On 10/11/23 9:09 PM, MarkE wrote:
On Thursday, October 12, 2023 at 1:16:06 PM UTC+11, John Harshman wrote:
On 10/11/23 5:22 PM, MarkE wrote:
On Thursday, October 12, 2023 at 10:21:08 AM UTC+11, John Harshman wrote: >>>> On 10/11/23 3:59 PM, MarkE wrote:
On Thursday, October 12, 2023 at 12:06:04 AM UTC+11, Ernest Major wrote:
which may interest some participants
https://www.youtube.com/watch?v=JOiGEI9pQBs
with sources
https://sites.google.com/view/sources-big-bang-life/
I think Hoylean panspermia is implicit here.
I believe the question as to how life survives 13 billion years of >>>>>> cosmic ray bombardment is unaddressed (though I guess one could
postulate cycles of regeneration in planetesimals in protoplanetary discs).
--
alias Ernest Major
Nicely produced video – almost too nice, in that the sparkling animations risk evoking flying unicorns which undermines the hypothesis presented.
I’ve always found panspermia to be both interesting and unsatisfactory. Interesting, because it gives greater freedom to noncreationists to question the origin of life on earth, and it offers a “cosmic” view of the history of life.
Unsatisfactory, because it seems to just kick the can down the road, with an appeal to a poorly specified cosmic teleology/causality (E.g.
https://www.panspermia.org/comparison.htm: “Origin of life? Undemonstrated. Source of life? The cosmos. Origin of
genetic programs? Undemonstrated. Source of genetic programs? The cosmos.“). >>>>>
The video exercises the abovementioned freedom by highlighting these OoL “paradoxes”, i.e. insufficient time in presumed earth history for first life to complexify, and the origin of transcription:
0:47 “To properly explain it let's first look at the paradox of life on Earth. The Life Paradox. For its first few hundred million years, Earth was a magma hell constantly bombarded by asteroids. But basically the second things calmed down and
the first oceans formed, life just appeared and zillions of microbes settled every nook and cranny they found. This is kind of strange – life on Earth seems to be almost as old as the planet itself. As if it was waiting around for an opportunity. But
life didn’t only appear extremely quickly: in that tiny time window, it also crossed a huge gap. To qualify as living things, even microbes need to eat, poop, grow and multiply. To do that, they need a genome, the biological instruction manual that
sets the inner workings of an organism.
1:44 How dead things with no genome became living things with genomes is one of the biggest riddles of science. Simplifying a lot, the problem is that to have a functioning genome you need proteins, and to make those proteins you need a functioning
genome. Both proteins and genomes are super long molecules made of pretty complex blocks that are extremely difficult to assemble by chance.
2:07 It is a chicken-egg paradox with several chickens and eggs. Once you have a finished cell, the whole system works efficiently. But starting from simple dead stuff and reaching that level of sophistication by pure chance should require an
amazing amount of time for trial and error. So how did the first living things manage to cross that gap in just a few hundred million years?
[“The essential problem is that in modern living systems, chemical reactions in cells are mediated by protein catalysts called enzymes. The information encoded in the nucleic acids DNA and RNA is required to make the proteins; yet the proteins
are required to make the nucleic acids. Furthermore, both proteins and nucleic acids are large molecules consisting of strings of small component molecules whose synthesis is supervised by proteins and nucleic acids. We have two chickens, two eggs, and
no answer to the old problem of which came first.”
https://www.americanscientist.org/article/the-origin-of-life]
2:31 Most theories about the origin of life try to explain that gap by theorizing how some primitive soup of prebiotic molecules could have efficiently produced the first self replicating entities. But we still don’t know how exactly this would
have worked.
...
3:35 When we put all these clues together, it seems that genomes have >>>>> been doubling in size on average every 350 million years or so. As if >>>>> evolution had been following an exponential inner clock. But it gets >>>>> even stranger. The very first microbes that emerged on Earth, even if >>>>> they look simple, already seem to have had pretty long and complex
genomes. But how could life have achieved that level of complexity in >>>>> such a short time?
What clues? I see no evidence for any such process, much less one that >>>> can be extrapolated back before the formation of the earth. How does
this person have any idea of the sizes of the genomes of
billions-of-year-ago organisms?
2:47 Maybe we need to think backwards. The Clock of Evolution Think
of genomes as a book telling the history of life. As time passed and
life evolved, more characters were introduced: Amoebae, fish,
amphibians, dinosaurs and mammals. Over billions of years, the story
of life got more and more complex. A genome can be viewed as a long
string of letters with biological instructions. And from microbes to
us today, functional genomes seem to have been increasing in size at
a fairly constant rate. The functional genome of fish is more than
twice that of worms; our functional genome is about twice bigger than
that of fish and so on. It is a bit more complicated, but for now
let’s run with this.
That's based on no data that I can see. There's no reason to think it's
true for the history of life, and the claims about current life just
aren't true at all. In fact, the functional genomes of most eukaryotes
are about the same size, and the nonfunctional bits vary by a factor of
100 or so. So better not run with that.
Note that I'm not defending the main thrust the video, just responding to it. They make this disclaimer too: "In this video we are going to put together two highly speculative yet scientifically grounded possibilities". As to data, they provide this
link
https://sites.google.com/view/sources-big-bang-life/ which the OP posted; from that here's some background material on the genomic clock:
#Sharov, A. (2006): “Genome increase as a clock for the origin and evolution of life”. Biology Direct, vol. 1, 17.
https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-17
Quote: “Biological complexity was recently defined by Adami et al. [8] as a size of functional and non-redundant genome. This measure does not depend on duplications, insertions, or deletions of non-functional or redundant sequences, and therefore it
is more stable in evolution than the total genome size.”
Quote: “Mammals (mouse, rat, and human), which appeared just recently in earth history, have a genome of ca. 3.2 × 109 bp, however only 5% of it is conserved between species [13]. Conserved regions are definitely functional but there may be
additional functional regulatory regions that are species-specific. These regions can be identified based on the absence of transposons, because transposons that are inserted in functional regions would interfere with normal gene regulation and
eventually disappear due to natural selection [14]. Transposon-free regions of 5 and 10 kb account for 20%, and 12% genome size, respectively [14]. If we take 15% as a rough estimate, then the size of functional and non-redundant genome in mammals is ca.
4.8 × 108 bp.”
If we now focus on the functional and non-redundant genomes of different kinds of organisms as they appeared over evolutionary history, a regular pattern emerges:
#Sharov, A. (2006): “Genome increase as a clock for the origin and evolution of life”. Biology Direct, vol. 1, 17.
https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-17
Quote: “Fish existed 0.5 billion years ago [15]. The genome size of the fugu fish is 4 × 108 bp and 1/3 of it is occupied by gene loci [16]. Worms existed at least for 1 billion years [17]. The genome of the worm Caenorhabditis elegans has size of 9.
7 × 107 bp and ca. 75% of its length is functional [18].”
The “more than twice” increase in genome length mentioned in the script is a rounding off that doesn’t correspond with the exact figures cited here (which correspond to particular examples) but with the average increase in genome length that will
be deduced from the regression explained below.
4:05 There may be an interesting way to solve this riddle: We just
take our exponential clock and extrapolate it back in time, to the
simplest conceivable life form – something equivalent to a being with >>>>> a genome containing just a few letters. But if we do that we end up
10 billion years in the past. More than twice the age of Earth, which >>>>> means: If life actually evolved like this, it did not start here, but >>>>> somewhere out there, in space.
There is no such exponential clock.
Yes, that exponential extrapolation is very debatable. In any case, your thoughts on the following?
"But life didn’t only appear extremely quickly: in that tiny time
window, it also crossed a huge gap. To qualify as living things, even
microbes need to eat, poop, grow and multiply. To do that, they need
a genome, the biological instruction manual that sets the inner
workings of an organism. How dead things with no genome became living
things with genomes is one of the biggest riddles of science.
Simplifying a lot, the problem is that to have a functioning genome
you need proteins, and to make those proteins you need a functioning
genome. Both proteins and genomes are super long molecules made of
pretty complex blocks that are extremely difficult to assemble by
chance. It is a chicken-egg paradox with several chickens and eggs."
That at least makes some sense. But the time window isn't all that tiny;
it's some hundreds of millions of years. And that claim ignores the
existence of ribozymes.
They allude to ribozymes in the background material referenced above:
#Trefil, J. et al. (2009): “The Origin of Life”. American Scientist, vol. 97, 3.
https://www.americanscientist.org/article/the-origin-of-life
Quote: “RNA World has been the prevailing theory for the origin of life since the 1980s. The emergence of a self-replicating catalytic molecule accounts for signature capabilities of living systems, but it doesn’t explain how the protobiological
molecule itself arose. Metabolism First seeks the answer in primitive reaction networks that generate their own constituents, offering a substrate for chemical selection and a launchpad for life.”
4:35 This would explain why life started to thrive so quickly on our young planet. If it was already present in space like a seed, it just needed water and warm temperatures to wake up and go on evolving. And it would also explain the high degree
of sophistication of the first life forms on Earth. They could have been complex already because they might have been evolving for billions of years somewhere else in the universe.
On 10/11/23 9:09 PM, MarkE wrote:
On Thursday, October 12, 2023 at 1:16:06 PM UTC+11, John Harshman wrote:
On 10/11/23 5:22 PM, MarkE wrote:
On Thursday, October 12, 2023 at 10:21:08 AM UTC+11, John Harshman wrote:
On 10/11/23 3:59 PM, MarkE wrote:
On Thursday, October 12, 2023 at 12:06:04 AM UTC+11, Ernest Major wrote:
which may interest some participants
https://www.youtube.com/watch?v=JOiGEI9pQBs
with sources
https://sites.google.com/view/sources-big-bang-life/
I think Hoylean panspermia is implicit here.
I believe the question as to how life survives 13 billion years of
cosmic ray bombardment is unaddressed (though I guess one could
postulate cycles of regeneration in planetesimals in
protoplanetary discs).
--
alias Ernest Major
Nicely produced video – almost too nice, in that the sparkling animations risk evoking flying unicorns which undermines the hypothesis presented.
I’ve always found panspermia to be both interesting and unsatisfactory. Interesting, because it gives greater freedom to noncreationists to question the origin of life on earth, and it offers a “cosmic” view of the history of life. Unsatisfactory, because it seems
to just kick the can down the road, with an appeal to a poorly specified
cosmic teleology/causality (E.g.
https://www.panspermia.org/comparison.htm: “Origin of life?
Undemonstrated. Source of life? The cosmos. Origin of genetic programs? Undemonstrated. Source of genetic programs? The cosmos.“).
The video exercises the abovementioned freedom by highlighting
these OoL “paradoxes”, i.e. insufficient time in presumed earth history
for first life to complexify, and the origin of transcription:
0:47 “To properly explain it let's first look at the paradox of
life on Earth. The Life Paradox. For its first few hundred million
years, Earth was a magma hell constantly bombarded by asteroids. But
basically the second things calmed down and the first oceans formed,
life just appeared and zillions of microbes settled every nook and
cranny they found. This is kind of strange – life on Earth seems to be
almost as old as the planet itself. As if it was waiting around for an opportunity. But life didn’t only appear extremely quickly: in that tiny
time window, it also crossed a huge gap. To qualify as living things,
even microbes need to eat, poop, grow and multiply. To do that, they
need a genome, the biological instruction manual that sets the inner
workings of an organism.
1:44 How dead things with no genome became living things with
genomes is one of the biggest riddles of science. Simplifying a lot, the problem is that to have a functioning genome you need proteins, and to
make those proteins you need a functioning genome. Both proteins and
genomes are super long molecules made of pretty complex blocks that are extremely difficult to assemble by chance.
2:07 It is a chicken-egg paradox with several chickens and eggs.
Once you have a finished cell, the whole system works efficiently. But
starting from simple dead stuff and reaching that level of
sophistication by pure chance should require an amazing amount of time
for trial and error. So how did the first living things manage to cross
that gap in just a few hundred million years?
[“The essential problem is that in modern living systems,
chemical reactions in cells are mediated by protein catalysts called
enzymes. The information encoded in the nucleic acids DNA and RNA is
required to make the proteins; yet the proteins are required to make the nucleic acids. Furthermore, both proteins and nucleic acids are large
molecules consisting of strings of small component molecules whose
synthesis is supervised by proteins and nucleic acids. We have two
chickens, two eggs, and no answer to the old problem of which came
first.”
https://www.americanscientist.org/article/the-origin-of-life]
2:31 Most theories about the origin of life try to explain that
gap by theorizing how some primitive soup of prebiotic molecules could
have efficiently produced the first self replicating entities. But we
still don’t know how exactly this would have worked.
...
3:35 When we put all these clues together, it seems that genomes have
been doubling in size on average every 350 million years or so. As if
evolution had been following an exponential inner clock. But it gets
even stranger. The very first microbes that emerged on Earth, even if
they look simple, already seem to have had pretty long and complex
genomes. But how could life have achieved that level of complexity in
such a short time?
What clues? I see no evidence for any such process, much less one that
can be extrapolated back before the formation of the earth. How does
this person have any idea of the sizes of the genomes of
billions-of-year-ago organisms?
2:47 Maybe we need to think backwards. The Clock of Evolution Think
of genomes as a book telling the history of life. As time passed and
life evolved, more characters were introduced: Amoebae, fish,
amphibians, dinosaurs and mammals. Over billions of years, the story
of life got more and more complex. A genome can be viewed as a long
string of letters with biological instructions. And from microbes to
us today, functional genomes seem to have been increasing in size at
a fairly constant rate. The functional genome of fish is more than
twice that of worms; our functional genome is about twice bigger than
that of fish and so on. It is a bit more complicated, but for now
let’s run with this.
That's based on no data that I can see. There's no reason to think it's
true for the history of life, and the claims about current life just
aren't true at all. In fact, the functional genomes of most eukaryotes
are about the same size, and the nonfunctional bits vary by a factor of
100 or so. So better not run with that.
Note that I'm not defending the main thrust the video, just
responding to it. They make this disclaimer too: "In this video we are
going to put together two highly speculative yet scientifically grounded possibilities". As to data, they provide this link
https://sites.google.com/view/sources-big-bang-life/ which the OP
posted; from that here's some background material on the genomic clock:
#Sharov, A. (2006): “Genome increase as a clock for the origin and
evolution of life”. Biology Direct, vol. 1, 17.
https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-17
Quote: “Biological complexity was recently defined by Adami et al.
[8] as a size of functional and non-redundant genome. This measure does
not depend on duplications, insertions, or deletions of non-functional
or redundant sequences, and therefore it is more stable in evolution
than the total genome size.”
Quote: “Mammals (mouse, rat, and human), which appeared just recently
in earth history, have a genome of ca. 3.2 × 109 bp, however only 5% of
it is conserved between species [13]. Conserved regions are definitely functional but there may be additional functional regulatory regions
that are species-specific. These regions can be identified based on the
absence of transposons, because transposons that are inserted in
functional regions would interfere with normal gene regulation and
eventually disappear due to natural selection [14]. Transposon-free
regions of 5 and 10 kb account for 20%, and 12% genome size,
respectively [14]. If we take 15% as a rough estimate, then the size of functional and non-redundant genome in mammals is ca. 4.8 × 108 bp.”
If we now focus on the functional and non-redundant genomes of
different kinds of organisms as they appeared over evolutionary history,
a regular pattern emerges:
#Sharov, A. (2006): “Genome increase as a clock for the origin and
evolution of life”. Biology Direct, vol. 1, 17.
https://biologydirect.biomedcentral.com/articles/10.1186/1745-6150-1-17
Quote: “Fish existed 0.5 billion years ago [15]. The genome size of
the fugu fish is 4 × 108 bp and 1/3 of it is occupied by gene loci [16].
Worms existed at least for 1 billion years [17]. The genome of the worm Caenorhabditis elegans has size of 9.7 × 107 bp and ca. 75% of its
length is functional [18].”
The “more than twice” increase in genome length mentioned in the
script is a rounding off that doesn’t correspond with the exact figures
cited here (which correspond to particular examples) but with the
average increase in genome length that will be deduced from the
regression explained below.
Useless. The only three data points are cherry-picked and considered
under different criteria. Lumping "fish" under a single species of
teleost is absurd. This is not science. This is garbage.
4:05 There may be an interesting way to solve this riddle: We just
take our exponential clock and extrapolate it back in time, to the
simplest conceivable life form – something equivalent to a being with
a genome containing just a few letters. But if we do that we end up
10 billion years in the past. More than twice the age of Earth, which
means: If life actually evolved like this, it did not start here, but
somewhere out there, in space.
There is no such exponential clock.
Yes, that exponential extrapolation is very debatable. In any case,
your thoughts on the following?
"But life didn’t only appear extremely quickly: in that tiny time
window, it also crossed a huge gap. To qualify as living things, even
microbes need to eat, poop, grow and multiply. To do that, they need
a genome, the biological instruction manual that sets the inner
workings of an organism. How dead things with no genome became living
things with genomes is one of the biggest riddles of science.
Simplifying a lot, the problem is that to have a functioning genome
you need proteins, and to make those proteins you need a functioning
genome. Both proteins and genomes are super long molecules made of
pretty complex blocks that are extremely difficult to assemble by
chance. It is a chicken-egg paradox with several chickens and eggs."
That at least makes some sense. But the time window isn't all that tiny;
it's some hundreds of millions of years. And that claim ignores the
existence of ribozymes.
They allude to ribozymes in the background material referenced above:
Then why do they ignore them in that quote?
#Trefil, J. et al. (2009): “The Origin of Life”. American
Scientist, vol. 97, 3.
https://www.americanscientist.org/article/the-origin-of-life
Quote: “RNA World has been the prevailing theory for the origin of
life since the 1980s. The emergence of a self-replicating catalytic
molecule accounts for signature capabilities of living systems, but it doesn’t explain how the protobiological molecule itself arose.
Metabolism First seeks the answer in primitive reaction networks that
generate their own constituents, offering a substrate for chemical
selection and a launchpad for life.”
That's irrelevant to the point, isn't it?
4:35 This would explain why life started to thrive so quickly on
our young planet. If it was already present in space like a seed, it
just needed water and warm temperatures to wake up and go on evolving.
And it would also explain the high degree of sophistication of the first
life forms on Earth. They could have been complex already because they
might have been evolving for billions of years somewhere else in the
universe.
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