Las universal common ancestor

[erik simpson]

The nature of the last universal common ancestor and its impact on the
early Earth system

Abstract
The nature of the last universal common ancestor (LUCA), its age and its
impact on the Earth system have been the subject of vigorous debate
across diverse disciplines, often based on disparate data and methods.
Age estimates for LUCA are usually based on the fossil record, varying
with every reinterpretation. The nature of LUCA’s metabolism has proven
equally contentious, with some attributing all core metabolisms to LUCA,
whereas others reconstruct a simpler life form dependent on
geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga)
through divergence time analysis of pre-LUCA gene duplicates, calibrated
using microbial fossils and isotope records under a new cross-bracing
implementation. Phylogenetic reconciliation suggests that LUCA had a
genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600
proteins, comparable to modern prokaryotes. Our results suggest LUCA was
a prokaryote-grade anaerobic acetogen that possessed an early immune
system. Although LUCA is sometimes perceived as living in isolation, we
infer LUCA to have been part of an established ecological system. The
metabolism of LUCA would have provided a niche for other microbial
community members and hydrogen recycling by atmospheric photochemistry
could have supported a modestly productive early ecosystem.

https://www.nature.com/articles/s41559-024-02461-1

[William Hyde]

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and its
impact on the Earth system have been the subject of vigorous debate
across diverse disciplines, often based on disparate data and methods.
Age estimates for LUCA are usually based on the fossil record, varying
with every reinterpretation. The nature of LUCA’s metabolism has proven
equally contentious, with some attributing all core metabolisms to LUCA,
whereas others reconstruct a simpler life form dependent on
geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga)
through divergence time analysis of pre-LUCA gene duplicates, calibrated
using microbial fossils and isotope records under a new cross-bracing
implementation. Phylogenetic reconciliation suggests that LUCA had a
genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600
proteins, comparable to modern prokaryotes. Our results suggest LUCA was
a prokaryote-grade anaerobic acetogen that possessed an early immune
system. Although LUCA is sometimes perceived as living in isolation, we
infer LUCA to have been part of an established ecological system. The
metabolism of LUCA would have provided a niche for other microbial
community members and hydrogen recycling by atmospheric photochemistry
could have supported a modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

Does not the existence of the immune system itself imply the existence
of other life forms? Smaller, parasitic or infectious? But since this
is LUCA they themselves cannot have left descendants.


So if they were virus-like they went extinct and the virus form evolved
again.

Corrections and comment welcome, as ever.

William Hyde

[erik simpson]

Post by William Hyde

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes perceived
as living in isolation, we infer LUCA to have been part of an
established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

Does not the existence of the immune system itself imply the existence
of other life forms?  Smaller, parasitic or infectious?  But since this
is LUCA they themselves cannot have left descendants.
So if they were virus-like they went extinct and the virus form evolved
again.
Corrections and comment welcome, as ever.
William Hyde

I'm not sure what "ancestral" means to a virus. Can someone with better
chops than I comment on that? I've never seen a phylogenetic tree for
viruses, or how that could be incorporated into a bacterial tree. The
authors mention "horizontal transfer awareness".

[Ernest Major]

Post by William Hyde

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes perceived
as living in isolation, we infer LUCA to have been part of an
established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

Does not the existence of the immune system itself imply the existence
of other life forms?  Smaller, parasitic or infectious?  But since this
is LUCA they themselves cannot have left descendants.
So if they were virus-like they went extinct and the virus form evolved
again.
Corrections and comment welcome, as ever.

You might think of this as LUCCA - last universal cellular common
ancestor. Coeval viruses might have "living" descendants.

When I read that this LUCA has an immune system I made the assumption
that this implied the existence of coeval viruses. But I now realise
that there are other alternatives, such as a prokaryote that injects a
copy of DNA into other cells, or still existing categories such as
viroids and plasmids.

I used to be agnostic between the 3 major hypotheses for viral origins,
but I am becoming increasingly convinced that at least some viral groups
are ancient. Viruses are now classified into 6 realms (and more than 2
dozen incertae sedae groups). One realm - the Adnaviria - seems to be as
old as the Archaea.

Post by William Hyde
William Hyde

[RonO]

Post by William Hyde

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes perceived
as living in isolation, we infer LUCA to have been part of an
established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

Does not the existence of the immune system itself imply the existence
of other life forms?  Smaller, parasitic or infectious?  But since this
is LUCA they themselves cannot have left descendants.
So if they were virus-like they went extinct and the virus form evolved
again.
Corrections and comment welcome, as ever.
William Hyde

Archaea and bacteria are only 2 lineages of life that have survived. If
you look at their inferred phylogeny (Figure 1) it looks like extant
lifeforms are derived from two lineages (Archaea and bacteria) seem to
have barely survived some event around a billion years after they first
diverged from the LUCA. The last Archaea common ancestor and the last
bacterial common ancestor existed over a billion years after LUCA. Just
think of how many lineages existed for all that time, and then only one
lineage of each survived to further diversify. Either something killed
everything off or by random chance only those single lineages
representing Archaea and bacteria managed to survive.

This just means that the existence of LUCA doesn't mean that there were
not a whole lot of other lifeforms that existed at the same time.

Ron Okimoto

[RonO]

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and its
impact on the Earth system have been the subject of vigorous debate
across diverse disciplines, often based on disparate data and methods.
Age estimates for LUCA are usually based on the fossil record, varying
with every reinterpretation. The nature of LUCA’s metabolism has proven
equally contentious, with some attributing all core metabolisms to LUCA,
whereas others reconstruct a simpler life form dependent on
geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga)
through divergence time analysis of pre-LUCA gene duplicates, calibrated
using microbial fossils and isotope records under a new cross-bracing
implementation. Phylogenetic reconciliation suggests that LUCA had a
genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600
proteins, comparable to modern prokaryotes. Our results suggest LUCA was
a prokaryote-grade anaerobic acetogen that possessed an early immune
system. Although LUCA is sometimes perceived as living in isolation, we
infer LUCA to have been part of an established ecological system. The
metabolism of LUCA would have provided a niche for other microbial
community members and hydrogen recycling by atmospheric photochemistry
could have supported a modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

It has been a long time since I published in this field, and they use
terminology that wasn't being used back then. I do not know why, but
they call genes "markers" and do not use gene names, but marker
designations that are in the NCBI database and give you a protein
sequence comparision and superfamily designation. TIGR01032 is a member
of superfamily cl00d393. You have to use the protein alignment names to
get the name of the gene. I clicked on P47440 in the protein sequence
alignment and found out that it was 50s ribosomal protein L20.

They identified 59 single copy markers in their 700 reference genomes,
and used 57 of them in their analysis. They created a phylogeny of
their 700 reference genomes by doing phylogenetic analysis on the 57
concatenated gene sequences.

They claim to use duplicated genes whose duplication preceded LUCA.
They did an analysis to identify all the gene families in their 700
reference genomes. They identified the genes and did a comparative
analysis and grouped them into families. They ended up with 5 groups of
related genes whose duplication may have occurred before LUCA existed.
They used analysis of these groups of related genes to estimate when
LUCA may have existed.

I do not know how accurate any estimate could be. They do have
phylogeny of their 700 reference genomes, and they do have the
duplicated sequence families. I do not know if they have enough nodes
to estimate how the protein sequences have evolved over the last 4
billion years. They have the extant sequence and are trying to recreate
the sequence of the original protein gene in order to make their clock
estimates. They are trying to infer how many substitutions have
occurred in 4 billion years for 700 reference genomes when it is likely
that a high percentage of the amino acid positions have been substituted
many times within each of their 700 lineages.

Their estimate of 4.2 Ga for the LUCA would mean that the genetic code
had evolved within 300 million years of their 4.5 Ga estimate for when
the earth's surface was essentially molten.

They reject the late heavy bombardment episode that was supposed to have
occurred around 3.8 Ga that would have sterilized the planet and note
that it has come into question as ever happening.

Ron Okimoto

[RonO]

Post by RonO

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes perceived
as living in isolation, we infer LUCA to have been part of an
established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

It has been a long time since I published in this field, and they use
terminology that wasn't being used back then.  I do not know why, but
they call genes "markers" and do not use gene names, but marker
designations that are in the NCBI database and give you a protein
sequence comparision and superfamily designation.  TIGR01032 is a member
of superfamily cl00d393.  You have to use the protein alignment names to
get the name of the gene.  I clicked on P47440 in the protein sequence
alignment and found out that it was 50s ribosomal protein L20.
They identified 59 single copy markers in their 700 reference genomes,
and used 57 of them in their analysis.  They created a phylogeny of
their 700 reference genomes by doing phylogenetic analysis on the 57
concatenated gene sequences.
They claim to use duplicated genes whose duplication preceded LUCA. They
did an analysis to identify all the gene families in their 700 reference
genomes. They identified the genes and did a comparative analysis and
grouped them into families.  They ended up with 5 groups of related
genes whose duplication may have occurred before LUCA existed. They used
analysis of these groups of related genes to estimate when LUCA may have
existed.
I do not know how accurate any estimate could be.  They do have
phylogeny of their 700 reference genomes, and they do have the
duplicated sequence families.  I do not know if they have enough nodes
to estimate how the protein sequences have evolved over the last 4
billion years.  They have the extant sequence and are trying to recreate
the sequence of the original protein gene in order to make their clock
estimates.  They are trying to infer how many substitutions have
occurred in 4 billion years for 700 reference genomes when it is likely
that a high percentage of the amino acid positions have been substituted
many times within each of their 700 lineages.
Their estimate of 4.2 Ga for the LUCA would mean that the genetic code
had evolved within 300 million years of their 4.5 Ga estimate for when
the earth's surface was essentially molten.
They reject the late heavy bombardment episode that was supposed to have
occurred around 3.8 Ga that would have sterilized the planet and note
that it has come into question as ever happening.
Ron Okimoto

The ID perps have their take on this study.

https://evolutionnews.org/2024/07/study-finds-lifes-origin-required-a-surprisingly-short-interval-of-geologic-time/

They make some stupid comments like:
QUOTE:
First, it infers the genetic and phenotypic traits of LUCA by assuming
that biological similarity always results from common ancestry — and
never from common design. This dubious logic is seen in the opening
statement from the technical paper which reads, “The common ancestry of
all extant cellular life is evidenced by the universal genetic code,
machinery for protein synthesis, shared chirality of the
almost-universal set of 20 amino acids and use of ATP as a common energy
currency.” It’s true that all life uses those components (although the
genetic code is not exactly universal), but this does not provide
special evidence for common ancestry because the commonality of these
similar features could be explained by common design due to their
functional utility.
END QUOTE:

The stupid thing about this IDiotic notion is that the study is only
possible because of descent with modification. If it were common design
there is no reason to have lineages accumulate the genetic changes that
make this study possible. Some designer could have created all
lifeforms with the same genetic code and related gene sets, but this
study relied on ancient gene families that started gene duplication
prior to the last common bacterial ancestor and the last common Archaea
ancestor. These genes duplicated and they started changing. The
lineages of these gene families existed before LUCA, and further
differentiated after the last common Archaea and bacterial common
ancestors. The phylogenies have been maintained in all the subsequent
Archaea and bacterial lineages including Eukarya. Behe and Denton
understand that this pattern of evolution could not have been due to a
common designer, but had to be created by descent with modification.
That is why Behe started claiming that he was looking for 3 neutral
mutations to alter a protein to do something different. These 3 neutral
mutations would have had to occur in a lineage that could be determined
not to have them until they occurred within some Beheian time limit.
Behe is a tweeker. His designer is duplicating genes and putting in a
few amino acid substitutions in them every once in a while. For the 5
gene families used in this study the genes started duplicating before
LUCA existed.

LUCA is only the last common ancestor of both Archaea and bacteria. As
crazy as it may seem this study indicates that around a billion years
after LUCA existed life was reduced to just two surviving lineages.
There were likely trillions of lifeforms that started lineages before
LUCA and after, but only two surviving lineages are represented by
extant lifeforms. If we had a third or a fourth surviving lineage we
could have a different LUCA. There were many different lineages of life
that existed at the same time as LUCA, but LUCA identified in this study
is the only one with surviving descendants.

Ron Okimoto

[John Harshman]

Post by RonO

Post by RonO

Post by erik simpson
The nature of the last universal common ancestor and its impact on
the early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes
perceived as living in isolation, we infer LUCA to have been part of
an established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

It has been a long time since I published in this field, and they use
terminology that wasn't being used back then.  I do not know why, but
they call genes "markers" and do not use gene names, but marker
designations that are in the NCBI database and give you a protein
sequence comparision and superfamily designation.  TIGR01032 is a
member of superfamily cl00d393.  You have to use the protein alignment
names to get the name of the gene.  I clicked on P47440 in the protein
sequence alignment and found out that it was 50s ribosomal protein L20.
They identified 59 single copy markers in their 700 reference genomes,
and used 57 of them in their analysis.  They created a phylogeny of
their 700 reference genomes by doing phylogenetic analysis on the 57
concatenated gene sequences.
They claim to use duplicated genes whose duplication preceded LUCA.
They did an analysis to identify all the gene families in their 700
reference genomes. They identified the genes and did a comparative
analysis and grouped them into families.  They ended up with 5 groups
of related genes whose duplication may have occurred before LUCA
existed. They used analysis of these groups of related genes to
estimate when LUCA may have existed.
I do not know how accurate any estimate could be.  They do have
phylogeny of their 700 reference genomes, and they do have the
duplicated sequence families.  I do not know if they have enough nodes
to estimate how the protein sequences have evolved over the last 4
billion years.  They have the extant sequence and are trying to
recreate the sequence of the original protein gene in order to make
their clock estimates.  They are trying to infer how many
substitutions have occurred in 4 billion years for 700 reference
genomes when it is likely that a high percentage of the amino acid
positions have been substituted many times within each of their 700
lineages.
Their estimate of 4.2 Ga for the LUCA would mean that the genetic code
had evolved within 300 million years of their 4.5 Ga estimate for when
the earth's surface was essentially molten.
They reject the late heavy bombardment episode that was supposed to
have occurred around 3.8 Ga that would have sterilized the planet and
note that it has come into question as ever happening.
Ron Okimoto

The ID perps have their take on this study.
https://evolutionnews.org/2024/07/study-finds-lifes-origin-required-a-surprisingly-short-interval-of-geologic-time/
First, it infers the genetic and phenotypic traits of LUCA by assuming
that biological similarity always results from common ancestry — and
never from common design. This dubious logic is seen in the opening
statement from the technical paper which reads, “The common ancestry of
all extant cellular life is evidenced by the universal genetic code,
machinery for protein synthesis, shared chirality of the
almost-universal set of 20 amino acids and use of ATP as a common energy
currency.” It’s true that all life uses those components (although the
genetic code is not exactly universal), but this does not provide
special evidence for common ancestry because the commonality of these
similar features could be explained by common design due to their
functional utility.
The stupid thing about this IDiotic notion is that the study is only
possible because of descent with modification.  If it were common design
there is no reason to have lineages accumulate the genetic changes that
make this study possible.  Some designer could have created all
lifeforms with the same genetic code and related gene sets, but this
study relied on ancient gene families that started gene duplication
prior to the last common bacterial ancestor and the last common Archaea
ancestor.  These genes duplicated and they started changing.  The
lineages of these gene families existed before LUCA, and further
differentiated after the last common Archaea and bacterial common
ancestors.  The phylogenies have been maintained in all the subsequent
Archaea and bacterial lineages including Eukarya.  Behe and Denton
understand that this pattern of evolution could not have been due to a
common designer, but had to be created by descent with modification.
That is why Behe started claiming that he was looking for 3 neutral
mutations to alter a protein to do something different.  These 3 neutral
mutations would have had to occur in a lineage that could be determined
not to have them until they occurred within some Beheian time limit.
Behe is a tweeker.  His designer is duplicating genes and putting in a
few amino acid substitutions in them every once in a while.  For the 5
gene families used in this study the genes started duplicating before
LUCA existed.
LUCA is only the last common ancestor of both Archaea and bacteria.  As
crazy as it may seem this study indicates that around a billion years
after LUCA existed life was reduced to just two surviving lineages.
There were likely trillions of lifeforms that started lineages before
LUCA and after, but only two surviving lineages are represented by
extant lifeforms.  If we had a third or a fourth surviving lineage we
could have a different LUCA.  There were many different lineages of life
that existed at the same time as LUCA, but LUCA identified in this study
is the only one with surviving descendants.

Hey, it's just coalescence. IDers seem unable to understand coalescence,
and creationists are generally worse. Also, Theobald 2010.

Theobald, D. A formal test of the theory of universal common ancestry.
Nature 465, 219–222 (2010)

https://www.nature.com/articles/nature09014

[RonO]

Post by John Harshman

Post by RonO

Post by RonO

Post by erik simpson
The nature of the last universal common ancestor and its impact on
the early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2
 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic
reconciliation suggests that LUCA had a genome of at least 2.5 Mb
(2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern
prokaryotes. Our results suggest LUCA was a prokaryote-grade
anaerobic acetogen that possessed an early immune system. Although
LUCA is sometimes perceived as living in isolation, we infer LUCA to
have been part of an established ecological system. The metabolism
of LUCA would have provided a niche for other microbial community
members and hydrogen recycling by atmospheric photochemistry could
have supported a modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

It has been a long time since I published in this field, and they use
terminology that wasn't being used back then.  I do not know why, but
they call genes "markers" and do not use gene names, but marker
designations that are in the NCBI database and give you a protein
sequence comparision and superfamily designation.  TIGR01032 is a
member of superfamily cl00d393.  You have to use the protein
alignment names to get the name of the gene.  I clicked on P47440 in
the protein sequence alignment and found out that it was 50s
ribosomal protein L20.
They identified 59 single copy markers in their 700 reference
genomes, and used 57 of them in their analysis.  They created a
phylogeny of their 700 reference genomes by doing phylogenetic
analysis on the 57 concatenated gene sequences.
They claim to use duplicated genes whose duplication preceded LUCA.
They did an analysis to identify all the gene families in their 700
reference genomes. They identified the genes and did a comparative
analysis and grouped them into families.  They ended up with 5 groups
of related genes whose duplication may have occurred before LUCA
existed. They used analysis of these groups of related genes to
estimate when LUCA may have existed.
I do not know how accurate any estimate could be.  They do have
phylogeny of their 700 reference genomes, and they do have the
duplicated sequence families.  I do not know if they have enough
nodes to estimate how the protein sequences have evolved over the
last 4 billion years.  They have the extant sequence and are trying
to recreate the sequence of the original protein gene in order to
make their clock estimates.  They are trying to infer how many
substitutions have occurred in 4 billion years for 700 reference
genomes when it is likely that a high percentage of the amino acid
positions have been substituted many times within each of their 700
lineages.
Their estimate of 4.2 Ga for the LUCA would mean that the genetic
code had evolved within 300 million years of their 4.5 Ga estimate
for when the earth's surface was essentially molten.
They reject the late heavy bombardment episode that was supposed to
have occurred around 3.8 Ga that would have sterilized the planet and
note that it has come into question as ever happening.
Ron Okimoto

The ID perps have their take on this study.
https://evolutionnews.org/2024/07/study-finds-lifes-origin-required-a-surprisingly-short-interval-of-geologic-time/
First, it infers the genetic and phenotypic traits of LUCA by assuming
that biological similarity always results from common ancestry — and
never from common design. This dubious logic is seen in the opening
statement from the technical paper which reads, “The common ancestry
of all extant cellular life is evidenced by the universal genetic
code, machinery for protein synthesis, shared chirality of the
almost-universal set of 20 amino acids and use of ATP as a common
energy currency.” It’s true that all life uses those components
(although the genetic code is not exactly universal), but this does
not provide special evidence for common ancestry because the
commonality of these similar features could be explained by common
design due to their functional utility.
The stupid thing about this IDiotic notion is that the study is only
possible because of descent with modification.  If it were common
design there is no reason to have lineages accumulate the genetic
changes that make this study possible.  Some designer could have
created all lifeforms with the same genetic code and related gene
sets, but this study relied on ancient gene families that started gene
duplication prior to the last common bacterial ancestor and the last
common Archaea ancestor.  These genes duplicated and they started
changing.  The lineages of these gene families existed before LUCA,
and further differentiated after the last common Archaea and bacterial
common ancestors.  The phylogenies have been maintained in all the
subsequent Archaea and bacterial lineages including Eukarya.  Behe and
Denton understand that this pattern of evolution could not have been
due to a common designer, but had to be created by descent with
modification. That is why Behe started claiming that he was looking
for 3 neutral mutations to alter a protein to do something different.
These 3 neutral mutations would have had to occur in a lineage that
could be determined not to have them until they occurred within some
Beheian time limit. Behe is a tweeker.  His designer is duplicating
genes and putting in a few amino acid substitutions in them every once
in a while.  For the 5 gene families used in this study the genes
started duplicating before LUCA existed.
LUCA is only the last common ancestor of both Archaea and bacteria.
As crazy as it may seem this study indicates that around a billion
years after LUCA existed life was reduced to just two surviving
lineages. There were likely trillions of lifeforms that started
lineages before LUCA and after, but only two surviving lineages are
represented by extant lifeforms.  If we had a third or a fourth
surviving lineage we could have a different LUCA.  There were many
different lineages of life that existed at the same time as LUCA, but
LUCA identified in this study is the only one with surviving descendants.

Hey, it's just coalescence. IDers seem unable to understand coalescence,
and creationists are generally worse. Also, Theobald 2010.
Theobald, D. A formal test of the theory of universal common ancestry.
Nature 465, 219–222 (2010)
https://www.nature.com/articles/nature09014

Gish used to use Yockey's numbers to claim that proteins could not have
assembled by chance. Yockey had estimated that there were something
like 10^69 possible protein sequences the same length as cytochrome c
(around 104 amino acid residues). Cytochrome c was a short protein so
it had been sequenced in a large number of taxa before we could sequence
DNA we had the protein sequences for several short proteins like cyt c
and hemoglobin. Yockey was able to estimate that there were something
like 10^45 possible functional cytochrome c sequences based on the
variation that was already known at that time, but this was still too
few to have the protein sequence assembled by chance. Gish would make a
big deal about how unlikely it was to form a functional cytochrome c
protein by chance, but Yockey turned it around and noted the
phylogenetic information contained in the known cytochrome c proteins
was much more unlikely to have been assembled by chance without descent
with modification. I recall an ID perp tried to claim that a common
designer could account for the phylogenetic information, but they never
could. I recall that one of the arguments was that similar lifestyles
would need more similar sequences, but that doesn't explain things like
intron variation, and lineages that have converged on the same
phenotypes like marsupial moles and eutherian moles. The ID perps do
not want to face the fact that their designer had to use an ape template
to create humans. That same designer would have needed to use a simian
template to create apes, and the apes would have to be created in some
type of sequence so that we are most closely related to chimps, next to
gorillas, orangs and gibbons, but all apes are about the same genetic
distance from our simian common ancestor. The common designer doesn't
make sense.

Ron Okimoto

[RonO]

Post by RonO

Post by erik simpson
The nature of the last universal common ancestor and its impact on the
early Earth system
Abstract
The nature of the last universal common ancestor (LUCA), its age and
its impact on the Earth system have been the subject of vigorous
debate across diverse disciplines, often based on disparate data and
methods. Age estimates for LUCA are usually based on the fossil
record, varying with every reinterpretation. The nature of LUCA’s
metabolism has proven equally contentious, with some attributing all
core metabolisms to LUCA, whereas others reconstruct a simpler life
form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga
(4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene
duplicates, calibrated using microbial fossils and isotope records
under a new cross-bracing implementation. Phylogenetic reconciliation
suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb),
encoding around 2,600 proteins, comparable to modern prokaryotes. Our
results suggest LUCA was a prokaryote-grade anaerobic acetogen that
possessed an early immune system. Although LUCA is sometimes perceived
as living in isolation, we infer LUCA to have been part of an
established ecological system. The metabolism of LUCA would have
provided a niche for other microbial community members and hydrogen
recycling by atmospheric photochemistry could have supported a
modestly productive early ecosystem.
https://www.nature.com/articles/s41559-024-02461-1

It has been a long time since I published in this field, and they use
terminology that wasn't being used back then.  I do not know why, but
they call genes "markers" and do not use gene names, but marker
designations that are in the NCBI database and give you a protein
sequence comparision and superfamily designation.  TIGR01032 is a member
of superfamily cl00d393.  You have to use the protein alignment names to
get the name of the gene.  I clicked on P47440 in the protein sequence
alignment and found out that it was 50s ribosomal protein L20.
They identified 59 single copy markers in their 700 reference genomes,
and used 57 of them in their analysis.  They created a phylogeny of
their 700 reference genomes by doing phylogenetic analysis on the 57
concatenated gene sequences.
They claim to use duplicated genes whose duplication preceded LUCA. They
did an analysis to identify all the gene families in their 700 reference
genomes. They identified the genes and did a comparative analysis and
grouped them into families.  They ended up with 5 groups of related
genes whose duplication may have occurred before LUCA existed. They used
analysis of these groups of related genes to estimate when LUCA may have
existed.
I do not know how accurate any estimate could be.  They do have
phylogeny of their 700 reference genomes, and they do have the
duplicated sequence families.  I do not know if they have enough nodes
to estimate how the protein sequences have evolved over the last 4
billion years.  They have the extant sequence and are trying to recreate
the sequence of the original protein gene in order to make their clock
estimates.  They are trying to infer how many substitutions have
occurred in 4 billion years for 700 reference genomes when it is likely
that a high percentage of the amino acid positions have been substituted
many times within each of their 700 lineages.
Their estimate of 4.2 Ga for the LUCA would mean that the genetic code
had evolved within 300 million years of their 4.5 Ga estimate for when
the earth's surface was essentially molten.
They reject the late heavy bombardment episode that was supposed to have
occurred around 3.8 Ga that would have sterilized the planet and note
that it has come into question as ever happening.
Ron Okimoto

I've looked at this paper again, and they do not discuss the fact that
their model indicates that all lineages derived from LUCA went to
extinction except for two (Archaea and bacteria). The last common
Archaea and independent last common ancestor of bacteria existed over a
billion years after LUCA. The paper doesn't discuss the point, but it
looks like there was some event that reduced the surviving lineages
derived from LUCA to just two around a billion years after the LUCA of
those two surviving lineages existed.

They dismiss the late heavy bombardment episode that would have
sterilized the earth between 4.1 and 3.8 billion years ago, but it could
explain the lack of diversification for the billion years after LUCA
existed. Both Archaea and bacteria inherited reverse gyrase from LUCA
and that seems to indicate that the lineages that survived this period
of lineage extinctions were thermophilic probably living around
hydrothermal vents in volcanically active areas that may have been
spawned by the late heavy bombardment if it wasn't as bad as they think
that it was. Their analysis indicates that somehow only two
thermophilic lineages survived to coalesce a billion years after LUCA
existed.

They think that LUCA may have been a heterotrophe and may have relied on
chemotrophes to fix carbon, but LUCA had ATPase (evolved in
chemotrophes) and they admit that LUCA could have been chemotrophic.
They think that LUCA existed in an ecology of diverse lifeforms, but
this ecology would have needed to be decimated in order for only two
lineages derived from LUCA to represent all extant life on earth.

It would seem that life nearly went extinct within a billion years after
LUCA existed. Something happened to all the lifeforms that shared the
planet with LUCA and all the lineages that were spawned from LUCA within
a billion year period after LUCA existed. Somehow only two lineages
survived and both independent lineages coalesce into two single lineages
around a billion years after LUCA existed.

Ron Okimoto