The steroid receptor
example involved gene duplication of some kind. Once you have two genes
there is less selection to maintain the same function and the two genes
can diverge from each other. This is obviously an important
evolutionary event, and it happens a lot more than we ever thought.
That just means that most of the duplication events will not amount to
anything, and just a few will be found to be useful for the further
evolution of the lineage. So it is a problem and an important issue and
if we don't find a way to identify the examples accurately there will be
some messed up inferences. So the technology isn't idiot proof and will
be far from IDiot proof in terms of what IDiots want to deny.
Will the issues with next generation sequencing exist in a few years?
My guess is that it will not. Assembly issues will become less of a
problem with implementation of accurate long single molecule DNA
sequencing, and this has already started. Will we find new problems,
probably, but they are going to be problems that we are glad to deal
with when you have more data than you can analyze. You can go deeper
into denial or you can start to better understand the diversity and
evolution of life on earth, that is the future.
Ron Okimoto
Genetics and Genomics and a lot of things are coming together to make it
much easier for anyone to make evolutionary inferences for just about
any taxonomic branch that you can imagine. The avian diversification
was just addressed in recent papers that I put up on TO and things like
where turtles fit in the evolution of terrestrial vertebrates has been
resolved. We aren't supposed to discuss the science of the meetings
outside the meetings because of the unpublished data presented, but
basically what has already been presented on this newsgroup is
accelerating. Just the rapidity with which new genomes can be sequenced
and assembled is mind boggling to me. In the late 1990's I submitted a
grant proposal to sequence 10 mitochondrial genomes (only around 170,000
base-pairs of DNA sequence) for over $250,000, about 5 years later I
sequenced 9 mitochondrial genomes for around $25,000 once our department
had it's own automated (Sanger type) DNA sequencers. Now with the next
generation DNA sequence technology. The new series of next generation
sequencing units is supposed to drop the cost of sequencing a human
genome (around a 3 gigabase genome) to much less than $1,000 for
reagents (the claim is less than 400 dollars) and since you can assemble
and do batch analysis of a bunch of human genomes at one time the cost
of sequencing and assembly of a human genome is less than $1,000.
We are dealing with terabases of DNA sequence instead of just a few
thousand base-pairs and it is more data than we can analyze at this
time. The avian example took over 400 years of processor time to
generate the bird phylogeny from whole genome sequence. This is only
possible using the massively parallel processor super computers. The
great thing about the technology is that we will identify the most
useful bits of the genome to make evolutionary inferences from and we
can deal with a few thousand genes instead of whole genomes in order to
answer the questions that we are asking. We will have the luxury to do
the analysis the most accurate way instead of the most economical or
practical.
Researchers are sequencing and assembling new genomes in months instead
of years. Soon just about any evolutionary issue will be able to be
addressed in detail. We have the 10,000 vertebrate genome project that
is on track. The avian papers that I put up on TO were just the latest
update on that project. They are sequencing a bunch of invertebrate
animals and pretty soon we will have a detailed description of the
evolution of vertebrates and the other major multicellular animal
lineages. Vertebrates are just one of the branches of the Cambrian
explosion. If we sequence the other phyla to the same extent we will
likely have enough sequence to start doing a top down type of analysis
that will allow us to map out the details both taxonomic and temporal
for the Cambrian diversification of animals.
Top down is just the type of analysis that Eddie put up for the steroid
receptor evolution where they were able to sequence a lot of steroid
receptor genes from a lot of different multicellular animals. In that
study they were able to do a backwards analysis to determine what
mutations occurred in what lineages and determine the order of the
mutations. They were able to determine that two mutations were
essential for the divergence of the two main steroid receptor families
that became major players in making the Cambrian explosion possible.
Once you have enough sequence from enough different branch points in the
phylogeny you can backtrack through the sequences and generate a ton of
inferences. This will be done for thousands of genes and not just two
receptor families. Even though the "explosion" occurred over just a few
million years details of events and what happened will be able to be
determined. Like the steroid receptor example, we will be able to
determine what event preceded the Cambrian diversification and the order
of such events, and we have a good chance of determining just what was
happening during the Cambrian diversification event. The steroid
receptor evolution was just one of the events that predated the Cambrian
explosion that had to happen in the common ancestor of multicellular
animals.
It is pretty definite that all extant vertebrates are descended from a
common ancestor that became a new species by duplicating it's genome
(tetraploid) or by two different species mating and a doubling of the
genome (amphidiploid tetraploid) to make a fertile individual. Like a
lot of plant examples where doubling the genome to make a tetraploid
individual facilitates speciation, doubling of the genome happened in
our vertebrate tetraploid ancestor. The vertebrate lineage has done a
lot with the extra genes provided by the doubling of the genome. Many
of the duplicate genes were lost, but many of the duplicated genes
evolved new uses for the animals, and that will all be mapped out.
The level of detail should become undeniable, but you just have to look
at IDiots like Eddie and Kalk to know that denial is all they already
have. It all isn't going to be roses. There are accuracy issues in
assembling new genomes. Even existing genome assemblies have issues
with the next generation technology. Things like duplicated sequences
(gene duplications) have been found to be much more prevalent than we
expected and they mess up assemblies and can do things like inflate
diversity measures if they are not accounted for. The steroid receptor
example involved gene duplication of some kind. Once you have two genes
there is less selection to maintain the same function and the two genes
can diverge from each other. This is obviously an important
evolutionary event, and it happens a lot more than we ever thought.
That just means that most of the duplication events will not amount to
anything, and just a few will be found to be useful for the further
evolution of the lineage. So it is a problem and an important issue and
if we don't find a way to identify the examples accurately there will be
some messed up inferences. So the technology isn't idiot proof and will
be far from IDiot proof in terms of what IDiots want to deny.
Will the issues with next generation sequencing exist in a few years?
My guess is that it will not. Assembly issues will become less of a
problem with implementation of accurate long single molecule DNA
sequencing, and this has already started. Will we find new problems,
probably, but they are going to be problems that we are glad to deal
with when you have more data than you can analyze. You can go deeper
into denial or you can start to better understand the diversity and
evolution of life on earth, that is the future.
Ron Okimoto
Paul Ciszek
Mar 3, 2015, 6:04:50 PM3/3/15
to
In article <mct0h9$gn1$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>any taxonomic branch that you can imagine. The avian diversification
>was just addressed in recent papers that I put up on TO and things like
>where turtles fit in the evolution of terrestrial vertebrates has been
>resolved. We aren't supposed to discuss the science of the meetings
>outside the meetings because of the unpublished data presented, but
>basically what has already been presented on this newsgroup is
>accelerating.
to point me to?
--
Please reply to: | "Evolution is a theory that accounts
pciszek at panix dot com | for variety, not superiority."
Autoreply has been disabled | -- Joan Pontius
RonO
Mar 3, 2015, 6:54:49 PM3/3/15
to
On 3/3/2015 5:00 PM, Paul Ciszek wrote:
> In article <mct0h9$gn1$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>> any taxonomic branch that you can imagine. The avian diversification
>> was just addressed in recent papers that I put up on TO and things like
>> where turtles fit in the evolution of terrestrial vertebrates has been
>> resolved. We aren't supposed to discuss the science of the meetings
>> outside the meetings because of the unpublished data presented, but
>> basically what has already been presented on this newsgroup is
>> accelerating.
>
> I am curious about the turtle thing. Is there anything you are allowed
> to point me to?
>
There is a complete turtle genome (possibly more than one by now) and
> In article <mct0h9$gn1$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>> any taxonomic branch that you can imagine. The avian diversification
>> was just addressed in recent papers that I put up on TO and things like
>> where turtles fit in the evolution of terrestrial vertebrates has been
>> resolved. We aren't supposed to discuss the science of the meetings
>> outside the meetings because of the unpublished data presented, but
>> basically what has already been presented on this newsgroup is
>> accelerating.
>
> I am curious about the turtle thing. Is there anything you are allowed
> to point me to?
>
the analysis has already been done.
http://www.ncbi.nlm.nih.gov/pubmed/25504731
http://www.ncbi.nlm.nih.gov/pubmed/25450099
http://www.ncbi.nlm.nih.gov/pubmed/23537068
Ron Okimoto
Gary Bohn
Mar 3, 2015, 10:04:49 PM3/3/15
to
RonO
Mar 4, 2015, 6:59:48 AM3/4/15
to
Paul Ciszek
Mar 4, 2015, 6:09:49 PM3/4/15
to
In article <md5hi5$es9$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>
>There is a complete turtle genome (possibly more than one by now) and
>the analysis has already been done.
>http://www.ncbi.nlm.nih.gov/pubmed/25504731
>
>http://www.ncbi.nlm.nih.gov/pubmed/25450099
>
>http://www.ncbi.nlm.nih.gov/pubmed/23537068
The tree makes it look like turtles belong squarely in the middle of
reptiles, next to the archosaurs (is that the right collective term for
crocodilians, dinosaurs, and birds?) rather than being an outgroup, as
I had been led to believe.
RonO
Mar 5, 2015, 7:54:47 AM3/5/15
to
On 3/4/2015 5:07 PM, Paul Ciszek wrote:
> In article <md5hi5$es9$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>>
>> There is a complete turtle genome (possibly more than one by now) and
>> the analysis has already been done.
>> http://www.ncbi.nlm.nih.gov/pubmed/25504731
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/25450099
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/23537068
>
> The last paper is the only one with pictures. :-/
> The tree makes it look like turtles belong squarely in the middle of
> reptiles, next to the archosaurs (is that the right collective term for
> crocodilians, dinosaurs, and birds?) rather than being an outgroup, as
> I had been led to believe.
>
Turtles have some extreme derived anatomical morphologies that made it
> In article <md5hi5$es9$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>>
>> There is a complete turtle genome (possibly more than one by now) and
>> the analysis has already been done.
>> http://www.ncbi.nlm.nih.gov/pubmed/25504731
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/25450099
>>
>> http://www.ncbi.nlm.nih.gov/pubmed/23537068
>
> The last paper is the only one with pictures. :-/
> The tree makes it look like turtles belong squarely in the middle of
> reptiles, next to the archosaurs (is that the right collective term for
> crocodilians, dinosaurs, and birds?) rather than being an outgroup, as
> I had been led to believe.
>
difficult to do classic morphological taxonomy on them. They had an
incorrect branch point in the vertebrate phylogeny. The first molecular
evidence indicated that the morphological phylogeny was incorrect, and
now whole genome analysis has been used to place turtles where they
likely belong in the evolution of vertebrates. They are more closely
related to our branch of amniotes (Crocs, birds, mammals) than they are
to snakes and lizards.
Ron Okimoto
Paul Ciszek
Mar 6, 2015, 7:56:34 PM3/6/15
to talk-o...@moderators.isc.org
In article <md9jbl$i3n$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>
>Turtles have some extreme derived anatomical morphologies that made it
>difficult to do classic morphological taxonomy on them. They had an
>incorrect branch point in the vertebrate phylogeny. The first molecular
>evidence indicated that the morphological phylogeny was incorrect, and
>now whole genome analysis has been used to place turtles where they
>likely belong in the evolution of vertebrates. They are more closely
>related to our branch of amniotes (Crocs, birds, mammals) than they are
>to snakes and lizards.
than they are to snakes and lizards? Whoa.
RonO
Mar 7, 2015, 9:40:00 AM3/7/15
to talk-o...@moderators.isc.org
On 3/6/2015 5:27 PM, Paul Ciszek wrote:
> In article <md9jbl$i3n$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>>
>> Turtles have some extreme derived anatomical morphologies that made it
>> difficult to do classic morphological taxonomy on them. They had an
>> incorrect branch point in the vertebrate phylogeny. The first molecular
>> evidence indicated that the morphological phylogeny was incorrect, and
>> now whole genome analysis has been used to place turtles where they
>> likely belong in the evolution of vertebrates. They are more closely
>> related to our branch of amniotes (Crocs, birds, mammals) than they are
>> to snakes and lizards.
>
> Are you saying that crocs and birds are more closely related to mammals
> than they are to snakes and lizards? Whoa.
>
That is how it has been for quite a while. Haven't you ever heard
> In article <md9jbl$i3n$1...@dont-email.me>, RonO <roki...@cox.net> wrote:
>>
>> Turtles have some extreme derived anatomical morphologies that made it
>> difficult to do classic morphological taxonomy on them. They had an
>> incorrect branch point in the vertebrate phylogeny. The first molecular
>> evidence indicated that the morphological phylogeny was incorrect, and
>> now whole genome analysis has been used to place turtles where they
>> likely belong in the evolution of vertebrates. They are more closely
>> related to our branch of amniotes (Crocs, birds, mammals) than they are
>> to snakes and lizards.
>
> Are you saying that crocs and birds are more closely related to mammals
> than they are to snakes and lizards? Whoa.
>
someone object to calling dinos reptiles? Dinos, crocs, and birds had
scutes instead of scales. Mammals apparently turned their scutes into
hair and some dinos turned the scutes into feathers.
RSNorman
Mar 7, 2015, 10:25:01 AM3/7/15
to talk-o...@moderators.isc.org
"reptiles" is no longer a scientific classification even though it
retains its value as an informal grouping. The "cold-blooded
amniotes" include really a very diverse mixture of things.
Sneaky O. Possum
Mar 7, 2015, 11:00:01 AM3/7/15
to talk-o...@moderators.isc.org
RSNorman <r_s_n...@comcast.net> wrote in
news:ok5mfa90ub7eecovt...@4ax.com:
Shouldn't that be 'ectothermic amniotes'?
--
S.O.P.
news:ok5mfa90ub7eecovt...@4ax.com:
--
S.O.P.
RSNorman
Mar 7, 2015, 11:20:00 AM3/7/15
to talk-o...@moderators.isc.org
"cold-blooded" which exists as a useful phrase in the same way that
"reptile" is useful. Neither one is proper in a scientific context.
Sneaky O. Possum
Mar 7, 2015, 11:55:00 AM3/7/15
to talk-o...@moderators.isc.org
RSNorman <r_s_n...@comcast.net> wrote in
news:gv8mfapf8ps50jvlp...@4ax.com:
But 'amniotes' is only proper in a scientific context, which makes the
phrase 'cold-blooded amniotes' a bit jarring. Was that your point?
--
S.O.P.
news:gv8mfapf8ps50jvlp...@4ax.com:
phrase 'cold-blooded amniotes' a bit jarring. Was that your point?
--
S.O.P.
RSNorman
Mar 7, 2015, 12:15:01 PM3/7/15
to talk-o...@moderators.isc.org
On Sat, 7 Mar 2015 16:51:38 +0000 (UTC), "Sneaky O. Possum"
There is no ordinary language non-scientific word to describe that
group.
The real point is that the notion of "reptile" is defunct. It
underlies the misconception that turtles and crocks are somehow more
closely related to snakes than to mammals and birds simply because
they share the lack of heat regulation and a four-chambered heart.
group.
The real point is that the notion of "reptile" is defunct. It
underlies the misconception that turtles and crocks are somehow more
closely related to snakes than to mammals and birds simply because
they share the lack of heat regulation and a four-chambered heart.
Bob Casanova
Mar 7, 2015, 1:35:00 PM3/7/15
to talk-o...@moderators.isc.org
On Sat, 07 Mar 2015 12:14:42 -0500, the following appeared
in talk.origins, posted by RSNorman
<r_s_n...@comcast.net>:
OK. I'm confused. Can I assume you meant "lack of heat
regulation and lack of a four-chambered heart" rather than
the other possibility your statement allows, that they share
a four-chambered heart with snakes but not with mammals and
birds?
Interesting side note: I clearly recall reading (probably
almost 60 years ago) that birds have *three*-chambered
hearts, but a quick Gurgle search says that's incorrect and
they have, as you note, four-chambered hearts, so apparently
I'm misremembering (not unknown). Always something new to
learn here (or, as the case may be, *un*learn). ;-)
--
Bob C.
"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"
- Isaac Asimov
in talk.origins, posted by RSNorman
<r_s_n...@comcast.net>:
regulation and lack of a four-chambered heart" rather than
the other possibility your statement allows, that they share
a four-chambered heart with snakes but not with mammals and
birds?
Interesting side note: I clearly recall reading (probably
almost 60 years ago) that birds have *three*-chambered
hearts, but a quick Gurgle search says that's incorrect and
they have, as you note, four-chambered hearts, so apparently
I'm misremembering (not unknown). Always something new to
learn here (or, as the case may be, *un*learn). ;-)
--
Bob C.
"The most exciting phrase to hear in science,
the one that heralds new discoveries, is not
'Eureka!' but 'That's funny...'"
- Isaac Asimov
RSNorman
Mar 7, 2015, 5:54:59 PM3/7/15
to talk-o...@moderators.isc.org
On Sat, 07 Mar 2015 11:30:32 -0700, Bob Casanova <nos...@buzz.off>
wrote:
Yes, I should have "share a lack of both a four-chambered heart and
heat regulation."
It used to be the standard teaching saw that amphibians have a
3-chambered heart, "reptiles" a 3-1/2, and birds and mammals a
4-chambered heart. The crocodilian heart is pretty much four separate
chambers. However there is no real evolutionary succession shown
because different groups divided the single ventricle now exhibited by
amphibians in different non-homologous ways and in different stages to
produce the completely separated two ventricles and four chambers in
different animals. What is more interesting to me is the fate of the
aortic arches. Fish have multiple bilaterally paired arches from the
heart passing through the different rows of gills on both the left and
the right sides.In mammals, a left aortic arche forms the main
systemic connection between the heart and the dorsal aorta. Birds
have the same pattern of complete separation of the pulmonary and
systemic loop but they use a right aortic arch to make the connection.
So obviously the completely divided double circulation of birds and
mammals evolved separately as did the process of division of the
ventricle.
wrote:
heat regulation."
It used to be the standard teaching saw that amphibians have a
3-chambered heart, "reptiles" a 3-1/2, and birds and mammals a
4-chambered heart. The crocodilian heart is pretty much four separate
chambers. However there is no real evolutionary succession shown
because different groups divided the single ventricle now exhibited by
amphibians in different non-homologous ways and in different stages to
produce the completely separated two ventricles and four chambers in
different animals. What is more interesting to me is the fate of the
aortic arches. Fish have multiple bilaterally paired arches from the
heart passing through the different rows of gills on both the left and
the right sides.In mammals, a left aortic arche forms the main
systemic connection between the heart and the dorsal aorta. Birds
have the same pattern of complete separation of the pulmonary and
systemic loop but they use a right aortic arch to make the connection.
So obviously the completely divided double circulation of birds and
mammals evolved separately as did the process of division of the
ventricle.
Sneaky O. Possum
Mar 7, 2015, 5:54:59 PM3/7/15
to talk-o...@moderators.isc.org
RSNorman <r_s_n...@comcast.net> wrote in
news:f2cmfadhqqua9kbg4...@4ax.com:
> On Sat, 7 Mar 2015 16:51:38 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>
>>RSNorman <r_s_n...@comcast.net> wrote in
>>news:gv8mfapf8ps50jvlp...@4ax.com:
>>
>>> On Sat, 7 Mar 2015 15:58:40 +0000 (UTC), "Sneaky O. Possum"
>>> <sneaky...@gmail.com> wrote:
>>>
>>>>RSNorman <r_s_n...@comcast.net> wrote in
>>>>news:ok5mfa90ub7eecovt...@4ax.com:
[snip]
modifier like 'cold-blooded' in front of it. If you assume that your
readers know what an amniote is, why not assume they know what
ectothermic means?
> The real point is that the notion of "reptile" is defunct.
As a scientific term, sure. But so is 'cold-blooded'.
> It underlies the misconception that turtles and crocks are somehow
> more closely related to snakes than to mammals and birds simply
> because they share the lack of heat regulation and a four-chambered
> heart.
The phylogram from the article about the Western painted turtle genome
doesn't indicate that turtles and crocs are more closely related to
mammals than snakes and lizards are.
As far as I know, the current thinking is that the Amniota diverged into
the Synapsida (whence the Therapsida, whence mammals) and the Sauropsida
(whence the Diapsida, whence all other extant amniotes.) Thus all other
extant amniotes are more closely related to each other than they are to
any given mammal.
Of course, it is true that 'reptile' obscures the fact that testudines
and crurotarsians are more closely related to each other than either is
to a lepidosaurian, but calling them all 'amniotes' doesn't clear that
up, does it?
--
S.O.P.
news:f2cmfadhqqua9kbg4...@4ax.com:
> On Sat, 7 Mar 2015 16:51:38 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>
>>RSNorman <r_s_n...@comcast.net> wrote in
>>news:gv8mfapf8ps50jvlp...@4ax.com:
>>
>>> On Sat, 7 Mar 2015 15:58:40 +0000 (UTC), "Sneaky O. Possum"
>>> <sneaky...@gmail.com> wrote:
>>>
>>>>RSNorman <r_s_n...@comcast.net> wrote in
>>>>news:ok5mfa90ub7eecovt...@4ax.com:
>>>>> This strange pattern of relationships is the basic reason why
>>>>> "reptiles" is no longer a scientific classification even though it
>>>>> retains its value as an informal grouping. The "cold-blooded
>>>>> amniotes" include really a very diverse mixture of things.
>>>>
>>>>Shouldn't that be 'ectothermic amniotes'?
>>>
>>> Yes in the proper context. I deliberately chose to write
>>> "cold-blooded" which exists as a useful phrase in the same way that
>>> "reptile" is useful. Neither one is proper in a scientific context.
>>
>>But 'amniotes' is only proper in a scientific context, which makes the
>>phrase 'cold-blooded amniotes' a bit jarring. Was that your point?
>
> There is no ordinary language non-scientific word to describe that
> group.
I know. That's why it's jarring to put an ordinary non-scientific
>>>>> "reptiles" is no longer a scientific classification even though it
>>>>> retains its value as an informal grouping. The "cold-blooded
>>>>> amniotes" include really a very diverse mixture of things.
>>>>
>>>>Shouldn't that be 'ectothermic amniotes'?
>>>
>>> Yes in the proper context. I deliberately chose to write
>>> "cold-blooded" which exists as a useful phrase in the same way that
>>> "reptile" is useful. Neither one is proper in a scientific context.
>>
>>But 'amniotes' is only proper in a scientific context, which makes the
>>phrase 'cold-blooded amniotes' a bit jarring. Was that your point?
>
> There is no ordinary language non-scientific word to describe that
> group.
modifier like 'cold-blooded' in front of it. If you assume that your
readers know what an amniote is, why not assume they know what
ectothermic means?
> The real point is that the notion of "reptile" is defunct.
> It underlies the misconception that turtles and crocks are somehow
> more closely related to snakes than to mammals and birds simply
> because they share the lack of heat regulation and a four-chambered
> heart.
doesn't indicate that turtles and crocs are more closely related to
mammals than snakes and lizards are.
As far as I know, the current thinking is that the Amniota diverged into
the Synapsida (whence the Therapsida, whence mammals) and the Sauropsida
(whence the Diapsida, whence all other extant amniotes.) Thus all other
extant amniotes are more closely related to each other than they are to
any given mammal.
Of course, it is true that 'reptile' obscures the fact that testudines
and crurotarsians are more closely related to each other than either is
to a lepidosaurian, but calling them all 'amniotes' doesn't clear that
up, does it?
--
S.O.P.
RSNorman
Mar 7, 2015, 6:29:59 PM3/7/15
to talk-o...@moderators.isc.org
On Sat, 7 Mar 2015 22:53:24 +0000 (UTC), "Sneaky O. Possum"
>news:f2cmfadhqqua9kbg4...@4ax.com:
>
<snip the part where we are completely agreeing on the subject but
arguing about my choice of words to describe it>
>> It underlies the misconception that turtles and crocks are somehow
>> more closely related to snakes than to mammals and birds simply
>> because they share the lack of heat regulation and a four-chambered
>> heart.
>
>The phylogram from the article about the Western painted turtle genome
>doesn't indicate that turtles and crocs are more closely related to
>mammals than snakes and lizards are.
>
>As far as I know, the current thinking is that the Amniota diverged into
>the Synapsida (whence the Therapsida, whence mammals) and the Sauropsida
>(whence the Diapsida, whence all other extant amniotes.) Thus all other
>extant amniotes are more closely related to each other than they are to
>any given mammal.
>
I took my cue from what RonO wrote earlier in the thread: " They
[turtles] are more closely related to our branch of amniotes (Crocs,
birds, mammals) than they are to snakes and lizards." That would
indicate that turtles are not more closely related to snakes and
lizards than to mammals. In other words, to say otherwise is a
misconception. Also RonO put "our branch" is including crocs, birds
and mammals, indicating that crocs are more closely related to us
(being in our branch) than to snakes and lizards.
So if you have a problem with my wording on this issue, please take it
up with RonO. He even repeated it in his answer to Paul Ciszek's
surprise at the statement.
>news:f2cmfadhqqua9kbg4...@4ax.com:
>
<snip the part where we are completely agreeing on the subject but
arguing about my choice of words to describe it>
>> It underlies the misconception that turtles and crocks are somehow
>> more closely related to snakes than to mammals and birds simply
>> because they share the lack of heat regulation and a four-chambered
>> heart.
>
>The phylogram from the article about the Western painted turtle genome
>doesn't indicate that turtles and crocs are more closely related to
>mammals than snakes and lizards are.
>
>As far as I know, the current thinking is that the Amniota diverged into
>the Synapsida (whence the Therapsida, whence mammals) and the Sauropsida
>(whence the Diapsida, whence all other extant amniotes.) Thus all other
>extant amniotes are more closely related to each other than they are to
>any given mammal.
>
[turtles] are more closely related to our branch of amniotes (Crocs,
birds, mammals) than they are to snakes and lizards." That would
indicate that turtles are not more closely related to snakes and
lizards than to mammals. In other words, to say otherwise is a
misconception. Also RonO put "our branch" is including crocs, birds
and mammals, indicating that crocs are more closely related to us
(being in our branch) than to snakes and lizards.
So if you have a problem with my wording on this issue, please take it
up with RonO. He even repeated it in his answer to Paul Ciszek's
surprise at the statement.
Sneaky O. Possum
Mar 7, 2015, 7:44:58 PM3/7/15
to talk-o...@moderators.isc.org
RSNorman <r_s_n...@comcast.net> wrote in
news:se1nfal7vsd27ve5u...@4ax.com:
> On Sat, 7 Mar 2015 22:53:24 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>
>>RSNorman <r_s_n...@comcast.net> wrote in
>>news:f2cmfadhqqua9kbg4...@4ax.com:
>>
> <snip the part where we are completely agreeing on the subject but
> arguing about my choice of words to describe it>
The choice of words *was* the subject.
>>> It underlies the misconception that turtles and crocks are somehow
>>> more closely related to snakes than to mammals and birds simply
>>> because they share the lack of heat regulation and a four-chambered
>>> heart.
>>
>>The phylogram from the article about the Western painted turtle genome
>>doesn't indicate that turtles and crocs are more closely related to
>>mammals than snakes and lizards are.
>>
>>As far as I know, the current thinking is that the Amniota diverged
>>into the Synapsida (whence the Therapsida, whence mammals) and the
>>Sauropsida (whence the Diapsida, whence all other extant amniotes.)
>>Thus all other extant amniotes are more closely related to each other
>>than they are to any given mammal.
>
> I took my cue from what RonO wrote earlier in the thread: " They
> [turtles] are more closely related to our branch of amniotes (Crocs,
> birds, mammals) than they are to snakes and lizards." That would
> indicate that turtles are not more closely related to snakes and
> lizards than to mammals. In other words, to say otherwise is a
> misconception. Also RonO put "our branch" is including crocs, birds
> and mammals, indicating that crocs are more closely related to us
> (being in our branch) than to snakes and lizards.
The fact that he wrote it isn't an excuse for repeating it. I had the
impression you were more intelligent and amenable to correction than he
is. If I erred in that, then I apologize.
> So if you have a problem with my wording on this issue, please take it
> up with RonO. He even repeated it in his answer to Paul Ciszek's
> surprise at the statement.
When you uncritically repeat other people's errors, that's not their
fault.
And you still haven't explained how 'amniote' is supposed to clear up
the misconception about the relationships among testudines,
crurotarsians, and lepidosaurians that 'reptile' supposedly encourages.
--
S.O.P.
news:se1nfal7vsd27ve5u...@4ax.com:
> On Sat, 7 Mar 2015 22:53:24 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>
>>RSNorman <r_s_n...@comcast.net> wrote in
>>news:f2cmfadhqqua9kbg4...@4ax.com:
>>
> <snip the part where we are completely agreeing on the subject but
> arguing about my choice of words to describe it>
>>> It underlies the misconception that turtles and crocks are somehow
>>> more closely related to snakes than to mammals and birds simply
>>> because they share the lack of heat regulation and a four-chambered
>>> heart.
>>
>>The phylogram from the article about the Western painted turtle genome
>>doesn't indicate that turtles and crocs are more closely related to
>>mammals than snakes and lizards are.
>>
>>As far as I know, the current thinking is that the Amniota diverged
>>into the Synapsida (whence the Therapsida, whence mammals) and the
>>Sauropsida (whence the Diapsida, whence all other extant amniotes.)
>>Thus all other extant amniotes are more closely related to each other
>>than they are to any given mammal.
>
> I took my cue from what RonO wrote earlier in the thread: " They
> [turtles] are more closely related to our branch of amniotes (Crocs,
> birds, mammals) than they are to snakes and lizards." That would
> indicate that turtles are not more closely related to snakes and
> lizards than to mammals. In other words, to say otherwise is a
> misconception. Also RonO put "our branch" is including crocs, birds
> and mammals, indicating that crocs are more closely related to us
> (being in our branch) than to snakes and lizards.
impression you were more intelligent and amenable to correction than he
is. If I erred in that, then I apologize.
> So if you have a problem with my wording on this issue, please take it
> up with RonO. He even repeated it in his answer to Paul Ciszek's
> surprise at the statement.
fault.
And you still haven't explained how 'amniote' is supposed to clear up
the misconception about the relationships among testudines,
crurotarsians, and lepidosaurians that 'reptile' supposedly encourages.
--
S.O.P.
RSNorman
Mar 7, 2015, 9:20:00 PM3/7/15
to talk-o...@moderators.isc.org
On Sun, 8 Mar 2015 00:39:09 +0000 (UTC), "Sneaky O. Possum"
I fully admit to accepting RonO's authority on this point and that I
did not get a second source to confirm its authenticity. If your
first source is right you don't need the second source and I am not at
all convinced he was not right. You have to understand that his
original post on this was in excitement having just returned from a
Gordon Conference. He wrote: " things like where turtles fit in the
You cite one of the papers Ron provided but, as he explained, this was
older data. Paul questioned Ron about turtles in particular and about
the phenogram you mention. Ron replied "They had an incorrect branch
point in the vertebrate phylogeny....now whole genome analysis has
reason to doubt Ron's presentation. After your comments, I still find
no reason to doubt what Ron wrote.
So I did not "uncritically" repeat other peoples' errors. I evaluated
the information and the surrounding supporting circumstances before
repeat the statement which has not been established to be in error.
If Ron withdraws his claim, then I will apologize profusely for being
so crass and gullible as to be pulled in.
As to the amniote business, I already explained. I wanted to show how
the concept of "reptile" was inappropriate even though the animals
that are generally called reptiles constitute amniotes that, as a
group, fail to thermoregulate. I used the word "amniote" simply
because there is no ordinary language word to indicate the group. I
used the word "cold-blooded" (as I already explained) because it, like
"reptile" is now an inappropriate terminology just as is the word
"reptile" even though both have their uses in ordinary language. I
used the word "amniote" because I had no other to use. The word
"amniote" includes birds and mammals which were excluded by the phrase
"cold-blooded". In short (maybe I should just go back and erase all
the previous), the "cold blooded amniotes" just happen to include the
turtles, the snakes and lizards, the crocs, and the tuatara. By some
strange coincidence, that just happens to be the group we call the
"reptiles". The misconception is that these form some kind of natural
grouping and that they should all be closely related because of that
grouping.
did not get a second source to confirm its authenticity. If your
first source is right you don't need the second source and I am not at
all convinced he was not right. You have to understand that his
original post on this was in excitement having just returned from a
Gordon Conference. He wrote: " things like where turtles fit in the
evolution of terrestrial vertebrates has been resolved. We aren't
supposed to discuss the science of the meetings outside the meetings
because of the unpublished data presented, ..."
supposed to discuss the science of the meetings outside the meetings
You cite one of the papers Ron provided but, as he explained, this was
older data. Paul questioned Ron about turtles in particular and about
the phenogram you mention. Ron replied "They had an incorrect branch
point in the vertebrate phylogeny....now whole genome analysis has
been used to place turtles where they likely belong in the evolution
of vertebrates. They are more closely related to our branch of
amniotes (Crocs, birds, mammals) than they are to snakes and lizards."
Given the circumstances surrounding this information, I found no
reason to doubt Ron's presentation. After your comments, I still find
no reason to doubt what Ron wrote.
So I did not "uncritically" repeat other peoples' errors. I evaluated
the information and the surrounding supporting circumstances before
repeat the statement which has not been established to be in error.
If Ron withdraws his claim, then I will apologize profusely for being
so crass and gullible as to be pulled in.
As to the amniote business, I already explained. I wanted to show how
the concept of "reptile" was inappropriate even though the animals
that are generally called reptiles constitute amniotes that, as a
group, fail to thermoregulate. I used the word "amniote" simply
because there is no ordinary language word to indicate the group. I
used the word "cold-blooded" (as I already explained) because it, like
"reptile" is now an inappropriate terminology just as is the word
"reptile" even though both have their uses in ordinary language. I
used the word "amniote" because I had no other to use. The word
"amniote" includes birds and mammals which were excluded by the phrase
"cold-blooded". In short (maybe I should just go back and erase all
the previous), the "cold blooded amniotes" just happen to include the
turtles, the snakes and lizards, the crocs, and the tuatara. By some
strange coincidence, that just happens to be the group we call the
"reptiles". The misconception is that these form some kind of natural
grouping and that they should all be closely related because of that
grouping.
Roger Shrubber
Mar 7, 2015, 10:05:02 PM3/7/15
to talk-o...@moderators.isc.org
RSNorman wrote:
> On Sun, 8 Mar 2015 00:39:09 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>> When you uncritically repeat other people's errors, that's not their
>> fault.
>>
>> And you still haven't explained how 'amniote' is supposed to clear up
>> the misconception about the relationships among testudines,
>> crurotarsians, and lepidosaurians that 'reptile' supposedly encourages.
>
> I fully admit to accepting RonO's authority on this point and that I
> did not get a second source to confirm its authenticity. If your
> first source is right you don't need the second source and I am not at
> all convinced he was not right. You have to understand that his
> original post on this was in excitement having just returned from a
> Gordon Conference. He wrote: " things like where turtles fit in the
> evolution of terrestrial vertebrates has been resolved. We aren't
> supposed to discuss the science of the meetings outside the meetings
> because of the unpublished data presented, ..."
Gordon Conferences are wondrous things. The scale is right, and the
> On Sun, 8 Mar 2015 00:39:09 +0000 (UTC), "Sneaky O. Possum"
> <sneaky...@gmail.com> wrote:
>> When you uncritically repeat other people's errors, that's not their
>> fault.
>>
>> And you still haven't explained how 'amniote' is supposed to clear up
>> the misconception about the relationships among testudines,
>> crurotarsians, and lepidosaurians that 'reptile' supposedly encourages.
>
> I fully admit to accepting RonO's authority on this point and that I
> did not get a second source to confirm its authenticity. If your
> first source is right you don't need the second source and I am not at
> all convinced he was not right. You have to understand that his
> original post on this was in excitement having just returned from a
> Gordon Conference. He wrote: " things like where turtles fit in the
> evolution of terrestrial vertebrates has been resolved. We aren't
> supposed to discuss the science of the meetings outside the meetings
> because of the unpublished data presented, ..."
participants are thus primed to share information in a very collegial
manner. It's intoxicating. It's easy to get carried away.
I have reservations about Ron. Crudely, I think he has a taste for
Kool-aid. But that's as much about me as it is about him. Someday
soon we'll have the actual data to check. That is what matters.
The confusion over the roots of turtles and other reptiles is
a long standing issue. I've seen some data suggesting some ancient
horizontal transfers that muddle the issue. I didn't really
understand the analysis I saw, and it was in a paper I reviewed
and rejected. So I'm waiting for somebody to explain it all to
this bear of very little brain. But with lots of data instead
of just with intoxicating words.
RSNorman
Mar 7, 2015, 10:19:59 PM3/7/15
to talk-o...@moderators.isc.org
Nobody now can tell whether it was just cruel cynicism because turtles
create chaos in any kind of reconstruction of the amniote line or
whether it was kindly guidance because someday turtles will be the key
to figuring it all out.
Roger Shrubber
Mar 7, 2015, 10:45:01 PM3/7/15
to talk-o...@moderators.isc.org
RSNorman wrote:
> The genius of the creator was in making it turtles all the way down.
> Nobody now can tell whether it was just cruel cynicism because turtles
> create chaos in any kind of reconstruction of the amniote line or
> whether it was kindly guidance because someday turtles will be the key
> to figuring it all out.
Back in the stone age, I used one of the drawers in my dorm
> The genius of the creator was in making it turtles all the way down.
> Nobody now can tell whether it was just cruel cynicism because turtles
> create chaos in any kind of reconstruction of the amniote line or
> whether it was kindly guidance because someday turtles will be the key
> to figuring it all out.
room for a pet turtle. I water-proofed it and, strangely enough,
then filled it with water and a turtle. I never saw her/him eat one
of the goldfish I also added but on occasion there were less
goldfish than there were the day before. He/she also seemed to
eat lettuce and kale. It worked quite well up until the point
where she/he died. That's some cruel cynicism for you.
Paul Ciszek
Mar 8, 2015, 8:19:58 AM3/8/15
to talk-o...@moderators.isc.org
In article <bjfnfat28c58l555h...@4ax.com>,
RSNorman <r_s_n...@comcast.net> wrote:
>
>The genius of the creator was in making it turtles all the way down.
>Nobody now can tell whether it was just cruel cynicism because turtles
>create chaos in any kind of reconstruction of the amniote line or
>whether it was kindly guidance because someday turtles will be the key
>to figuring it all out.
Perhaps the two of you could stop you infighting long enough to comment
>
>The genius of the creator was in making it turtles all the way down.
>Nobody now can tell whether it was just cruel cynicism because turtles
>create chaos in any kind of reconstruction of the amniote line or
>whether it was kindly guidance because someday turtles will be the key
>to figuring it all out.
on the cladogram of Amniota included in Wikipedia:
http://en.wikipedia.org/wiki/Reptile#Phylogeny
According to this, "Reptile" is not a defunct term (it would seem to
correspond to "Eureptilia" on the cladogram) provided you are willing
to include birds. I also take it that whatever arrangement Ron0 was
talking about from the Gordon conference disagrees with Wikipedia (not
that there is anything wrong with that.)
RSNorman
Mar 8, 2015, 9:39:57 AM3/8/15
to talk-o...@moderators.isc.org
On Sun, 8 Mar 2015 12:19:32 +0000 (UTC), nos...@nospam.com (Paul
Ciszek) wrote:
>
>In article <bjfnfat28c58l555h...@4ax.com>,
>RSNorman <r_s_n...@comcast.net> wrote:
>>
>>The genius of the creator was in making it turtles all the way down.
>>Nobody now can tell whether it was just cruel cynicism because turtles
>>create chaos in any kind of reconstruction of the amniote line or
>>whether it was kindly guidance because someday turtles will be the key
>>to figuring it all out.
>
>Perhaps the two of you could stop you infighting long enough to comment
>on the cladogram of Amniota included in Wikipedia:
>
>http://en.wikipedia.org/wiki/Reptile#Phylogeny
>
>According to this, "Reptile" is not a defunct term (it would seem to
>correspond to "Eureptilia" on the cladogram) provided you are willing
>to include birds. I also take it that whatever arrangement Ron0 was
>talking about from the Gordon conference disagrees with Wikipedia (not
>that there is anything wrong with that.)
Nobody is willing to include birds as belonging to the reptiles. Well,
Ciszek) wrote:
>
>In article <bjfnfat28c58l555h...@4ax.com>,
>RSNorman <r_s_n...@comcast.net> wrote:
>>
>>The genius of the creator was in making it turtles all the way down.
>>Nobody now can tell whether it was just cruel cynicism because turtles
>>create chaos in any kind of reconstruction of the amniote line or
>>whether it was kindly guidance because someday turtles will be the key
>>to figuring it all out.
>
>Perhaps the two of you could stop you infighting long enough to comment
>on the cladogram of Amniota included in Wikipedia:
>
>http://en.wikipedia.org/wiki/Reptile#Phylogeny
>
>According to this, "Reptile" is not a defunct term (it would seem to
>correspond to "Eureptilia" on the cladogram) provided you are willing
>to include birds. I also take it that whatever arrangement Ron0 was
>talking about from the Gordon conference disagrees with Wikipedia (not
>that there is anything wrong with that.)
perhaps somebody is -- in teaching I would dismiss birds as simply
warm reptiles with feathers. But then intro biology has an awful lot
of material to get through in one semester and you have to short
change many things.
My impression is that RonO was talking about new and as yet
unpublished data that does disagree with the traditional thinking.
Since it is unpublished, I do not have access to it. And, as Roger
Shrubber points out, very often there is data that is presented at
meetings but fails to pass peer review and so never gets published.
RSNorman
Mar 8, 2015, 9:44:58 AM3/8/15
to talk-o...@moderators.isc.org
children. This was before people understood that they were not pets
but rather Salmonella breeding grounds. In any event, you would get
special turtle food for them. Unfortunately, the food had very little
nutritive value for the turtles. Turtles starve to death very slowly
and you can't see how skinny they are so the kids were happy for a
while and anyway they got bored with the turtle long before it died.
So everybody was happy, except the turtles.
RonO
Mar 8, 2015, 10:09:57 AM3/8/15
to talk-o...@moderators.isc.org
vertebrates.
Ron Okimoto
John Harshman
Mar 8, 2015, 10:19:57 AM3/8/15
to talk-o...@moderators.isc.org
really claiming that diapsids are polyphyletic?
RonO
Mar 8, 2015, 11:19:57 AM3/8/15
to talk-o...@moderators.isc.org
Ron Okimoto
John Harshman
Mar 8, 2015, 12:19:57 PM3/8/15
to talk-o...@moderators.isc.org
RSNorman
Mar 8, 2015, 12:54:56 PM3/8/15
to talk-o...@moderators.isc.org
abjectly apologize for repeating what RonO wrote. So leave out mammal
completely from the argument: it is still true that turtles are
closer to birds than they are to snakes and lizards.
Bob Casanova
Mar 10, 2015, 2:04:50 PM3/10/15
to talk-o...@moderators.isc.org
On Sat, 07 Mar 2015 17:52:48 -0500, the following appeared
OK; thanks. ;-)
>It used to be the standard teaching saw that amphibians have a
>3-chambered heart, "reptiles" a 3-1/2, and birds and mammals a
>4-chambered heart. The crocodilian heart is pretty much four separate
>chambers. However there is no real evolutionary succession shown
>because different groups divided the single ventricle now exhibited by
>amphibians in different non-homologous ways and in different stages to
>produce the completely separated two ventricles and four chambers in
>different animals. What is more interesting to me is the fate of the
>aortic arches. Fish have multiple bilaterally paired arches from the
>heart passing through the different rows of gills on both the left and
>the right sides.In mammals, a left aortic arche forms the main
>systemic connection between the heart and the dorsal aorta. Birds
>have the same pattern of complete separation of the pulmonary and
>systemic loop but they use a right aortic arch to make the connection.
>So obviously the completely divided double circulation of birds and
>mammals evolved separately as did the process of division of the
>ventricle.
Thanks! Apparently (as I suspected might be the case) my
memory was a bit defective, as the conflation of "birds" and
"three-chambered heart" shows.
The different paths taken by birds and mammals is
interesting, and indicates (to me) that the change started
after the split from a common ancestor, probably an
amphibian. True?
>It used to be the standard teaching saw that amphibians have a
>3-chambered heart, "reptiles" a 3-1/2, and birds and mammals a
>4-chambered heart. The crocodilian heart is pretty much four separate
>chambers. However there is no real evolutionary succession shown
>because different groups divided the single ventricle now exhibited by
>amphibians in different non-homologous ways and in different stages to
>produce the completely separated two ventricles and four chambers in
>different animals. What is more interesting to me is the fate of the
>aortic arches. Fish have multiple bilaterally paired arches from the
>heart passing through the different rows of gills on both the left and
>the right sides.In mammals, a left aortic arche forms the main
>systemic connection between the heart and the dorsal aorta. Birds
>have the same pattern of complete separation of the pulmonary and
>systemic loop but they use a right aortic arch to make the connection.
>So obviously the completely divided double circulation of birds and
>mammals evolved separately as did the process of division of the
>ventricle.
memory was a bit defective, as the conflation of "birds" and
"three-chambered heart" shows.
The different paths taken by birds and mammals is
interesting, and indicates (to me) that the change started
after the split from a common ancestor, probably an
amphibian. True?
RSNorman
Mar 10, 2015, 2:29:52 PM3/10/15
to talk-o...@moderators.isc.org
On Tue, 10 Mar 2015 11:03:39 -0700, Bob Casanova <nos...@buzz.off>
I don't know the physiology of ancient amphibians but once you abandon
using gills even in larval stages or using the skin as a major
respiratory structure (both are seen in modern amphibians), then a
complete double circulation separating the lungs (pulmonary loop) from
the body (systemic loop) is a major advantage. So the changes no
doubt began early in the amniote evolutionary stages with multiple
lines using different approaches with different successes in that
direction. Eventually there were two winners, birds and mammals.
using gills even in larval stages or using the skin as a major
respiratory structure (both are seen in modern amphibians), then a
complete double circulation separating the lungs (pulmonary loop) from
the body (systemic loop) is a major advantage. So the changes no
doubt began early in the amniote evolutionary stages with multiple
lines using different approaches with different successes in that
direction. Eventually there were two winners, birds and mammals.
Bob Casanova
Mar 12, 2015, 12:34:45 PM3/12/15
to talk-o...@moderators.isc.org
On Tue, 10 Mar 2015 14:28:20 -0400, the following appeared
Makes sense. Thanks again!
Walter Bushell
Mar 23, 2015, 6:24:11 AM3/23/15
to talk-o...@moderators.isc.org
In article <mct0h9$gn1$1...@dont-email.me>, RonO <roki...@cox.net>
wrote:
> You can go deeper
> into denial or you can start to better understand the diversity and
> evolution of life on earth, that is the future.
Sounds like they will need scuba gear to go that deep in de Nile.
--
Never attribute to stupidity that which can be explained by greed. Me.
wrote:
> You can go deeper
> into denial or you can start to better understand the diversity and
> evolution of life on earth, that is the future.
Sounds like they will need scuba gear to go that deep in de Nile.
--
Never attribute to stupidity that which can be explained by greed. Me.
Walter Bushell
Mar 23, 2015, 6:29:10 AM3/23/15
to talk-o...@moderators.isc.org
> n the late 1990's I submitted a
> grant proposal to sequence 10 mitochondrial genomes (only around 170,000
> base-pairs of DNA sequence) for over $250,000, about 5 years later I
> sequenced 9 mitochondrial genomes for around $25,000 once our department
> had it's own automated (Sanger type) DNA sequencers. Now with the next
> generation DNA sequence technology. The new series of next generation
> sequencing units is supposed to drop the cost of sequencing a human
> genome (around a 3 gigabase genome) to much less than $1,000 for
> reagents (the claim is less than 400 dollars) and since you can assemble
> and do batch analysis of a bunch of human genomes at one time the cost
> of sequencing and assembly of a human genome is less than $1,000.
Wow. Shades of the computer revolution, which IIUC is a major part of
this.
> grant proposal to sequence 10 mitochondrial genomes (only around 170,000
> base-pairs of DNA sequence) for over $250,000, about 5 years later I
> sequenced 9 mitochondrial genomes for around $25,000 once our department
> had it's own automated (Sanger type) DNA sequencers. Now with the next
> generation DNA sequence technology. The new series of next generation
> sequencing units is supposed to drop the cost of sequencing a human
> genome (around a 3 gigabase genome) to much less than $1,000 for
> reagents (the claim is less than 400 dollars) and since you can assemble
> and do batch analysis of a bunch of human genomes at one time the cost
> of sequencing and assembly of a human genome is less than $1,000.
Wow. Shades of the computer revolution, which IIUC is a major part of
this.
RonO
Mar 27, 2015, 7:38:58 AM3/27/15
to talk-o...@moderators.isc.org
genome project started in the 1990's the goal was to get the cost of
sequencing down to 1 dollar per base. By the time that the human genome
was completed (ahead of schedule and under budget by around 60%) the
cost of DNA sequencing a human genome was only around 100 million
dollars instead of 3 billion dollars. The first human genome still cost
around 3 billion dollars to sequence, but they started out with pretty
basic technology and developed the tech needed along the way. The
chicken genome was one of the first genomes picked to be sequenced after
the human genome was published and it was only 0.4 the size of the human
genome and cost around 25 million dollars to sequence. Now just about
anyone can sequence a chicken genome for around $1,000, and if you use
the newest machines it is a fraction of that cost, but they are using
the new machines for the mega projects sequencing thousands of genomes.
Most of the cost is likely in the analysis today. There has been a
leveling out of the advances in cost efficiency, but if they get the
nanopore sequencing tech worked out there will likely be another
dramatic drop in sequencing costs. These guys are sequencing single
strands of DNA as they move through a nanopore and they can have
hundreds of thousands of nanopores in a membrane.
http://www.genome.gov/sequencingcosts/
Ron Okimoto
christi...@brown.edu
Mar 29, 2015, 2:08:53 PM3/29/15
to talk-o...@moderators.isc.org
>
> I don't know the physiology of ancient amphibians but once you abandon
> using gills even in larval stages or using the skin as a major
> respiratory structure (both are seen in modern amphibians), then a
> complete double circulation separating the lungs (pulmonary loop) from
> the body (systemic loop) is a major advantage. So the changes no
> doubt began early in the amniote evolutionary stages with multiple
> lines using different approaches with different successes in that
> direction. Eventually there were two winners, birds and mammals.
The division of the basic truncus arteriosus leaving the heart (ie. the ventral aorta of gilled vertebrates) into distinct pulmonary and systemic vessels leaving the heart separately is probably a within-amniote feature done convergently between synapsids (mammals) and sauropsids ("reptiles" and birds), as there is no evidence that ancestors of mammals ever had the two separate systemic arches system seen in non-avian sauropsids.
Given the fact that there are around 9000 extant species of squamates (lizards and snakes), as opposed to around 5500 extant species of mammals, it's a matter of debate as to who has been the "winners".
Öö Tiib
Mar 30, 2015, 4:48:49 AM3/30/15
to talk-o...@moderators.isc.org
On Sunday, 29 March 2015 21:08:53 UTC+3, christi...@brown.edu wrote:
>
> Given the fact that there are around 9000 extant species of
> squamates (lizards and snakes), as opposed to around 5500 extant
> species of mammals, it's a matter of debate as to who has been
> the "winners".
It seems that more versatile and flexible life-forms are more
>
> Given the fact that there are around 9000 extant species of
> squamates (lizards and snakes), as opposed to around 5500 extant
> species of mammals, it's a matter of debate as to who has been
> the "winners".
competitive on wider area and more primitive life-forms need more
species for adaptation. Why else beetles got more than 350,000
species? On the other hand jackals, coyotes, wolves and so on can
hybrid healthy puppies so are these species or subspecies? Different
human races look sometimes more distant side by side than those
"species" of Canini to me.
Bob Casanova
Mar 30, 2015, 2:08:47 PM3/30/15
to talk-o...@moderators.isc.org
On Mon, 30 Mar 2015 01:44:31 -0700 (PDT), the following
appeared in talk.origins, posted by 嘱 Tiib <oot...@hot.ee>:
This Wiki article...
http://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus
....shows the various subspecies of Canis lupus worldwide.
Interestingly, the coyote (Canis latrans) is *not*
apparently considered a subspecies (and has quite a few
subspecies of its own), although hybridization with domestic
dogs, and especially with gray wolves, is apparently far
from unknown. See:
http://en.wikipedia.org/wiki/Coyote
I suspect the accepted taxonomy may well change in the
future, given the ability of different defined species to
have fertile hybrid offspring.
appeared in talk.origins, posted by 嘱 Tiib <oot...@hot.ee>:
http://en.wikipedia.org/wiki/Subspecies_of_Canis_lupus
....shows the various subspecies of Canis lupus worldwide.
Interestingly, the coyote (Canis latrans) is *not*
apparently considered a subspecies (and has quite a few
subspecies of its own), although hybridization with domestic
dogs, and especially with gray wolves, is apparently far
from unknown. See:
http://en.wikipedia.org/wiki/Coyote
I suspect the accepted taxonomy may well change in the
future, given the ability of different defined species to
have fertile hybrid offspring.
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