What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:Most genes in complex organisms express regulatory RNAs” [5].
2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]
10% - “90% of your genome is junk” (Laurence Moran) [2]
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those inother animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the majority
Are Larry and Dan DNA dinosaurs?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On 11/25/2023 4:41 AM, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a
controversial and developing issue, but also that there appears to be
an ongoing movement away from “Junk DNA”, even to the proposal of a “A >> Kuhnian revolution
in molecular biology: Most genes in complex organisms expressDenial isn't anyway forward. Obfuscation and science denial are what
regulatory RNAs” [5].
the ID perps call the switch scam. They tell rubes like you that the
switch scam has nothing to do with ID nor creationism because they do
not want the stupidity associated with losers that are still making the
god-of-the-gaps claims to support IDiocy and creationism. This is just
the same type of obfuscation and science denial that the scientific
creationists used to employ. It is the same type of stupidity like
their "90% water" and humans share 50% of their genes with bananas.
They are just attempts to obfuscate and deny the existing science. All
the evidence still supports biological evolution, creationists just make
it sound like it doesn't.
2% - “Our 21,000 or so protein-coding genes account for less than 2% of
the genome's total nucleotides.” [1]
This has been the estimate since we figured out that the average protein
was 300 amino acids in length, and had a rough order of magnitude
estimate of the number of proteins were in plants and animals. Once we
could estimate the amount of DNA in the nucleus everyone started asking
why there was so much extra DNA in the genome.
10% - “90% of your genome is junk” (Laurence Moran) [2]
In the 1960's regulatory sequences were identified, and it was proposed
that a lot of the DNA was used for regulatory purposes, but we also had
research indicating that a lot of the DNA was composed of repetitive
sequences. Heterochromatin are stretches of DNA composed of short
tandem repeats. They were first identified by how they could be
differentially stained for cytological analysis. Early research that
could only depend on genetic recombination and chromosome structural
features that could be identified under a microscope determined that
heterochromatin was deficient in genes. It seems to be some type of
spacer between gene containing DNA sequence. In the 1970's and 80's
transposons and retrovirus were verified to exist, and they were
determined to be DNA parasites. Many retrovirus can make complete virus
that can make you sick and can infect other individuals. The AIDs virus
is a retrovirus that inserts into your genome. Transposons are shorter
bits of DNA that mostly seem to have evolved from retrovirus, but some
transposable elements seem to have other origins. There were also DNA
virus that insert into DNA like herpes. Heterochromatin and DNA
parasites compose most of the genome, and of the around 35% of our
genome thought to be composed of single copy sequence most of that
sequence is just fossil DNA of transposons and retrovirus that have
decayed by mutation into sequence that we can't tell from random DNA
sequence. Parasitic DNA was classified as part of the "junk" DNA even
though it had a selfish function. McClintock's initial work starting in
the 1930's on transposable elements indicated that they could affect
gene regulation, and she initially proposed that they were gene
regulatory elements that could move around the genome. She detected
them on how they could turn genes on and off. Later research determined
that their affect on genes was mostly due to them jumping into or near a
gene and affecting normal gene regulation. Transposons are just like
any other insertion mutation that might happen. They usually carry
their own trancriptional regulatory sequences and they can kill a gene
or alter it's expression. Like any other mutation this can be good,
bad, or neutral, but mostly bad. ENCODE screwed up by counting the
regulatory sequences found in transposons and retrovirus as legitimate
regulatory sequences. They do regulate genes around them, but mostly
this altered regulation is just tolerated. Most of the time it would
have a significant effect it would be deleterious, and sometimes just
like any mutation they can be beneficial.
It just turned out that a whole lot of DNA in our genome is due to DNA
parasites. There is a recently evolved transposon in primates called
ALU, and in the last 80 million years it accounts for over 10% of the
human genome, but was zero in our distant ancestors. Our genome is full
of even older transposon families that we share with other mammals, and
sometimes even reptiles, but if you go back too far the transposons have
evolved so much that it gets difficult to determine if they are related
or not. Life forms are in a constant battle to reduce the transposon
load in their genomes. One proposed use of heterochromatin is as
transposon and retrovirus traps because the sequence evolves rapidly by
recombination and replication skipping and the inserted transposons are
eliminated more rapidly from the genome.
15% - “Mutational load considerations lead to the conclusion that the
functional fraction within the human genome cannot exceed 15%.”(Dan
Graur) [3]
This is a proposed limit of how much functional DNA we can have in our
genome, and my guess is that it could be off by a significant amount,
but that doesn't matter. That likely doesn't matter because as
indicated above most of the DNA in our genome is due to transposons and
retrovirus, and heterochromatin that may function as transposon traps
and the mutation rate in heterochromatin is supposed to be high. We
want mutations in transposons and retrovirus because we don't want them
jumping around and messing up existing gene function. DNA parasites
account for a significant fraction of the mutational load on functional
sequences. You just have to look up ALU and note all the genetic
diseases that seem to occur within a single family that they are
responsible for (new genetic defects not ancient ones like Tay Sachs or
sickle cell anemia). We want mutations to inactivate transposons, but
ENCODE chose to include them in functional DNA.
We are likely safely within that 15% limit for the DNA that we rely on
to make us humans. Sure transposons affect gene function, but the gene
functions that they affect are what made us human in the first place.
Like any mutation it can be good, bad, or neutral, and throughout our
evolutionary history including the present, transposon activity is
mostly bad for us. What is sad is that some of the transposition
effects likely have been beneficial, and have likely had a significant
impact on the evolution of humans from our primate ancestors, but it is
the mutator activity of transposons and retrovirus that have done that.
The mutator activity is what lifeforms have been selecting against
likely since DNA parasites evolved. In research organisms like
Drosophila we can mess up the systems that suppress transposition and
you can go from something like 10^-8 specific gene knockouts to 10^-5 to
10^-4 gene knockouts for a single gene that they are screening for, and
the gene knockouts will be due to transposon insertions.
If you include transposons as functional DNA you are including a
significant cause of the mutational load on the organism. Really, the
mutational load would be less if we didn't have transposons.
80% - “The ENCODE Consortium reported that its members were able to
assign biochemical functions to over 80% of the genome.”[4]
They have taken a beating for their estimate,
and it has all been
justified. They were just stupid.
??% - “The genomic programming of developmentally complex organisms was
misunderstood for much of the last century. The mammalian genome
harbors only ∼20 000 protein-coding genes, similar in number and with
largely orthologous functions as those in other animals, including
simple nematodes. On the other hand, the extent of non-protein-coding
DNA increases with increasing developmental and cognitive complexity,
reaching 98.5% in humans. Moreover, high throughput analyses have shown
that the majority of the mammalian genome is differentially and
dynamically transcribed during development to produce tens if not
hundreds of thousands of short and long non-protein-coding RNAs that
show highly specific expression patterns and subcellular locations.
These RNAs function at many different levels of gene expression and
cell biology, including translational control, subcellular domain
formation, and guidance of the epigenetic processes that underpin
development, brain function and physiological adaptation, augmented by
the superimposition of plasticity by RNA editing, RNA modification and
retrotransposon mobilization. The evidence is now overwhelming that
there is a massive network of RNA-directed regulatory transactions in
architecturally organised and spatially specialised multicellular
organisms, which extends to transgenerational inheritance.” [5]
This is only a tendency across animals, and pretty much ends as being
very predictive when vertebrates evolved due to the whole genome
duplication from a cordate. That seems to have been enough DNA to
create all the diversity among vertebrates. Birds have less than half
the DNA of humans, dogs and cats, but some birds are likely smarter than
your dog or cat, and they can fly. Birds have a lot fewer transposable
than mammals.
Are Larry and Dan DNA dinosaurs?
DNA realists. Can you find any wide spread scientific support for the
ENCODE stupidity?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur
established a valid falsifiability criterion for evolution? Or would
even a 100% functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of function
in non-protein-coding DNA?
Just try to find any widespread scientific support for your ENCODE
claims. They aren't supported because transposable elements were placed
among the junk DNA for a very good reason. They obviously need to be
tracked for medical purposes because of their deleterious effects, but
in terms of being functional sequence, their evolutionary significance
has only been a very minor fraction of parasitic multiplication events
that have done something interesting enough to be selected for in our
ancestors.
Really, most of what is called single copy sequence in our genome is
likely ancient transposable element sequences that have mutated beyond
recognition. They now look like random sequence. Transposable elements
have likely been a plague before eukaryotes evolved. Once a mutation
inactivates them they can no longer jump around the genome and are stuck
in place, and they slowly degenerate into unrecognizable sequence or get
removed by the random deletions that may occur. We have transposon
insertion sites in common with our primate relatives, and these
transposon sequences have evolved just as much as the surrounding DNA.
One proposal is that we have a lot of extra DNA in order for
transposition events to cause less damage. If we didn't have so much
extra DNA a transposable element would be more likely to jump into a
required functional sequence and kill it.
You still do not want to believe in the designer of our genomes, so why
make this argument? Just think of how the design progressed from the
first vertebrate ancestor. The Reason to Believe old earth creationists
claim that the new genome designs came to be by "recreation" events over
time. The genomes created could be so closely related that the two
creations could still interbreed. They do throw their model out the
window in order to have whales created before land animals, and they
have issues with the Cambrian explosion occurring before land plants
existed, but can you believe in the designer of our genome.
Ron Okimoto
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2]
https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On 2023-11-25 15:20:57 +0000, RonO said:
On 11/25/2023 4:41 AM, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a
controversial and developing issue, but also that there appears to be
an ongoing movement away from “Junk DNA”, even to the proposal of a
“A Kuhnian revolution
Whenever I see the phrase "Kuhnian revolution" I know that some nonsense
is going to follow.
in molecular biology: Most genes in complex organisms expressDenial isn't anyway forward. Obfuscation and science denial are what
regulatory RNAs” [5].
the ID perps call the switch scam. They tell rubes like you that the
switch scam has nothing to do with ID nor creationism because they do
not want the stupidity associated with losers that are still making the
god-of-the-gaps claims to support IDiocy and creationism. This is just
the same type of obfuscation and science denial that the scientific
creationists used to employ. It is the same type of stupidity like
their "90% water" and humans share 50% of their genes with bananas.
They are just attempts to obfuscate and deny the existing science. All
the evidence still supports biological evolution, creationists just make
it sound like it doesn't.
2% - “Our 21,000 or so protein-coding genes account for less than 2%
of the genome's total nucleotides.” [1]
This has been the estimate since we figured out that the average protein
was 300 amino acids in length, and had a rough order of magnitude
estimate of the number of proteins were in plants and animals. Once we
could estimate the amount of DNA in the nucleus everyone started asking
why there was so much extra DNA in the genome.
10% - “90% of your genome is junk” (Laurence Moran) [2]
In the 1960's regulatory sequences were identified, and it was proposed
that a lot of the DNA was used for regulatory purposes, but we also had
research indicating that a lot of the DNA was composed of repetitive
sequences. Heterochromatin are stretches of DNA composed of short
tandem repeats. They were first identified by how they could be
differentially stained for cytological analysis. Early research that
could only depend on genetic recombination and chromosome structural
features that could be identified under a microscope determined that
heterochromatin was deficient in genes. It seems to be some type of
spacer between gene containing DNA sequence. In the 1970's and 80's
transposons and retrovirus were verified to exist, and they were
determined to be DNA parasites. Many retrovirus can make complete virus
that can make you sick and can infect other individuals. The AIDs virus
is a retrovirus that inserts into your genome. Transposons are shorter
bits of DNA that mostly seem to have evolved from retrovirus, but some
transposable elements seem to have other origins. There were also DNA
virus that insert into DNA like herpes. Heterochromatin and DNA
parasites compose most of the genome, and of the around 35% of our
genome thought to be composed of single copy sequence most of that
sequence is just fossil DNA of transposons and retrovirus that have
decayed by mutation into sequence that we can't tell from random DNA
sequence. Parasitic DNA was classified as part of the "junk" DNA even
though it had a selfish function. McClintock's initial work starting in
the 1930's on transposable elements indicated that they could affect
gene regulation, and she initially proposed that they were gene
regulatory elements that could move around the genome. She detected
them on how they could turn genes on and off. Later research determined
that their affect on genes was mostly due to them jumping into or near a
gene and affecting normal gene regulation. Transposons are just like
any other insertion mutation that might happen. They usually carry
their own trancriptional regulatory sequences and they can kill a gene
or alter it's expression. Like any other mutation this can be good,
bad, or neutral, but mostly bad. ENCODE screwed up by counting the
regulatory sequences found in transposons and retrovirus as legitimate
regulatory sequences. They do regulate genes around them, but mostly
this altered regulation is just tolerated. Most of the time it would
have a significant effect it would be deleterious, and sometimes just
like any mutation they can be beneficial.
It just turned out that a whole lot of DNA in our genome is due to DNA
parasites. There is a recently evolved transposon in primates called
ALU, and in the last 80 million years it accounts for over 10% of the
human genome, but was zero in our distant ancestors. Our genome is full
of even older transposon families that we share with other mammals, and
sometimes even reptiles, but if you go back too far the transposons have
evolved so much that it gets difficult to determine if they are related
or not. Life forms are in a constant battle to reduce the transposon
load in their genomes. One proposed use of heterochromatin is as
transposon and retrovirus traps because the sequence evolves rapidly by
recombination and replication skipping and the inserted transposons are
eliminated more rapidly from the genome.
15% - “Mutational load considerations lead to the conclusion that the
functional fraction within the human genome cannot exceed 15%.”(Dan
Graur) [3]
This is a proposed limit of how much functional DNA we can have in our
genome, and my guess is that it could be off by a significant amount,
but that doesn't matter. That likely doesn't matter because as
indicated above most of the DNA in our genome is due to transposons and
retrovirus, and heterochromatin that may function as transposon traps
and the mutation rate in heterochromatin is supposed to be high. We
want mutations in transposons and retrovirus because we don't want them
jumping around and messing up existing gene function. DNA parasites
account for a significant fraction of the mutational load on functional
sequences. You just have to look up ALU and note all the genetic
diseases that seem to occur within a single family that they are
responsible for (new genetic defects not ancient ones like Tay Sachs or
sickle cell anemia). We want mutations to inactivate transposons, but
ENCODE chose to include them in functional DNA.
We are likely safely within that 15% limit for the DNA that we rely on
to make us humans. Sure transposons affect gene function, but the gene
functions that they affect are what made us human in the first place.
Like any mutation it can be good, bad, or neutral, and throughout our
evolutionary history including the present, transposon activity is
mostly bad for us. What is sad is that some of the transposition
effects likely have been beneficial, and have likely had a significant
impact on the evolution of humans from our primate ancestors, but it is
the mutator activity of transposons and retrovirus that have done that.
The mutator activity is what lifeforms have been selecting against
likely since DNA parasites evolved. In research organisms like
Drosophila we can mess up the systems that suppress transposition and
you can go from something like 10^-8 specific gene knockouts to 10^-5 to
10^-4 gene knockouts for a single gene that they are screening for, and
the gene knockouts will be due to transposon insertions.
If you include transposons as functional DNA you are including a
significant cause of the mutational load on the organism. Really, the
mutational load would be less if we didn't have transposons.
80% - “The ENCODE Consortium reported that its members were able to
assign biochemical functions to over 80% of the genome.”[4]
They have taken a beating for their estimate,
I wish that were true, but Larry Moran's blog suggests that there are
still plenty of people who ought to know better but don't.
and it has all been
justified. They were just stupid.
??% - “The genomic programming of developmentally complex organisms
was misunderstood for much of the last century. The mammalian genome
harbors only ∼20 000 protein-coding genes, similar in number and with
largely orthologous functions as those in other animals, including
simple nematodes. On the other hand, the extent of non-protein-coding
DNA increases with increasing developmental and cognitive complexity,
reaching 98.5% in humans. Moreover, high throughput analyses have
shown that the majority of the mammalian genome is differentially and
dynamically transcribed during development to produce tens if not
hundreds of thousands of short and long non-protein-coding RNAs that
show highly specific expression patterns and subcellular locations.
These RNAs function at many different levels of gene expression and
cell biology, including translational control, subcellular domain
formation, and guidance of the epigenetic processes that underpin
development, brain function and physiological adaptation, augmented
by the superimposition of plasticity by RNA editing, RNA modification
and retrotransposon mobilization. The evidence is now overwhelming
that there is a massive network of RNA-directed regulatory
transactions in architecturally organised and spatially specialised
multicellular organisms, which extends to transgenerational
inheritance.” [5]
This is only a tendency across animals, and pretty much ends as being
very predictive when vertebrates evolved due to the whole genome
duplication from a cordate. That seems to have been enough DNA to
create all the diversity among vertebrates. Birds have less than half
the DNA of humans, dogs and cats, but some birds are likely smarter than
your dog or cat, and they can fly. Birds have a lot fewer transposable
than mammals.
Onion plants have five times more DNA than we have. I could believe that onions are more intelligent than JTEM, MarkE etc., but in general it's absurd. Onions are not even the most intelligent by that silly
criterion: the Australian lungfish has 14 times as much DNA as we have.
Are Larry and Dan DNA dinosaurs?
Larry Moran and, even more, Dan Graur are among the most intelligent
people I've come across.
DNA realists. Can you find any wide spread scientific support for the
ENCODE stupidity?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur
established a valid falsifiability criterion for evolution? Or would
even a 100% functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of
function in non-protein-coding DNA?
Just try to find any widespread scientific support for your ENCODE
claims. They aren't supported because transposable elements were placed
among the junk DNA for a very good reason. They obviously need to be
tracked for medical purposes because of their deleterious effects, but
in terms of being functional sequence, their evolutionary significance
has only been a very minor fraction of parasitic multiplication events
that have done something interesting enough to be selected for in our
ancestors.
Really, most of what is called single copy sequence in our genome is
likely ancient transposable element sequences that have mutated beyond
recognition. They now look like random sequence. Transposable elements >> have likely been a plague before eukaryotes evolved. Once a mutation
inactivates them they can no longer jump around the genome and are stuck
in place, and they slowly degenerate into unrecognizable sequence or get
removed by the random deletions that may occur. We have transposon
insertion sites in common with our primate relatives, and these
transposon sequences have evolved just as much as the surrounding DNA.
One proposal is that we have a lot of extra DNA in order for
transposition events to cause less damage. If we didn't have so much
extra DNA a transposable element would be more likely to jump into a
required functional sequence and kill it.
You still do not want to believe in the designer of our genomes, so why
make this argument? Just think of how the design progressed from the
first vertebrate ancestor. The Reason to Believe old earth creationists
claim that the new genome designs came to be by "recreation" events over
time. The genomes created could be so closely related that the two
creations could still interbreed. They do throw their model out the
window in order to have whales created before land animals, and they
have issues with the Cambrian explosion occurring before land plants
existed, but can you believe in the designer of our genome.
Ron Okimoto
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2]
https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On 11/25/2023 10:46 AM, Athel Cornish-Bowden wrote:
On 2023-11-25 15:20:57 +0000, RonO said:
On 11/25/2023 4:41 AM, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a
controversial and developing issue, but also that there appears to
be an ongoing movement away from “Junk DNA”, even to the proposal of >>>> a “A Kuhnian revolution
Whenever I see the phrase "Kuhnian revolution" I know that some
nonsense is going to follow.
in molecular biology: Most genes in complex organisms expressDenial isn't anyway forward. Obfuscation and science denial are what
regulatory RNAs” [5].
the ID perps call the switch scam. They tell rubes like you that the
switch scam has nothing to do with ID nor creationism because they do
not want the stupidity associated with losers that are still making the
god-of-the-gaps claims to support IDiocy and creationism. This is just >>> the same type of obfuscation and science denial that the scientific
creationists used to employ. It is the same type of stupidity like
their "90% water" and humans share 50% of their genes with bananas.
They are just attempts to obfuscate and deny the existing science. All >>> the evidence still supports biological evolution, creationists just make >>> it sound like it doesn't.
2% - “Our 21,000 or so protein-coding genes account for less than 2% >>>> of the genome's total nucleotides.” [1]
This has been the estimate since we figured out that the average protein >>> was 300 amino acids in length, and had a rough order of magnitude
estimate of the number of proteins were in plants and animals. Once we >>> could estimate the amount of DNA in the nucleus everyone started asking
why there was so much extra DNA in the genome.
10% - “90% of your genome is junk” (Laurence Moran) [2]
In the 1960's regulatory sequences were identified, and it was proposed
that a lot of the DNA was used for regulatory purposes, but we also had
research indicating that a lot of the DNA was composed of repetitive
sequences. Heterochromatin are stretches of DNA composed of short
tandem repeats. They were first identified by how they could be
differentially stained for cytological analysis. Early research that
could only depend on genetic recombination and chromosome structural
features that could be identified under a microscope determined that
heterochromatin was deficient in genes. It seems to be some type of
spacer between gene containing DNA sequence. In the 1970's and 80's
transposons and retrovirus were verified to exist, and they were
determined to be DNA parasites. Many retrovirus can make complete virus >>> that can make you sick and can infect other individuals. The AIDs virus >>> is a retrovirus that inserts into your genome. Transposons are shorter >>> bits of DNA that mostly seem to have evolved from retrovirus, but some
transposable elements seem to have other origins. There were also DNA
virus that insert into DNA like herpes. Heterochromatin and DNA
parasites compose most of the genome, and of the around 35% of our
genome thought to be composed of single copy sequence most of that
sequence is just fossil DNA of transposons and retrovirus that have
decayed by mutation into sequence that we can't tell from random DNA
sequence. Parasitic DNA was classified as part of the "junk" DNA even
though it had a selfish function. McClintock's initial work starting in >>> the 1930's on transposable elements indicated that they could affect
gene regulation, and she initially proposed that they were gene
regulatory elements that could move around the genome. She detected
them on how they could turn genes on and off. Later research determined >>> that their affect on genes was mostly due to them jumping into or near a >>> gene and affecting normal gene regulation. Transposons are just like
any other insertion mutation that might happen. They usually carry
their own trancriptional regulatory sequences and they can kill a gene
or alter it's expression. Like any other mutation this can be good,
bad, or neutral, but mostly bad. ENCODE screwed up by counting the
regulatory sequences found in transposons and retrovirus as legitimate
regulatory sequences. They do regulate genes around them, but mostly
this altered regulation is just tolerated. Most of the time it would
have a significant effect it would be deleterious, and sometimes just
like any mutation they can be beneficial.
It just turned out that a whole lot of DNA in our genome is due to DNA
parasites. There is a recently evolved transposon in primates called
ALU, and in the last 80 million years it accounts for over 10% of the
human genome, but was zero in our distant ancestors. Our genome is full >>> of even older transposon families that we share with other mammals, and
sometimes even reptiles, but if you go back too far the transposons have >>> evolved so much that it gets difficult to determine if they are related
or not. Life forms are in a constant battle to reduce the transposon
load in their genomes. One proposed use of heterochromatin is as
transposon and retrovirus traps because the sequence evolves rapidly by
recombination and replication skipping and the inserted transposons are
eliminated more rapidly from the genome.
15% - “Mutational load considerations lead to the conclusion that
the functional fraction within the human genome cannot exceed
15%.”(Dan Graur) [3]
This is a proposed limit of how much functional DNA we can have in our
genome, and my guess is that it could be off by a significant amount,
but that doesn't matter. That likely doesn't matter because as
indicated above most of the DNA in our genome is due to transposons and
retrovirus, and heterochromatin that may function as transposon traps
and the mutation rate in heterochromatin is supposed to be high. We
want mutations in transposons and retrovirus because we don't want them
jumping around and messing up existing gene function. DNA parasites
account for a significant fraction of the mutational load on functional
sequences. You just have to look up ALU and note all the genetic
diseases that seem to occur within a single family that they are
responsible for (new genetic defects not ancient ones like Tay Sachs or
sickle cell anemia). We want mutations to inactivate transposons, but
ENCODE chose to include them in functional DNA.
We are likely safely within that 15% limit for the DNA that we rely on
to make us humans. Sure transposons affect gene function, but the gene >>> functions that they affect are what made us human in the first place.
Like any mutation it can be good, bad, or neutral, and throughout our
evolutionary history including the present, transposon activity is
mostly bad for us. What is sad is that some of the transposition
effects likely have been beneficial, and have likely had a significant
impact on the evolution of humans from our primate ancestors, but it is
the mutator activity of transposons and retrovirus that have done that.
The mutator activity is what lifeforms have been selecting against
likely since DNA parasites evolved. In research organisms like
Drosophila we can mess up the systems that suppress transposition and
you can go from something like 10^-8 specific gene knockouts to 10^-5 to >>> 10^-4 gene knockouts for a single gene that they are screening for, and
the gene knockouts will be due to transposon insertions.
If you include transposons as functional DNA you are including a
significant cause of the mutational load on the organism. Really, the
mutational load would be less if we didn't have transposons.
80% - “The ENCODE Consortium reported that its members were able to
assign biochemical functions to over 80% of the genome.”[4]
They have taken a beating for their estimate,
I wish that were true, but Larry Moran's blog suggests that there are
still plenty of people who ought to know better but don't.
and it has all been
justified. They were just stupid.
??% - “The genomic programming of developmentally complex organisms
was misunderstood for much of the last century. The mammalian genome
harbors only ∼20 000 protein-coding genes, similar in number and
with largely orthologous functions as those in other animals,
including simple nematodes. On the other hand, the extent of
non-protein-coding DNA increases with increasing developmental and
cognitive complexity, reaching 98.5% in humans. Moreover, high
throughput analyses have shown that the majority of the mammalian
genome is differentially and dynamically transcribed during
development to produce tens if not hundreds of thousands of short
and long non-protein-coding RNAs that show highly specific
expression patterns and subcellular locations. These RNAs function
at many different levels of gene expression and cell biology,
including translational control, subcellular domain formation, and
guidance of the epigenetic processes that underpin development,
brain function and physiological adaptation, augmented by the
superimposition of plasticity by RNA editing, RNA modification and
retrotransposon mobilization. The evidence is now overwhelming that
there is a massive network of RNA-directed regulatory transactions
in architecturally organised and spatially specialised multicellular
organisms, which extends to transgenerational inheritance.” [5]
This is only a tendency across animals, and pretty much ends as being
very predictive when vertebrates evolved due to the whole genome
duplication from a cordate. That seems to have been enough DNA to
create all the diversity among vertebrates. Birds have less than half
the DNA of humans, dogs and cats, but some birds are likely smarter than >>> your dog or cat, and they can fly. Birds have a lot fewer transposable >>> than mammals.
Onion plants have five times more DNA than we have. I could believe
that onions are more intelligent than JTEM, MarkE etc., but in general
it's absurd. Onions are not even the most intelligent by that silly
criterion: the Australian lungfish has 14 times as much DNA as we have.
Salamanders are terrestrial vertebrates with a vertebrate brain and some salamanders have 120 pg genomes. That is 40 times the size of the human genome, but those salamanders are not the dominant species on this earth.
Salamander genome size and some correlations with their evolution: https://pubmed.ncbi.nlm.nih.gov/30588701/
On 11/25/2023 10:46 AM, Athel Cornish-Bowden wrote:
On 2023-11-25 15:20:57 +0000, RonO said:
[ … ]
Onion plants have five times more DNA than we have. I could believe
that onions are more intelligent than JTEM, MarkE etc., but in general
it's absurd. Onions are not even the most intelligent by that silly
criterion: the Australian lungfish has 14 times as much DNA as we have.
Salamanders are terrestrial vertebrates with a vertebrate brain and
some salamanders have 120 pg genomes. That is 40 times the size of the
human genome, but those salamanders are not the dominant species on
this earth.
Salamander genome size and some correlations with their evolution: https://pubmed.ncbi.nlm.nih.gov/30588701/
--Athel -- French and British, living in Marseilles for 36 years; mainly
On 2023-11-25 18:32:34 +0000, RonO said:
On 11/25/2023 10:46 AM, Athel Cornish-Bowden wrote:
On 2023-11-25 15:20:57 +0000, RonO said:
[ … ]
Onion plants have five times more DNA than we have. I could believe
that onions are more intelligent than JTEM, MarkE etc., but in
general it's absurd. Onions are not even the most intelligent by that
silly criterion: the Australian lungfish has 14 times as much DNA as
we have.
Salamanders are terrestrial vertebrates with a vertebrate brain and
some salamanders have 120 pg genomes. That is 40 times the size of
the human genome, but those salamanders are not the dominant species
on this earth.
Salamander genome size and some correlations with their evolution:
https://pubmed.ncbi.nlm.nih.gov/30588701/
I forgot about the salamanders. I tend to think of them mainly as an approximate example of a ring species (in California).
--Athel -- French and British, living in Marseilles for 36 years; mainly
in England until 1987.
On 11/25/23 2:41 AM, MarkE wrote:Most genes in complex organisms express regulatory RNAs” [5].
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:
in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]
10% - “90% of your genome is junk” (Laurence Moran) [2]
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those
Are Larry and Dan DNA dinosaurs?No. I would suggest that you actually find and read Larry's book, and
that you google "c-value paradox", "onion test", and "dog's ass plot".
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or wouldGraur was wrong (or just misspoke) about that. What he probably meant
even a 100% functional genome be explained as evolution’s parsimony?
was that if ENCODE is right, natural selection doesn't work the way we
think it does. It was all about mutational load. Of course ENCODE walked back their claim almost immediately, so the point is moot.
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?Very little. None of those ongoing discoveries have moved the percentage
of junk DNA in humans to less than 90%.
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:Most genes in complex organisms express regulatory RNAs” [5].
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:
Everybody wants to make a "paradigm shift."
2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those
Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift.""functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do anything
Second, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying around alot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding a mammalian
And in any case design is not a competing hypothesis - an unspecified designer of unspecified, and potentially limitless, abilities with unspecified intentions is compatible with all possible evidence, including a genome full of junk DNA.
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?There have been known functions in non-protein-coding DNA for many decades. Some more are being found. That's interesting.
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:Most genes in complex organisms express regulatory RNAs” [5].
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:
those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that theEverybody wants to make a "paradigm shift."
I'm including this a as lower bound. However, at the following point in the history of genetics it appears that all non-coding DNA was termed "junk":2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
I'm aware of the disputation of ENCODE results, and that "biochemical function" does not automatically amount to biological effect.80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as
anything "functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift."
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do
a lot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding aSecond, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying around
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:Most genes in complex organisms express regulatory RNAs” [5].
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:
Everybody wants to make a "paradigm shift."
2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those
Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift.""functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do anything
Second, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying around alot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding a mammalian
And in any case design is not a competing hypothesis - an unspecified designer of unspecified, and potentially limitless, abilities with unspecified intentions is compatible with all possible evidence, including a genome full of junk DNA.
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?There have been known functions in non-protein-coding DNA for many decades. Some more are being found. That's interesting.
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:biology: Most genes in complex organisms express regulatory RNAs” [5].
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular
those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that theEverybody wants to make a "paradigm shift."
I'm including this a as lower bound. However, at the following point in the history of genetics it appears that all non-coding DNA was termed "junk":2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
I'm aware of the disputation of ENCODE results, and that "biochemical function" does not automatically amount to biological effect.80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as
anything "functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift."
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do
around a lot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding aSecond, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:biology: Most genes in complex organisms express regulatory RNAs” [5].
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular
those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that theEverybody wants to make a "paradigm shift."
I'm including this a as lower bound. However, at the following point in the history of genetics it appears that all non-coding DNA was termed "junk":2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
I'm aware of the disputation of ENCODE results, and that "biochemical function" does not automatically amount to biological effect.80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as
anything "functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift."
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do
around a lot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding aSecond, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on askingThe question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.
loaded questions that are in fact insinuations about things you don't even understand.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?
On 11/25/2023 4:41 AM, MarkE wrote:Most genes in complex organisms express regulatory RNAs” [5].
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:
Denial isn't anyway forward. Obfuscation and science denial are whatin other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the
the ID perps call the switch scam. They tell rubes like you that the
switch scam has nothing to do with ID nor creationism because they do
not want the stupidity associated with losers that are still making the god-of-the-gaps claims to support IDiocy and creationism. This is just
the same type of obfuscation and science denial that the scientific creationists used to employ. It is the same type of stupidity like
their "90% water" and humans share 50% of their genes with bananas.
They are just attempts to obfuscate and deny the existing science. All
the evidence still supports biological evolution, creationists just make
it sound like it doesn't.
2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]This has been the estimate since we figured out that the average protein
was 300 amino acids in length, and had a rough order of magnitude
estimate of the number of proteins were in plants and animals. Once we
could estimate the amount of DNA in the nucleus everyone started asking
why there was so much extra DNA in the genome.
10% - “90% of your genome is junk” (Laurence Moran) [2]In the 1960's regulatory sequences were identified, and it was proposed
that a lot of the DNA was used for regulatory purposes, but we also had research indicating that a lot of the DNA was composed of repetitive sequences. Heterochromatin are stretches of DNA composed of short
tandem repeats. They were first identified by how they could be differentially stained for cytological analysis. Early research that
could only depend on genetic recombination and chromosome structural features that could be identified under a microscope determined that heterochromatin was deficient in genes. It seems to be some type of
spacer between gene containing DNA sequence. In the 1970's and 80's transposons and retrovirus were verified to exist, and they were
determined to be DNA parasites. Many retrovirus can make complete virus
that can make you sick and can infect other individuals. The AIDs virus
is a retrovirus that inserts into your genome. Transposons are shorter
bits of DNA that mostly seem to have evolved from retrovirus, but some transposable elements seem to have other origins. There were also DNA
virus that insert into DNA like herpes. Heterochromatin and DNA
parasites compose most of the genome, and of the around 35% of our
genome thought to be composed of single copy sequence most of that
sequence is just fossil DNA of transposons and retrovirus that have
decayed by mutation into sequence that we can't tell from random DNA sequence. Parasitic DNA was classified as part of the "junk" DNA even
though it had a selfish function. McClintock's initial work starting in
the 1930's on transposable elements indicated that they could affect
gene regulation, and she initially proposed that they were gene
regulatory elements that could move around the genome. She detected
them on how they could turn genes on and off. Later research determined
that their affect on genes was mostly due to them jumping into or near a gene and affecting normal gene regulation. Transposons are just like
any other insertion mutation that might happen. They usually carry
their own trancriptional regulatory sequences and they can kill a gene
or alter it's expression. Like any other mutation this can be good,
bad, or neutral, but mostly bad. ENCODE screwed up by counting the regulatory sequences found in transposons and retrovirus as legitimate regulatory sequences. They do regulate genes around them, but mostly
this altered regulation is just tolerated. Most of the time it would
have a significant effect it would be deleterious, and sometimes just
like any mutation they can be beneficial.
It just turned out that a whole lot of DNA in our genome is due to DNA parasites. There is a recently evolved transposon in primates called
ALU, and in the last 80 million years it accounts for over 10% of the
human genome, but was zero in our distant ancestors. Our genome is full
of even older transposon families that we share with other mammals, and sometimes even reptiles, but if you go back too far the transposons have evolved so much that it gets difficult to determine if they are related
or not. Life forms are in a constant battle to reduce the transposon
load in their genomes. One proposed use of heterochromatin is as
transposon and retrovirus traps because the sequence evolves rapidly by recombination and replication skipping and the inserted transposons are eliminated more rapidly from the genome.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]This is a proposed limit of how much functional DNA we can have in our genome, and my guess is that it could be off by a significant amount,
but that doesn't matter. That likely doesn't matter because as
indicated above most of the DNA in our genome is due to transposons and retrovirus, and heterochromatin that may function as transposon traps
and the mutation rate in heterochromatin is supposed to be high. We
want mutations in transposons and retrovirus because we don't want them jumping around and messing up existing gene function. DNA parasites
account for a significant fraction of the mutational load on functional sequences. You just have to look up ALU and note all the genetic
diseases that seem to occur within a single family that they are
responsible for (new genetic defects not ancient ones like Tay Sachs or sickle cell anemia). We want mutations to inactivate transposons, but
ENCODE chose to include them in functional DNA.
We are likely safely within that 15% limit for the DNA that we rely on
to make us humans. Sure transposons affect gene function, but the gene functions that they affect are what made us human in the first place.
Like any mutation it can be good, bad, or neutral, and throughout our evolutionary history including the present, transposon activity is
mostly bad for us. What is sad is that some of the transposition
effects likely have been beneficial, and have likely had a significant impact on the evolution of humans from our primate ancestors, but it is
the mutator activity of transposons and retrovirus that have done that.
The mutator activity is what lifeforms have been selecting against
likely since DNA parasites evolved. In research organisms like
Drosophila we can mess up the systems that suppress transposition and
you can go from something like 10^-8 specific gene knockouts to 10^-5 to 10^-4 gene knockouts for a single gene that they are screening for, and
the gene knockouts will be due to transposon insertions.
If you include transposons as functional DNA you are including a
significant cause of the mutational load on the organism. Really, the mutational load would be less if we didn't have transposons.
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]They have taken a beating for their estimate, and it has all been
justified. They were just stupid.
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those
This is only a tendency across animals, and pretty much ends as being
very predictive when vertebrates evolved due to the whole genome
duplication from a cordate. That seems to have been enough DNA to
create all the diversity among vertebrates. Birds have less than half
the DNA of humans, dogs and cats, but some birds are likely smarter than your dog or cat, and they can fly. Birds have a lot fewer transposable
than mammals.
Are Larry and Dan DNA dinosaurs?DNA realists. Can you find any wide spread scientific support for the
ENCODE stupidity?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?Just try to find any widespread scientific support for your ENCODE
claims. They aren't supported because transposable elements were placed among the junk DNA for a very good reason. They obviously need to be
tracked for medical purposes because of their deleterious effects, but
in terms of being functional sequence, their evolutionary significance
has only been a very minor fraction of parasitic multiplication events
that have done something interesting enough to be selected for in our ancestors.
Really, most of what is called single copy sequence in our genome is
likely ancient transposable element sequences that have mutated beyond recognition. They now look like random sequence. Transposable elements
have likely been a plague before eukaryotes evolved. Once a mutation inactivates them they can no longer jump around the genome and are stuck
in place, and they slowly degenerate into unrecognizable sequence or get removed by the random deletions that may occur. We have transposon
insertion sites in common with our primate relatives, and these
transposon sequences have evolved just as much as the surrounding DNA.
One proposal is that we have a lot of extra DNA in order for
transposition events to cause less damage. If we didn't have so much
extra DNA a transposable element would be more likely to jump into a required functional sequence and kill it.
You still do not want to believe in the designer of our genomes, so why
make this argument? Just think of how the design progressed from the
first vertebrate ancestor. The Reason to Believe old earth creationists claim that the new genome designs came to be by "recreation" events over time. The genomes created could be so closely related that the two
creations could still interbreed. They do throw their model out the
window in order to have whales created before land animals, and they
have issues with the Cambrian explosion occurring before land plants existed, but can you believe in the designer of our genome.
Ron Okimoto
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
On Sunday, November 26, 2023 at 2:21:50 AM UTC+11, RonO wrote:
On 11/25/2023 4:41 AM, MarkE wrote:
Ron, great post, appreciated.
Regarding the ENCODE results, it is true that "biochemical function" does not necessarily
translate to significant biological effect. Determining the function of TEs does seem to
be a major issue. You've prompted me to investigate this further.
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:biology: Most genes in complex organisms express regulatory RNAs” [5].
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular
those in other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that theEverybody wants to make a "paradigm shift."
I'm including this a as lower bound. However, at the following point in the history of genetics it appears that all non-coding DNA was termed "junk":2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]The claim that only about 1.5% of a mammalian genome consists of protein coding sequence is not a claim that 98.5% of the genome is junk. People have known about functional RNAs and regulatory sequences for a long time.
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."
10% - “90% of your genome is junk” (Laurence Moran) [2]Given the C-value paradox, this does not seem like an unreasonable claim.
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]Seems consistent with the rest of what we know.
I'm aware of the disputation of ENCODE results, and that "biochemical function" does not automatically amount to biological effect.80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]Look carefully at what ENCODE means by a "biochemical function,' and read the section in your wiki article about criticisms of ENCODE's claims, or at least of the popular press interpretation of them.
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as
anything "functional." RNA polymerase may be sloppy enough to make low level transcripts of essentially all DNA in the cell.Yes, gene regulation is complex. This fellow rather overstates how little this was understood in the 20th century because, as I said above, everybody loves a "paradigm shift."
Are Larry and Dan DNA dinosaurs?No.
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?First, the question is not whether ENCODE is right, but whether their definition of function means what most people mean by a function. Most of that 80% consists of very low level transcription with no evidence that the transcripts actually do
around a lot of useless sequences, so functionless DNA is minimized. It would be surprising if the same happened in big multicellular organisms for whom the slow steps in reproduction are factors other than the speed of genome replication. And finding aSecond, there are certainly organisms with very little, if any, "junk DNA," many prokaryotes, for example. When a major aspect of how well you can grow is how fast you can replicate your DNA, then there's a selective advantage to not carrying
.....Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
I'm including this a as lower bound. However, at the following point in
the history of genetics it appears that all non-coding DNA was termed
"junk":
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."
On Monday, November 27, 2023 at 7:06:51 AM UTC-5, MarkE wrote:
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.Can you repeat that in English ? Check your subject verb and object. You asked a question
alright but it assumes a flawed premise, actually multiple false premises because you had
followed up with some nonsense about how going one way or the other would falsify the
theory of evolution. To explain your confusion would likely be a waste if you don't even
understand Dan's paper.
But before we even get there, there's a big confusion on your part as different species have very
different proportions of junk. Ultimately, you aren't making sense and it looks like you don't
understand what scientists are arguing about. Further, you demonstrate little desire to learn,
just to throw what you imagine to be dirt.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?It's not a trivial answer the way you ask, but you're clearly asking for opinions about topics
you haven't bothered to learn about. Ask an honest question.
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
What are your thoughts on this? Acknowledging this is still a controversial and developing issue, but also that there appears to be an ongoing movement away from “Junk DNA”, even to the proposal of a “A Kuhnian revolution in molecular biology:Most genes in complex organisms express regulatory RNAs” [5].
2% - “Our 21,000 or so protein-coding genes account for less than 2% of the genome's total nucleotides.” [1]other animals, including simple nematodes. On the other hand, the extent of non-protein-coding DNA increases with increasing developmental and cognitive complexity, reaching 98.5% in humans. Moreover, high throughput analyses have shown that the majority
10% - “90% of your genome is junk” (Laurence Moran) [2]
15% - “Mutational load considerations lead to the conclusion that the functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]
80% - “The ENCODE Consortium reported that its members were able to assign biochemical functions to over 80% of the genome.”[4]
??% - “The genomic programming of developmentally complex organisms was misunderstood for much of the last century. The mammalian genome harbors only ∼20 000 protein-coding genes, similar in number and with largely orthologous functions as those in
Are Larry and Dan DNA dinosaurs?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established a valid falsifiability criterion for evolution? Or would even a 100% functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
On Monday, November 27, 2023 at 7:06:51 AM UTC-5, MarkE wrote:
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.Can you repeat that in English ? Check your subject verb and object. You asked a question
alright but it assumes a flawed premise, actually multiple false premises because you had
followed up with some nonsense about how going one way or the other would falsify the
theory of evolution. To explain your confusion would likely be a waste if you don't even
understand Dan's paper.
But before we even get there, there's a big confusion on your part as different species have very
different proportions of junk. Ultimately, you aren't making sense and it looks like you don't
understand what scientists are arguing about. Further, you demonstrate little desire to learn,
just to throw what you imagine to be dirt.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?It's not a trivial answer the way you ask, but you're clearly asking for opinions about topics
you haven't bothered to learn about. Ask an honest question.
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
On 27/11/2023 11:17, MarkE wrote:
I'm including this a as lower bound. However, at the following point in the history of genetics it appears that all non-coding DNA was termed "junk":
"In 1972 the late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding sections of a genome, most of which consist of repeated segments scattered randomly throughout the genome."That appears to have come from the Scientific American website.
When you are going to put words in Susumu Ohno's mouth, it's desirable
to see what he actually wrote. Unfortunately the relevant paper is not easily accessible.
Answers in Genesis writes
"A geneticist, Susumu Ohno, was the first to coin the term “junk” DNA in 1972.1 He used the term to refer to pseudogenes (commonly thought of as defunct relatives of known genes that do not code for proteins), but
with time its meaning broadened to include all non-coding DNA (DNA that
does not contain genes and does not produce proteins)."
https://answersingenesis.org/genetics/junk-dna/junk-dna-past-present-and-future-part-1/
Larry Moran writes
"First, Ohno did not coin the term "junk DNA" - it was commonly used in discussions about genomes and even appeared in print many years before Ohno's paper. Second, Ohno specifically addresses regulatory sequences
in his paper so it's clear that he knew about functional noncoding DNA
that was not junk. He also mentions centromeres and I think it's safe to assume that he knew about ribosomal RNA genes and tRNA genes."
https://sandwalk.blogspot.com/2022/08/junk-dna-vs-noncoding-dna.html
Dan Graur looked into the history of the term junk DNA
https://judgestarling.tumblr.com/post/64504735261/the-origin-of-the-term-junk-dna-a-historical
Palazzo and Gregory say the same about Ohno as AIG.
"Although the term “junk DNA” was already in use as early as the 1960s [10]–[12], the term's origin is usually attributed to Susumu Ohno [13].
As Ohno pointed out, gene duplication can alleviate the constraint
imposed by natural selection on changes to important gene regions by allowing one copy to maintain the original function as the other
undergoes mutation. Rarely, these mutations will turn out to be
beneficial, and a new gene may arise (“neofunctionalization”) [14]. Most of the time, however, one copy sustains a mutation that eliminates its ability to encode a functional protein, turning it into a pseudogene.
These sequences are what Ohno initially referred to as “junk” [13], although the term was quickly extended to include many types of
noncoding DNA [15]. Today, “junk DNA” is often used in the broad sense of referring to any DNA sequence that does not play a functional role in development, physiology, or some other organism-level capacity. This
broader sense of the term is at the centre of most current debate about
the quantity—or even the existence—of “junk DNA” in the genomes of humans and other organisms.
It has now become something of a cliché to begin both media stories and journal articles with the simplistic claim that most or all noncoding
DNA was “long dismissed as useless junk.” The implication, of course, is that current research is revealing function in much of the supposed junk that was unwisely ignored as biologically uninteresting by past investigators. Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early
commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant” [10], [16], and possible functions were discussed each time a new type of nonprotein-coding sequence was
identified (including pseudogenes, transposable elements, satellite DNA,
and introns; for a compilation of relevant literature, see [17])."
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004351
--
alias Ernest Major
On Monday, November 27, 2023 at 11:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 7:06:51 AM UTC-5, MarkE wrote:
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
I'm not disputing Graur's 15% claim here. Rather, I'm asking what are the implications should a significantly higher percentage be confirmed.The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.Can you repeat that in English ? Check your subject verb and object. You asked a question
alright but it assumes a flawed premise, actually multiple false premises because you had
followed up with some nonsense about how going one way or the other would falsify the
theory of evolution. To explain your confusion would likely be a waste if you don't even
understand Dan's paper.
My interest in population genetics led me to write a program to simulate a large population with
sexual reproduction, recombination and crossover, mutations using various selection coefficient
profiles, etc, in an attempt to explore fixation, viable selection coefficient distribution, genetic loading
and so on. Not conclusive so far, but the exercise has necessitated a reasonable understanding
of the principles involved.
But before we even get there, there's a big confusion on your part as different species have very
different proportions of junk. Ultimately, you aren't making sense and it looks like you don't
understand what scientists are arguing about. Further, you demonstrate little desire to learn,
just to throw what you imagine to be dirt.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
On Monday, November 27, 2023 at 11:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 7:06:51 AM UTC-5, MarkE wrote:
On Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Question: Is Graur's deduction valid, i.e. the genetic load problem requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
I'm not disputing Graur's 15% claim here. Rather, I'm asking what are the implications should a significantly higher percentage be confirmed.The question legitimately holds this predication accountable - which is pertinent in view of the trend against the 90% junk hypothesis.Can you repeat that in English ? Check your subject verb and object. You asked a question
alright but it assumes a flawed premise, actually multiple false premises because you had
followed up with some nonsense about how going one way or the other would falsify the
theory of evolution. To explain your confusion would likely be a waste if you don't even
understand Dan's paper.
My interest in population genetics led me to write a program to simulate a large population with sexual reproduction, recombination and crossover, mutations using various selection coefficient profiles, etc, in an attempt to explore fixation, viableselection coefficient distribution, genetic loading and so on. Not conclusive so far, but the exercise has necessitated a reasonable understanding of the principles involved.
But before we even get there, there's a big confusion on your part as different species have very
different proportions of junk. Ultimately, you aren't making sense and it looks like you don't
understand what scientists are arguing about. Further, you demonstrate little desire to learn,
just to throw what you imagine to be dirt.
Moran emphatically endorses it (and Graur): https://sandwalk.blogspot.com/2017/07/revisiting-genetic-load-argument-with.html
Do you share their conviction?It's not a trivial answer the way you ask, but you're clearly asking for opinions about topics
you haven't bothered to learn about. Ask an honest question.
If you want help understanding it, it's possible that polite requests will be responded to,
to help you understand. I'm not personally in the mood to tutor as you've made some comments
above that don't seem quite candid. In particular, the bit where you try to claim that science
did consider all non-protein coding DNA to be junk is not supportable. I'm sure you imagine
that you've supported it with an isolated quote, but that quote simply doesn't hold up against
a much larger body of evidence, available through sources you seem to know exist. If you
think it's kosher to do what you did, you don't understand science in the least.
On Saturday, November 25, 2023 at 9:46:49 PM UTC+11, MarkE wrote:
What are your thoughts on this? Acknowledging this is still a
controversial and developing issue, but also that there appears to be an
ongoing movement away from “Junk DNA”, even to the proposal of a “A
Kuhnian revolution in molecular biology: Most genes in complex organisms
express regulatory RNAs” [5].
2% - “Our 21,000 or so protein-coding genes account for less than 2% of
the genome's total nucleotides.” [1]
10% - “90% of your genome is junk” (Laurence Moran) [2]
15% - “Mutational load considerations lead to the conclusion that the
functional fraction within the human genome cannot exceed 15%.”(Dan Graur) [3]
80% - “The ENCODE Consortium reported that its members were able to
assign biochemical functions to over 80% of the genome.”[4]
??% - “The genomic programming of developmentally complex organisms was
misunderstood for much of the last century. The mammalian genome harbors
only ∼20 000 protein-coding genes, similar in number and with largely
orthologous functions as those in other animals, including simple
nematodes. On the other hand, the extent of non-protein-coding DNA
increases with increasing developmental and cognitive complexity,
reaching 98.5% in humans. Moreover, high throughput analyses have shown
that the majority of the mammalian genome is differentially and
dynamically transcribed during development to produce tens if not
hundreds of thousands of short and long non-protein-coding RNAs that
show highly specific expression patterns and subcellular locations.
These RNAs function at many different levels of gene expression and cell
biology, including translational control, subcellular domain formation,
and guidance of the epigenetic processes that underpin development,
brain function and physiological adaptation, augmented by the
superimposition of plasticity by RNA editing, RNA modification and
retrotransposon mobilization. The evidence is now overwhelming that
there is a massive network of RNA-directed regulatory transactions in
architecturally organised and spatially specialised multicellular
organisms, which extends to transgenerational inheritance.” [5]
Are Larry and Dan DNA dinosaurs?
“If ENCODE is right, then evolution is wrong.” Has Dan Graur established >> a valid falsifiability criterion for evolution? Or would even a 100%
functional genome be explained as evolution’s parsimony?
What is the implication of the trend of ongoing discoveries of function in >> non-protein-coding DNA?
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
"Researchers are only just beginning to unravel the subtleties and interconnections in the vast networks of junk DNA. The field is controversial. At one extreme we have scientists claiming experimental
proof is lacking to support sometimes sweeping claims. At the other are
those who feel there is a whole generation of scientists (if not more) trapped in an outdated model and unable to see or understand the new
world order. Part of the problem is that the systems we can use to probe
the functions of junk DNA are still relatively underdeveloped. This can sometimes make it hard for researchers to use experimental approaches to
test their hypotheses."
Carey, Nessa. Junk DNA: A Journey Through the Dark Matter of the Genome
(p. 6). Icon Books, 2015. Kindle Edition.
On Wednesday, November 29, 2023 at 7:31:53 AM UTC-5, MarkE wrote:
On Monday, November 27, 2023 at 11:36:52 PM UTC+11, Lawyer Daggett wrote: >>> On Monday, November 27, 2023 at 7:06:51 AM UTC-5, MarkE wrote:
I'm not disputing Graur's 15% claim here. Rather, I'm asking what areOn Monday, November 27, 2023 at 10:36:52 PM UTC+11, Lawyer Daggett wrote:
On Monday, November 27, 2023 at 6:21:51 AM UTC-5, MarkE wrote:
On Saturday, November 25, 2023 at 11:01:50 PM UTC+11, broger...@gmail.com wrote:
On Saturday, November 25, 2023 at 5:46:49 AM UTC-5, MarkE wrote:
Can you repeat that in English ? Check your subject verb and object.Question: Is Graur's deduction valid, i.e. the genetic load problem >>>>>> requires the majority of the human genome to be junk?Why don't you read Dan's paper on the topic and offer us an informed opinion.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570035/
And if you aren't prepared to understand it, perhaps you might hold off on asking
loaded questions that are in fact insinuations about things you don't even understand.
The question legitimately holds this predication accountable - which
is pertinent in view of the trend against the 90% junk hypothesis.
You asked a question
alright but it assumes a flawed premise,
actually multiple false premises because you had
followed up with some nonsense about how going one way or the other would falsify the
theory of evolution. To explain your confusion would likely be a waste if you don't even
understand Dan's paper.
the implications should a significantly higher percentage be confirmed.
My interest in population genetics led me to write a program to simulate
a large population with
sexual reproduction, recombination and crossover, mutations using
various selection coefficient
profiles, etc, in an attempt to explore fixation, viable selection
coefficient distribution, genetic loading
and so on. Not conclusive so far, but the exercise has necessitated a
reasonable understanding
of the principles involved.
I can't help but point out that writing a program that attempts to investigate something does
not mean you understand said something. Over the years, I was often referred papers to
referee that included computer software that propertied to simulate a problem, or solve
a problem or similar. I would have to dig in and see what they claimed their software was
doing, and then sometimes dig and see what their software was actually doing. Sometimes submissions got rejected because their code didn't actually do what they
said it did. Other times,, people failed to actually understand the underlying principles.
So saying "but I wrote a population genetics program" doesn't accomplish what you think.
Again, read Dan Graur's paper. It shouldn't be a problem for you if you
have the understanding
you want to claim. And you wouldn't need to be asking us.
Meanwhile, in a prior post, you replied to Ernest Major's post which documented that your
citation of Sci. Amer. regards Ohno was a bad citation but didn't acknowledge your error.
If you think you should be forgiven because Sci. Amer. did indeed make a the claim,
you fail to understand how to cite things. The mere existence of a citation isn't enough,
especially not when there's good documentation that said citation is wrong. And the
evidence is clear that the claim that people believed "junk DNA" meant all non-protein
coding DNA is wrong. That is completely clear from the evidence spoon fed to you.
MarkE <me22over7@gmail.com> wrote:
On Saturday, November 25, 2023 at 9:46:49?PM UTC+11, MarkE wrote:What is gained conceptually by referring to these genomic regions as dark >matter?
What are your thoughts on this? Acknowledging this is still a
controversial and developing issue, but also that there appears to be an >>> ongoing movement away from Junk DNA, even to the proposal of a A
Kuhnian revolution in molecular biology: Most genes in complex organisms >>> express regulatory RNAs [5].
2% - Our 21,000 or so protein-coding genes account for less than 2% of
the genome's total nucleotides. [1]
10% - 90% of your genome is junk (Laurence Moran) [2]
15% - Mutational load considerations lead to the conclusion that the
functional fraction within the human genome cannot exceed 15%.(Dan Graur) [3]
80% - The ENCODE Consortium reported that its members were able to
assign biochemical functions to over 80% of the genome.[4]
??% - The genomic programming of developmentally complex organisms was
misunderstood for much of the last century. The mammalian genome harbors >>> only ?20 000 protein-coding genes, similar in number and with largely
orthologous functions as those in other animals, including simple
nematodes. On the other hand, the extent of non-protein-coding DNA
increases with increasing developmental and cognitive complexity,
reaching 98.5% in humans. Moreover, high throughput analyses have shown
that the majority of the mammalian genome is differentially and
dynamically transcribed during development to produce tens if not
hundreds of thousands of short and long non-protein-coding RNAs that
show highly specific expression patterns and subcellular locations.
These RNAs function at many different levels of gene expression and cell >>> biology, including translational control, subcellular domain formation,
and guidance of the epigenetic processes that underpin development,
brain function and physiological adaptation, augmented by the
superimposition of plasticity by RNA editing, RNA modification and
retrotransposon mobilization. The evidence is now overwhelming that
there is a massive network of RNA-directed regulatory transactions in
architecturally organised and spatially specialised multicellular
organisms, which extends to transgenerational inheritance. [5]
Are Larry and Dan DNA dinosaurs?
If ENCODE is right, then evolution is wrong. Has Dan Graur established >>> a valid falsifiability criterion for evolution? Or would even a 100%
functional genome be explained as evolutions parsimony?
What is the implication of the trend of ongoing discoveries of function in >>> non-protein-coding DNA?
-------
[1] https://learn.genetics.utah.edu/content/basics/geneanatomy/
[2] https://sandwalk.blogspot.com/2023/11/two-heidelberg-graduate-students-reject.html
[3] https://academic.oup.com/gbe/article/9/7/1880/3952726
[4] https://en.wikipedia.org/wiki/ENCODE
[5] https://onlinelibrary.wiley.com/doi/full/10.1002/bies.202300080
"Researchers are only just beginning to unravel the subtleties and
interconnections in the vast networks of junk DNA. The field is
controversial. At one extreme we have scientists claiming experimental
proof is lacking to support sometimes sweeping claims. At the other are
those who feel there is a whole generation of scientists (if not more)
trapped in an outdated model and unable to see or understand the new
world order. Part of the problem is that the systems we can use to probe
the functions of junk DNA are still relatively underdeveloped. This can
sometimes make it hard for researchers to use experimental approaches to
test their hypotheses."
Carey, Nessa. Junk DNA: A Journey Through the Dark Matter of the Genome
(p. 6). Icon Books, 2015. Kindle Edition.
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?
On 25/11/2023 10:41, MarkE wrote:
What is the implication of the trend of ongoing discoveries of function in >> non-protein-coding DNA?
A naive understanding of evolution predicts no junk DNA, because junk
DNA poses a cost of replication on the organism, and as such would
undergo negative selection.
A naive design hypothesis predicts no junk DNA, because superfluous DNA
would be bad design.
From the viewpoint of evolutionary there are at least two processes
that account for the existence of junk DNA. Firstly the existence of
genetic drift means that selection is poor at getting rid of very mildly deleterious DNA sequences; for sufficiently weak selection pressures in
a sufficiently small population the effects of drift dominate over those
of selection.
Second much junk DNA can be seen as active or dead
parasitic DNA - the selection pressure on a transposon to copy itself
strikes me as being greater than the selection pressure on an organism
to delete an individual copy of a transposon; I wouldn't be surprised if
the damage to genes and regulatory sites by a transposon causes a
greater cost on the host than the cost of replicating the additional
copies of transposons.
Ernest Major <{$to$}@meden.demon.co.uk> wrote:
On 25/11/2023 10:41, MarkE wrote:
What is the implication of the trend of ongoing discoveries of function in >>> non-protein-coding DNA?
A naive understanding of evolution predicts no junk DNA, because junk
DNA poses a cost of replication on the organism, and as such would
undergo negative selection.
A naive design hypothesis predicts no junk DNA, because superfluous DNA
would be bad design.
From the viewpoint of evolutionary there are at least two processes
that account for the existence of junk DNA. Firstly the existence of
genetic drift means that selection is poor at getting rid of very mildly
deleterious DNA sequences; for sufficiently weak selection pressures in
a sufficiently small population the effects of drift dominate over those
of selection.
Is this along the lines of nearly neutral theory?
Second much junk DNA can be seen as active or deadIsn’t active parasitic DNA more aligned with the selfish DNA concept than junk DNA? Taking Dawkins’ Necker Cube into account as framing, the actual selection is occurring at a lower level than the host organism at that of parasitic sequences. If these are knocked out in their key adaptive regions they remain as decaying inactive fossils…junk from POV of organismic level.
parasitic DNA - the selection pressure on a transposon to copy itself
strikes me as being greater than the selection pressure on an organism
to delete an individual copy of a transposon; I wouldn't be surprised if
the damage to genes and regulatory sites by a transposon causes a
greater cost on the host than the cost of replicating the additional
copies of transposons.
One interesting non-junk aspect of viral insertions is how retroviral elements seem integral in developing mammalian placentas:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177113/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3758191/
On the other side though former yolking genes in placental mammals seem to have degraded to junky pseudogenes.
On 25/11/2023 10:41, MarkE wrote:
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?A naive understanding of evolution predicts no junk DNA, because junk
DNA poses a cost of replication on the organism, and as such would
undergo negative selection.
A naive design hypothesis predicts no junk DNA, because superfluous DNA would be bad design.
From the viewpoint of evolutionary there are at least two processes
that account for the existence of junk DNA. Firstly the existence of
genetic drift means that selection is poor at getting rid of very mildly deleterious DNA sequences; for sufficiently weak selection pressures in
a sufficiently small population the effects of drift dominate over those
of selection. Second much junk DNA can be seen as active or dead
parasitic DNA - the selection pressure on a transposon to copy itself strikes me as being greater than the selection pressure on an organism
to delete an individual copy of a transposon; I wouldn't be surprised if
the damage to genes and regulatory sites by a transposon causes a
greater cost on the host than the cost of replicating the additional
copies of transposons.
From a design viewpoint the existence of junk DNA can be accounted for
by assuming a designer incapable of perfect design, or a designer that deliberately introduced flaws, or that the design occurred in the
distant past and junk DNA has accumulated since. For some reason the Intelligent Design movement has tied its flag to the mast of no junk
DNA. The implicit assumption of an omnipotent, omniscient,
omnibenevolent designer doesn't fit comfortably with their claims that Intelligent Design is a secular hypothesis. It's also somewhat
YEC-friendly; a counterargument that life was designed so that junk DNA couldn't appear is met with observations of processes that add it.
You might wish to consider whether the claim you wish to entertain is
that the human genome is 100% functional, or that all genomes are 100% functional.
--
alias Ernest Major
On Thursday, November 30, 2023 at 5:26:54 AM UTC+11, Ernest Major wrote:
On 25/11/2023 10:41, MarkE wrote:
What is the implication of the trend of ongoing discoveries of function in non-protein-coding DNA?A naive understanding of evolution predicts no junk DNA, because junk
DNA poses a cost of replication on the organism, and as such would
undergo negative selection.
A naive design hypothesis predicts no junk DNA, because superfluous DNA
would be bad design.
From the viewpoint of evolutionary there are at least two processes
that account for the existence of junk DNA. Firstly the existence of
genetic drift means that selection is poor at getting rid of very mildly
deleterious DNA sequences; for sufficiently weak selection pressures in
a sufficiently small population the effects of drift dominate over those
of selection. Second much junk DNA can be seen as active or dead
parasitic DNA - the selection pressure on a transposon to copy itself
strikes me as being greater than the selection pressure on an organism
to delete an individual copy of a transposon; I wouldn't be surprised if
the damage to genes and regulatory sites by a transposon causes a
greater cost on the host than the cost of replicating the additional
copies of transposons.
From a design viewpoint the existence of junk DNA can be accounted for
by assuming a designer incapable of perfect design, or a designer that
deliberately introduced flaws, or that the design occurred in the
distant past and junk DNA has accumulated since. For some reason the
Intelligent Design movement has tied its flag to the mast of no junk
DNA. The implicit assumption of an omnipotent, omniscient,
omnibenevolent designer doesn't fit comfortably with their claims that
Intelligent Design is a secular hypothesis. It's also somewhat
YEC-friendly; a counterargument that life was designed so that junk DNA
couldn't appear is met with observations of processes that add it.
You might wish to consider whether the claim you wish to entertain is
that the human genome is 100% functional, or that all genomes are 100%
functional.
I'm not imagining 100%. For this discussion, I'm contemplating an amount comfortably higher than Graur's upper bound.
But good assessment on your part: one could be unduly influenced by ideologically based assumptions either way. As you say, for ID there naturally is a strong bias to not concede "junk" in the designer's work. >
--
alias Ernest Major
On Thu, 30 Nov 2023 14:15:19 -0800 (PST)
MarkE <me22over7@gmail.com> wrote:
On Thursday, November 30, 2023 at 3:01:55?PM UTC+11, Lawyer Daggett wrote:[cost of junk DNA]
The energy cost argument does deserve testing, which you've had a go at.
Is the cost of carrying junk DNA more than just energy? E.g. the cost of material? Although efficient recycling within the cell may partially
offset that. Or the cost of occupied volume, processing speed (you
mention time to replicate), the requirement for proportionally more DNA management resources (error correction etc)?
If the cell as-a-factory analogy has merit, the idea of burning that proportion of time and money is highly questionable. At the same time, beware of simplistic comparisons - e.g. checking against biological realities is necessary, e.g. your selection coefficient calculation.
Interesting to see where the science goes from here.
It's a poorly designed factory. But it seems to work, and that's all evolution cares about.
On Monday, December 4, 2023 at 8:01:58 AM UTC+11, J. J. Lodder wrote:
Kerr-Mudd, John <ad...@127.0.0.1> wrote:
On Thu, 30 Nov 2023 14:15:19 -0800 (PST)Not just that. It is the worst possible factory that still works.
MarkE <me22...@gmail.com> wrote:
On Thursday, November 30, 2023 at 3:01:55?PM UTC+11, Lawyer Daggett wrote: >>> [cost of junk DNA]
The energy cost argument does deserve testing, which you've had a go at. >>>> Is the cost of carrying junk DNA more than just energy? E.g. the cost of >>>> material? Although efficient recycling within the cell may partially
offset that. Or the cost of occupied volume, processing speed (you
mention time to replicate), the requirement for proportionally more DNA >>>> management resources (error correction etc)?
If the cell as-a-factory analogy has merit, the idea of burning that
proportion of time and money is highly questionable. At the same time, >>>> beware of simplistic comparisons - e.g. checking against biological
realities is necessary, e.g. your selection coefficient calculation.
Interesting to see where the science goes from here.
It's a poorly designed factory. But it seems to work, and that's all
evolution cares about.
Jan
--
"Entropy always increases"
On what basis do you both assert this?
The opposite may in fact be the case, e.g. "The astonishing efficiency of life" https://phys.org/news/2017-11-astonishing-efficiency-life.html
On Mon, 4 Dec 2023 13:24:11 +0000, Ernest Major
<{$to$}@meden.demon.co.uk> wrote:
On 03/12/2023 23:28, MarkE wrote:
On Monday, December 4, 2023 at 8:01:58?AM UTC+11, J. J. Lodder wrote:
Kerr-Mudd, John <ad...@127.0.0.1> wrote:
On Thu, 30 Nov 2023 14:15:19 -0800 (PST)Not just that. It is the worst possible factory that still works.
MarkE <me22...@gmail.com> wrote:
On Thursday, November 30, 2023 at 3:01:55?PM UTC+11, Lawyer Daggett wrote:[cost of junk DNA]
The energy cost argument does deserve testing, which you've had a go at. >>>>>> Is the cost of carrying junk DNA more than just energy? E.g. the cost of >>>>>> material? Although efficient recycling within the cell may partially >>>>>> offset that. Or the cost of occupied volume, processing speed (you >>>>>> mention time to replicate), the requirement for proportionally more DNA >>>>>> management resources (error correction etc)?
If the cell as-a-factory analogy has merit, the idea of burning that >>>>>> proportion of time and money is highly questionable. At the same time, >>>>>> beware of simplistic comparisons - e.g. checking against biological >>>>>> realities is necessary, e.g. your selection coefficient calculation. >>>>>>
Interesting to see where the science goes from here.
It's a poorly designed factory. But it seems to work, and that's all >>>>> evolution cares about.
Jan
--
"Entropy always increases"
On what basis do you both assert this?
The opposite may in fact be the case, e.g. "The astonishing efficiency of life" https://phys.org/news/2017-11-astonishing-efficiency-life.html
Following the link to the paper on which that report is based, and then
to a work cited therein, I find numbers being put on why bacteria are so
much more effective at suppressing junk.
https://www.pnas.org/doi/full/10.1073/pnas.1514974112
https://www.pnas.org/doi/full/10.1073/pnas.1514974112
IIUC the limiting factor for bacteria is the speed of duplication.
Since most bacteria have but a single DNA string, larger genomes
necessarily mean longer strings necessarily mean slower duplication.
--
To know less than we don't know is the nature of most knowledge
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