https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release: https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have homologous gene ancestors. It seems to be a new gene that is associated
with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release: >https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have >homologous gene ancestors. It seems to be a new gene that is associated >with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the >elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
Ron Okimoto
On 7/25/2023 3:47 AM, Glenn wrote:
On Monday, July 24, 2023 at 3:50:50 PM UTC-7, RonO wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeasSo why is this called an orphan gene?
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated
with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
It doesn't have any gene parents in terms of homologous sequences.
There are no homologous genes to this orphan gene in vertebrates. When
you evolve a new gene by gene duplication, like the flatellar genes
that Minnich was involved with, you can see how that gene was derived
from another gene that already existed. It turns out that this gene
seems to have evolved from noncoding sequence. The ancestral sequence
was a bit of the elastin gene, but it was a noncoding bit of the
elastin gene, and not only that, but the protein encoded by the new
gene is coded off the anti sense strand of the elastin gene.
So it seems to have evolved from a duplicated bit of DNA, but that DNA
did not code for any existing protein sequence. It evolved from a
noncoding sequence.
Ron Okimoto
On Monday, July 24, 2023 at 3:50:50 PM UTC-7, RonO wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeasSo why is this called an orphan gene?
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated
with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
On 7/25/2023 3:47 AM, Glenn wrote:
On Monday, July 24, 2023 at 3:50:50 PM UTC-7, RonO wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeasSo why is this called an orphan gene?
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene >> that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
It doesn't have any gene parents in terms of homologous sequences.
There are no homologous genes to this orphan gene in vertebrates. When
you evolve a new gene by gene duplication, like the flatellar genes that Minnich was involved with, you can see how that gene was derived from another gene that already existed. It turns out that this gene seems to
have evolved from noncoding sequence. The ancestral sequence was a bit
of the elastin gene, but it was a noncoding bit of the elastin gene, and
not only that, but the protein encoded by the new gene is coded off the
anti sense strand of the elastin gene.
So it seems to have evolved from a duplicated bit of DNA, but that DNA
did not code for any existing protein sequence. It evolved from a
noncoding sequence.
On Tuesday, July 25, 2023 at 3:25:51 AM UTC-7, RonO wrote:
On 7/25/2023 3:47 AM, Glenn wrote:It appears this noncoding sequence has homologous gene ancestors, so where is the "mystery" in how a mutation that happened in a particular place created a coding gene in one species?
On Monday, July 24, 2023 at 3:50:50 PM UTC-7, RonO wrote:It doesn't have any gene parents in terms of homologous sequences.
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeasSo why is this called an orphan gene?
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >>>> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the >>>> elastin gene got associated with some transposons and formed a new gene >>>> that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit >>>> of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
There are no homologous genes to this orphan gene in vertebrates. When
you evolve a new gene by gene duplication, like the flatellar genes that
Minnich was involved with, you can see how that gene was derived from
another gene that already existed. It turns out that this gene seems to
have evolved from noncoding sequence. The ancestral sequence was a bit
of the elastin gene, but it was a noncoding bit of the elastin gene, and
not only that, but the protein encoded by the new gene is coded off the
anti sense strand of the elastin gene.
So it seems to have evolved from a duplicated bit of DNA, but that DNA
did not code for any existing protein sequence. It evolved from a
noncoding sequence.
On 7/25/2023 5:24 AM, jillery wrote:
On Mon, 24 Jul 2023 17:45:50 -0500, RonO <roki...@cox.net> wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene >> that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
Ron Okimoto
Ron, It looks to me like Jillery was agreeing with you.If in fact the gene responsible for flame cone cells had no
identifiable precursor, that would be the kind of gene Behe and other cdesign proponentsists should point to as evidence of purposeful
design. OTOH if in fact that gene is homologous to the antisense
strand of a noncoding region, it no longer qualifies as having no identifiable precursor, and Behe et al still lack the evidence they
need to make that case.
This isn't true. Where do you expect new genes to come from? They
pretty much have to come from preexisting DNA. The DNA has to exist in
order to change into a new gene. In this case the sequence was within
the transcribed region of an existing gene, but it wasn't part of the transcript because it was on the anti sense strand and would not have
been transcribed. It also was part of a noncoding sequence, so even if
it had been on the sense strand it wouldn't have coded for any protein sequence. De novo genes really do have to evolve from existing DNA
sequence. In this case the bit of sequence got associated with
transposons in another part of the genome and started to get transcribed
and it turned out to code for something that the sea horse could use.
It is about as mind boggling of an example of a new gene as you can get.
The original DNA sequence wasn't coding for any protein where it
previously had existed. What is the chance that such a bit of noncoding
DNA could evolve into a useful gene?
Ron Okimoto
On Mon, 24 Jul 2023 17:45:50 -0500, RonO <rokimoto@cox.net> wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated
with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
Ron Okimoto
If in fact the gene responsible for flame cone cells had no
identifiable precursor, that would be the kind of gene Behe and other
cdesign proponentsists should point to as evidence of purposeful
design. OTOH if in fact that gene is homologous to the antisense
strand of a noncoding region, it no longer qualifies as having no identifiable precursor, and Behe et al still lack the evidence they
need to make that case.
On 7/25/2023 5:24 AM, jillery wrote:
On Mon, 24 Jul 2023 17:45:50 -0500, RonO <rokimoto@cox.net> wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >>> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the
elastin gene got associated with some transposons and formed a new gene
that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit
of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
Ron Okimoto
If in fact the gene responsible for flame cone cells had no
identifiable precursor, that would be the kind of gene Behe and other
cdesign proponentsists should point to as evidence of purposeful
design. OTOH if in fact that gene is homologous to the antisense
strand of a noncoding region, it no longer qualifies as having no
identifiable precursor, and Behe et al still lack the evidence they
need to make that case.
This isn't true. Where do you expect new genes to come from? They
pretty much have to come from preexisting DNA. The DNA has to exist in >order to change into a new gene. In this case the sequence was within
the transcribed region of an existing gene, but it wasn't part of the >transcript because it was on the anti sense strand and would not have
been transcribed. It also was part of a noncoding sequence, so even if
it had been on the sense strand it wouldn't have coded for any protein >sequence. De novo genes really do have to evolve from existing DNA >sequence. In this case the bit of sequence got associated with
transposons in another part of the genome and started to get transcribed
and it turned out to code for something that the sea horse could use.
It is about as mind boggling of an example of a new gene as you can get.
The original DNA sequence wasn't coding for any protein where it
previously had existed. What is the chance that such a bit of noncoding
DNA could evolve into a useful gene?
On Tue, 25 Jul 2023 18:25:40 -0500, RonO <rokimoto@cox.net> wrote:
On 7/25/2023 5:24 AM, jillery wrote:
On Mon, 24 Jul 2023 17:45:50 -0500, RonO <rokimoto@cox.net> wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >>>> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to
code for this new protein gene. They think that a noncoding bit of the >>>> elastin gene got associated with some transposons and formed a new gene >>>> that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit >>>> of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding
for anything before.
Ron Okimoto
If in fact the gene responsible for flame cone cells had no
identifiable precursor, that would be the kind of gene Behe and other
cdesign proponentsists should point to as evidence of purposeful
design. OTOH if in fact that gene is homologous to the antisense
strand of a noncoding region, it no longer qualifies as having no
identifiable precursor, and Behe et al still lack the evidence they
need to make that case.
This isn't true. Where do you expect new genes to come from? They
pretty much have to come from preexisting DNA. The DNA has to exist in
order to change into a new gene. In this case the sequence was within
the transcribed region of an existing gene, but it wasn't part of the
transcript because it was on the anti sense strand and would not have
been transcribed. It also was part of a noncoding sequence, so even if
it had been on the sense strand it wouldn't have coded for any protein
sequence. De novo genes really do have to evolve from existing DNA
sequence. In this case the bit of sequence got associated with
transposons in another part of the genome and started to get transcribed
and it turned out to code for something that the sea horse could use.
It is about as mind boggling of an example of a new gene as you can get.
The original DNA sequence wasn't coding for any protein where it
previously had existed. What is the chance that such a bit of noncoding
DNA could evolve into a useful gene?
What I wrote above is true and correct. The phrase relevant to my
comment above is "identifiable precursor". Your previous comment
implied that only existing functioning genes qualify, which raises the question you ask above; "where do new genes come from?" My point is
that any identifiable sequence, whether functional or not, is an "identifiable precursor" by definition as far as "de novo" applies to
Behe et al's concept of ID.
WRT your last question, I have no idea what are the chances of
non-coding DNA to become functional. As a first approximation, I
presume it's non-zero and happens via unguided natural processes; no purposeful intelligent agent required.
For completeness, I acknowledge the standard way to create "new genes"
is for existing genes, with or without prior duplication, to change
function, and that the pathway you describe above would be a
non-standard but still identifiable way. My impression is there are
several non-standard yet identifiable ways for non-coding DNA
sequences to become functional genes.
On 7/26/2023 3:48 AM, jillery wrote:
On Tue, 25 Jul 2023 18:25:40 -0500, RonO <rokimoto@cox.net> wrote:
On 7/25/2023 5:24 AM, jillery wrote:
On Mon, 24 Jul 2023 17:45:50 -0500, RonO <rokimoto@cox.net> wrote:
https://link.springer.com/article/10.1007/s00441-023-03779-1#citeas
The article is paywalled.
Press Release:
https://www.sophia.ac.jp/eng/article/news/release/release20230724/
They found a gene that seems to be an orphan gene that doesn't have
homologous gene ancestors. It seems to be a new gene that is associated >>>>> with the pouch of sea horses. It looks like the coding sequence is
derived from the antisense strand of the elastin gene. It is a
noncoding bit of the elastin gene, but the antisense strand seems to >>>>> code for this new protein gene. They think that a noncoding bit of the >>>>> elastin gene got associated with some transposons and formed a new gene >>>>> that is now expressed in the pouches of sea horses.
I guess Behe can't look for his three neutral mutations because the
whole coding sequence was once the antisense strand of a noncoding bit >>>>> of the elastin gene. Instead you have to try to calculate what the
chances are of creating a new gene from a sequence that wasn't coding >>>>> for anything before.
Ron Okimoto
If in fact the gene responsible for flame cone cells had no
identifiable precursor, that would be the kind of gene Behe and other
cdesign proponentsists should point to as evidence of purposeful
design. OTOH if in fact that gene is homologous to the antisense
strand of a noncoding region, it no longer qualifies as having no
identifiable precursor, and Behe et al still lack the evidence they
need to make that case.
This isn't true. Where do you expect new genes to come from? They
pretty much have to come from preexisting DNA. The DNA has to exist in
order to change into a new gene. In this case the sequence was within
the transcribed region of an existing gene, but it wasn't part of the
transcript because it was on the anti sense strand and would not have
been transcribed. It also was part of a noncoding sequence, so even if
it had been on the sense strand it wouldn't have coded for any protein
sequence. De novo genes really do have to evolve from existing DNA
sequence. In this case the bit of sequence got associated with
transposons in another part of the genome and started to get transcribed >>> and it turned out to code for something that the sea horse could use.
It is about as mind boggling of an example of a new gene as you can get. >>> The original DNA sequence wasn't coding for any protein where it
previously had existed. What is the chance that such a bit of noncoding >>> DNA could evolve into a useful gene?
What I wrote above is true and correct. The phrase relevant to my
comment above is "identifiable precursor". Your previous comment
implied that only existing functioning genes qualify, which raises the
question you ask above; "where do new genes come from?" My point is
that any identifiable sequence, whether functional or not, is an
"identifiable precursor" by definition as far as "de novo" applies to
Behe et al's concept of ID.
Behe's definition just doesn't apply to reality. The Drosophila example
put up a few years ago was an example of a noncoding sequence between
genes that had evolved recently so that they could identify that the >precursor sequence still existed in the closely related species, and it
was still noncoding sequence, but in that one species it had acquired >mutations that allowed the previously noncoding sequence to start to be >transcribed and produce a protein product. You really can't have de
novo gene creation without using existing sequence. How are you going
to evolve a new gene without first having the sequence to use to make
the new gene? It looks like even the designer uses existing sequence to >evolve new genes.
If Behe wants to claim that his designer wasn't involved in the new gene >creation it would make the argument as stupid as his whale devolution >argument. Just claiming that the designer didn't have to be involved in >breaking the whale genes, and that normal evolutionary mechanisms would
be expected to select for such changes, does not mean that, that
evolution did not happen. It obviously did happen, but the designer
just wasn't needed to do anything.
WRT your last question, I have no idea what are the chances of
non-coding DNA to become functional. As a first approximation, I
presume it's non-zero and happens via unguided natural processes; no
purposeful intelligent agent required.
It is non zero, and it looks like whatever happened just happened. Once
it did happen a protein was produced that got involved in something that >gave the animal some type of selective advantage. It doesn't matter how >improbable something is once it happens, it has happened and there isn't >anything that anyone can do about it. These rare events become part of
the evolution of that biological lineage because it doesn't have to
happen again. Descent with modification just means that it can further >evolve as it is reproduced in that lineage.
For completeness, I acknowledge the standard way to create "new genes"
is for existing genes, with or without prior duplication, to change
function, and that the pathway you describe above would be a
non-standard but still identifiable way. My impression is there are
several non-standard yet identifiable ways for non-coding DNA
sequences to become functional genes.
In this reality a new gene pretty much has to evolve from preexisting >sequence. There are enzymes that can make polymers of nucleic acid, but >they are limited in what they can do like poly adenylation. DNA
replication polymerase skipping or slipping is using existing DNA
template to make a new sequence. Virus can bring in new DNA, but that
DNA already exists, but may not exist in the host genome.
Ron Okimoto
| Sysop: | Keyop |
|---|---|
| Location: | Huddersfield, West Yorkshire, UK |
| Users: | 307 |
| Nodes: | 16 (2 / 14) |
| Uptime: | 69:00:44 |
| Calls: | 6,915 |
| Files: | 12,380 |
| Messages: | 5,431,893 |