From Newsgroup: talk.origins

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the challenges
facing OOL becomes, including:

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the prebiotic assembly of complex molecules and structures needed before Darwinian
evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule affect
the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already encode
highly specific functions. These are not merely complex molecules, are functionally specified molecules operating in a coordinated coding
system, i.e. information-bearing and highly specified.

This links to 1. How do you evolve and refine enzymes and other proteins needed by a protocell (like SpudCell) before the first protocell?
Outside this context, an enzymerCOs biological function does not confer reproductive advantage because there is no reproducing protocell to
benefit from it.

Even if they evolved as naked polymers or in some other chemical system
(e.g. autocatalytic set), they have not been selected and evolved for
the unrelated context of a protocell. You can only ask so much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation and
to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane lipids, ribosomes, enzymes, polymerases, translation components and small
molecules. [2]

A first protocell would require similar coddling, which seems extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without any proposed solutions (however speculative). However, what SpudCell does is
bring into sharper focus the nature and magnitude of the chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects
SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And Replication https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full?utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or bottom-up (SpudCell) - the clearer our understanding of the challenges facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs.
ID has just been a bait and switch scam that the ID perps perpetrate on creationist rubes like yourself for decades.

Below is just GIGO. SpudCells were never intended to figure out how
life came to be on this planet. The first cells did not have DNA
genomes, and did not have the genetic code. Really, just think for a
moment. The current system that maintains life had to have evolved
after there were already replicating cells. These cells would have had
a mimimal metabolism that helped them replicate.

My take is that there was some type or possibly multiple types of self replicating molecules. Initially they would have replicated themselves
using materials available in their environment. Some people think that
they may have evolved in clay matrix and initially used mineral
catalysis to help them replicate themselves. Replication would not have
been perfect so the best replicators would evolve. My take is that
these self replicating molecules would be selected to have multiple
functions (parts of their structure that was not used for self
replication could have other enzymatic activity like lipid production or making nucleotides to be used as energy transfer molecules that would
help them replicate and make things like their component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate. These RNA components would maintain the cellular metabolism that existed before
the RNAs existed. The current system would evolve once the RNAs started
to make peptides, likely, to store useful amino acids and keep them from defusing out of the cell (amino acids are needed to make nucleotides).
My take is that the genetic code first evolved to store only the amino
acids that these early lifeforms wanted to store. Charging RNAs with
amino acids may have started in order to maintain a higher concentration
of the desired amino acids in the cell, but an added benefit to
attaching an amino acid to RNA is that the amino acid becomes more
amenable to peptide bond formation and amino acid polymers would start
to be made.

SpudCells are so far away from what is needed to be done to recreate the initial self replicating cells that your whole argument is GIGO.

Ron Okimoto

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the-a prebiotic assembly of complex molecules and structures needed before Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule affect
the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already encode highly specific functions. These are not merely complex molecules, are functionally specified molecules operating in a coordinated coding
system, i.e. information-bearing and highly specified.

This links to 1. How do you evolve and refine enzymes and other proteins needed by a protocell (like SpudCell) before the first protocell?
Outside this context, an enzymerCOs biological function does not confer reproductive advantage because there is no reproducing protocell to
benefit from it.

Even if they evolved as naked polymers or in some other chemical system (e.g. autocatalytic set), they have not been selected and evolved for
the unrelated context of a protocell. You can only ask so much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation and
to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane lipids, ribosomes, enzymes, polymerases, translation components and small
molecules. [2]

A first protocell would require similar coddling, which seems extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without any proposed solutions (however speculative). However, what SpudCell does is bring into sharper focus the nature and magnitude of the chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And Replication https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full? utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 26/07/2026 11:59 pm, RonO wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the challenges
facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs. ID
has just been a bait and switch scam that the ID perps perpetrate on creationist rubes like yourself for decades.

Below is just GIGO.-a SpudCells were never intended to figure out how
life came to be on this planet.-a The first cells did not have DNA
genomes, and did not have the genetic code.-a Really, just think for a moment.-a The current system that maintains life had to have evolved
after there were already replicating cells.-a These cells would have had
a mimimal metabolism that helped them replicate.

My take is that there was some type or possibly multiple types of self replicating molecules.-a Initially they would have replicated themselves using materials available in their environment.-a Some people think that they may have evolved in clay matrix and initially used mineral
catalysis to help them replicate themselves.-a Replication would not have been perfect so the best replicators would evolve.-a My take is that
these self replicating molecules would be selected to have multiple functions (parts of their structure that was not used for self
replication could have other enzymatic activity like lipid production or making nucleotides to be used as energy transfer molecules that would
help them replicate and make things like their component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate.-a These RNA components would maintain the cellular metabolism that existed before
the RNAs existed.-a The current system would evolve once the RNAs started
to make peptides, likely, to store useful amino acids and keep them from defusing out of the cell (amino acids are needed to make nucleotides).
My take is that the genetic code first evolved to store only the amino
acids that these early lifeforms wanted to store.-a Charging RNAs with
amino acids may have started in order to maintain a higher concentration
of the desired amino acids in the cell, but an added benefit to
attaching an amino acid to RNA is that the amino acid becomes more
amenable to peptide bond formation and amino acid polymers would start
to be made.

SpudCells are so far away from what is needed to be done to recreate the initial self replicating cells that your whole argument is GIGO.

Perhaps I should have stated this explicitly: I'm not suggesting that
SpudCell itself directly models OOL, or intends to. Rather, the exercise
of creating a synthetic cell illuminates some of the fundamental
problems with OOL. What I am suggesting is that further advances will
deepen these. Actually attempting to construct even a partially
functioning cell will shut down much of the hand waving and hype that
passes for OOL science. Bring it on.

Ron Okimoto

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already encode
highly specific functions. These are not merely complex molecules, are
functionally specified molecules operating in a coordinated coding
system, i.e. information-bearing and highly specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function does
not confer reproductive advantage because there is no reproducing
protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask so
much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects
SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And Replication
https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full?
utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 27/07/2026 7:05 am, MarkE wrote:

On 26/07/2026 11:59 pm, RonO wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs.
ID has just been a bait and switch scam that the ID perps perpetrate
on creationist rubes like yourself for decades.

Below is just GIGO.-a SpudCells were never intended to figure out how
life came to be on this planet.-a The first cells did not have DNA
genomes, and did not have the genetic code.-a Really, just think for a
moment.-a The current system that maintains life had to have evolved
after there were already replicating cells.-a These cells would have
had a mimimal metabolism that helped them replicate.

In fact, I did make this qualification at the start of my original post:

"While this does not directly correlate with presumed natural assembly
of protocells and their precursors, it does give a sense of the
difficulties with the prebiotic assembly of complex molecules and
structures needed before Darwinian evolution can begin."

Your take following is an example of hand-waving I'm referring to.

My take is that there was some type or possibly multiple types of self
replicating molecules.-a Initially they would have replicated
themselves using materials available in their environment.-a Some
people think that they may have evolved in clay matrix and initially
used mineral catalysis to help them replicate themselves.-a Replication
would not have been perfect so the best replicators would evolve.-a My
take is that these self replicating molecules would be selected to
have multiple functions (parts of their structure that was not used
for self replication could have other enzymatic activity like lipid
production or making nucleotides to be used as energy transfer
molecules that would help them replicate and make things like their
component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate.-a These RNA
components would maintain the cellular metabolism that existed before
the RNAs existed.-a The current system would evolve once the RNAs
started to make peptides, likely, to store useful amino acids and keep
them from defusing out of the cell (amino acids are needed to make
nucleotides). My take is that the genetic code first evolved to store
only the amino acids that these early lifeforms wanted to store.
Charging RNAs with amino acids may have started in order to maintain a
higher concentration of the desired amino acids in the cell, but an
added benefit to attaching an amino acid to RNA is that the amino acid
becomes more amenable to peptide bond formation and amino acid
polymers would start to be made.

SpudCells are so far away from what is needed to be done to recreate
the initial self replicating cells that your whole argument is GIGO.

Perhaps I should have stated this explicitly: I'm not suggesting that SpudCell itself directly models OOL, or intends to. Rather, the exercise
of creating a synthetic cell illuminates some of the fundamental
problems with OOL. What I am suggesting is that further advances will
deepen these. Actually attempting to construct even a partially
functioning cell will shut down much of the hand waving and hype that
passes for OOL science. Bring it on.

Ron Okimoto

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already
encode highly specific functions. These are not merely complex
molecules, are functionally specified molecules operating in a
coordinated coding system, i.e. information-bearing and highly
specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function does >>> not confer reproductive advantage because there is no reproducing
protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask so
much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects
SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And
Replication
https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full?
utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/26/2026 4:05 PM, MarkE wrote:

On 26/07/2026 11:59 pm, RonO wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs.
ID has just been a bait and switch scam that the ID perps perpetrate
on creationist rubes like yourself for decades.

Below is just GIGO.-a SpudCells were never intended to figure out how
life came to be on this planet.-a The first cells did not have DNA
genomes, and did not have the genetic code.-a Really, just think for a
moment.-a The current system that maintains life had to have evolved
after there were already replicating cells.-a These cells would have
had a mimimal metabolism that helped them replicate.

My take is that there was some type or possibly multiple types of self
replicating molecules.-a Initially they would have replicated
themselves using materials available in their environment.-a Some
people think that they may have evolved in clay matrix and initially
used mineral catalysis to help them replicate themselves.-a Replication
would not have been perfect so the best replicators would evolve.-a My
take is that these self replicating molecules would be selected to
have multiple functions (parts of their structure that was not used
for self replication could have other enzymatic activity like lipid
production or making nucleotides to be used as energy transfer
molecules that would help them replicate and make things like their
component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate.-a These RNA
components would maintain the cellular metabolism that existed before
the RNAs existed.-a The current system would evolve once the RNAs
started to make peptides, likely, to store useful amino acids and keep
them from defusing out of the cell (amino acids are needed to make
nucleotides). My take is that the genetic code first evolved to store
only the amino acids that these early lifeforms wanted to store.
Charging RNAs with amino acids may have started in order to maintain a
higher concentration of the desired amino acids in the cell, but an
added benefit to attaching an amino acid to RNA is that the amino acid
becomes more amenable to peptide bond formation and amino acid
polymers would start to be made.

SpudCells are so far away from what is needed to be done to recreate
the initial self replicating cells that your whole argument is GIGO.

Perhaps I should have stated this explicitly: I'm not suggesting that SpudCell itself directly models OOL, or intends to. Rather, the exercise
of creating a synthetic cell illuminates some of the fundamental
problems with OOL. What I am suggesting is that further advances will
deepen these. Actually attempting to construct even a partially
functioning cell will shut down much of the hand waving and hype that
passes for OOL science. Bring it on.

This model does not do that. It has nothing to do with the origin of
life. All these guys did was figure out how to get the needed
components into their "cell" in order to replicate the DNA strand.

They understood what they needed to add to the cell, but they didn't
have a means of getting it all into the cell in one step, so they first created the "cell" containing the DNA, and then they fused other lipid
bubbles with that one, and the other lipid bubbles contained the
material needed to start transcribing the DNA and included things like ribosomes so that the mRNA could be translated into protein. That is
all that they did. It had nothing to do with the origin of life. It
was just a way to create a minimal replicating cell, but it wasn't very
good at replicating. They just have the minimum number of genes needed
to replicate the DNA. They haven't tried to put in the genes needed to
insure that the two daughter cells have enough of the cellular
components to maintain replication. The first systems to insure that
fission produced two functional cells likely evolved before DNA was used
as the genetic material. This was before things like ribosomes existed.
The initial system was likely adapted to deal with new functional
units like ribosomes, and could have eventually been replaced by
something that worked better.

All we have to go by are Archaea and Eubacteria and their common
ancestor had already evolved the genetic code and the cellular system
needed to support it and both share the same means of dividing a double membrane cell. Archaea started messing with linear DNA molecules and
had to evolve a system to get a functional set into all daughter cells. Eubacteria never evolved such a system, so plasmids are routinely lost
by accident. One lineage of Archaea is likely the ancestor of our
eukaryotic nucleus and eukaryotes perfected mitosis so that the multiple linear chromosomes could be equally divided between the two new daughter cells.

Your effort is just GIGO.

Ron Okimoto

Ron Okimoto

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already
encode highly specific functions. These are not merely complex
molecules, are functionally specified molecules operating in a
coordinated coding system, i.e. information-bearing and highly
specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function does >>> not confer reproductive advantage because there is no reproducing
protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask so
much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects
SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And
Replication
https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full?
utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/26/2026 4:22 PM, MarkE wrote:

On 27/07/2026 7:05 am, MarkE wrote:

On 26/07/2026 11:59 pm, RonO wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs.
ID has just been a bait and switch scam that the ID perps perpetrate
on creationist rubes like yourself for decades.

Below is just GIGO.-a SpudCells were never intended to figure out how
life came to be on this planet.-a The first cells did not have DNA
genomes, and did not have the genetic code.-a Really, just think for a
moment.-a The current system that maintains life had to have evolved
after there were already replicating cells.-a These cells would have
had a mimimal metabolism that helped them replicate.

In fact, I did make this qualification at the start of my original post:

"While this does not directly correlate with presumed natural assembly
of protocells and their precursors, it does give a sense of the
difficulties with the-a prebiotic assembly of complex molecules and structures needed before Darwinian evolution can begin."

Your take following is an example of hand-waving I'm referring to.

Your effort is just GIGO. You have less than hand-waving. That is why
you have to support a stupid bait and switch scam that is never going to produce any valid science that you would ever want to believe. You
still keep wallowing in the denial when you understand that you never
want any designer to be responsible for the origin of life on earth.
That designer would not be Biblical and any real ID science would just
be more science for you to deny, just as you have to deny all the valid science that tells you that biological evolution is a fact of nature.

Ron Okimoto

My take is that there was some type or possibly multiple types of
self replicating molecules.-a Initially they would have replicated
themselves using materials available in their environment.-a Some
people think that they may have evolved in clay matrix and initially
used mineral catalysis to help them replicate themselves.
Replication would not have been perfect so the best replicators would
evolve.-a My take is that these self replicating molecules would be
selected to have multiple functions (parts of their structure that
was not used for self replication could have other enzymatic activity
like lipid production or making nucleotides to be used as energy
transfer molecules that would help them replicate and make things
like their component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate.-a These RNA
components would maintain the cellular metabolism that existed before
the RNAs existed.-a The current system would evolve once the RNAs
started to make peptides, likely, to store useful amino acids and
keep them from defusing out of the cell (amino acids are needed to
make nucleotides). My take is that the genetic code first evolved to
store only the amino acids that these early lifeforms wanted to
store. Charging RNAs with amino acids may have started in order to
maintain a higher concentration of the desired amino acids in the
cell, but an added benefit to attaching an amino acid to RNA is that
the amino acid becomes more amenable to peptide bond formation and
amino acid polymers would start to be made.

SpudCells are so far away from what is needed to be done to recreate
the initial self replicating cells that your whole argument is GIGO.

Perhaps I should have stated this explicitly: I'm not suggesting that
SpudCell itself directly models OOL, or intends to. Rather, the
exercise of creating a synthetic cell illuminates some of the
fundamental problems with OOL. What I am suggesting is that further
advances will deepen these. Actually attempting to construct even a
partially functioning cell will shut down much of the hand waving and
hype that passes for OOL science. Bring it on.

Ron Okimoto

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already
encode highly specific functions. These are not merely complex
molecules, are functionally specified molecules operating in a
coordinated coding system, i.e. information-bearing and highly
specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function
does not confer reproductive advantage because there is no
reproducing protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask
so much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the >>>> internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

_______

[1] Did Scientists Just Create Life? The Conversations Team Dissects
SpudCell
https://www.youtube.com/watch?v=mYDrfCrRqOk&t=1s

[2] A Chemically Defined Synthetic Cell Capable Of Growth And
Replication
https://www.biorxiv.org/content/10.64898/2026.07.01.735724v1.full?
utm_source=chatgpt.com

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 27/07/2026 9:09 am, RonO wrote:

This model does not do that.-a It has nothing to do with the origin of life.-a All these guys did was figure out how to get the needed
components into their "cell" in order to replicate the DNA strand.

They understood what they needed to add to the cell, but they didn't
have a means of getting it all into the cell in one step, so they first created the "cell" containing the DNA, and then they fused other lipid bubbles with that one, and the other lipid bubbles contained the
material needed to start transcribing the DNA and included things like ribosomes so that the mRNA could be translated into protein.-a That is
all that they did.-a It had nothing to do with the origin of life.-a It
was just a way to create a minimal replicating cell, but it wasn't very
good at replicating.-a They just have the minimum number of genes needed
to replicate the DNA.-a They haven't tried to put in the genes needed to insure that the two daughter cells have enough of the cellular
components to maintain replication.-a The first systems to insure that fission produced two functional cells likely evolved before DNA was used
as the genetic material.-a This was before things like ribosomes existed.
-aThe initial system was likely adapted to deal with new functional
units like ribosomes, and could have eventually been replaced by
something that worked better.

All we have to go by are Archaea and Eubacteria and their common
ancestor had already evolved the genetic code and the cellular system
needed to support it and both share the same means of dividing a double membrane cell.-a Archaea started messing with linear DNA molecules and
had to evolve a system to get a functional set into all daughter cells. Eubacteria never evolved such a system, so plasmids are routinely lost
by accident.-a One lineage of Archaea is likely the ancestor of our eukaryotic nucleus and eukaryotes perfected mitosis so that the multiple linear chromosomes could be equally divided between the two new daughter cells.

Your effort is just GIGO.

Ron Okimoto

You keep assuming materialistic OOL, which is begging the question, and
head in the sand.

I look forward to the impact of this emerging research on OOL.

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

RonO wrote:

On 7/26/2026 4:05 PM, MarkE wrote:

On 26/07/2026 11:59 pm, RonO wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

ID's best friend seems to be that other fellow that works downstairs.
ID has just been a bait and switch scam that the ID perps perpetrate
on creationist rubes like yourself for decades.

Below is just GIGO.-a SpudCells were never intended to figure out how
life came to be on this planet.-a The first cells did not have DNA
genomes, and did not have the genetic code.-a Really, just think for a
moment.-a The current system that maintains life had to have evolved
after there were already replicating cells.-a These cells would have
had a mimimal metabolism that helped them replicate.

My take is that there was some type or possibly multiple types of
self replicating molecules.-a Initially they would have replicated
themselves using materials available in their environment.-a Some
people think that they may have evolved in clay matrix and initially
used mineral catalysis to help them replicate themselves.
Replication would not have been perfect so the best replicators would
evolve.-a My take is that these self replicating molecules would be
selected to have multiple functions (parts of their structure that
was not used for self replication could have other enzymatic activity
like lipid production or making nucleotides to be used as energy
transfer molecules that would help them replicate and make things
like their component parts.

Once nucleotides were being made the RNA world would be possible, and
RNAs would evolve to help the self replicators replicate.-a These RNA
components would maintain the cellular metabolism that existed before
the RNAs existed.-a The current system would evolve once the RNAs
started to make peptides, likely, to store useful amino acids and
keep them from defusing out of the cell (amino acids are needed to
make nucleotides). My take is that the genetic code first evolved to
store only the amino acids that these early lifeforms wanted to
store. Charging RNAs with amino acids may have started in order to
maintain a higher concentration of the desired amino acids in the
cell, but an added benefit to attaching an amino acid to RNA is that
the amino acid becomes more amenable to peptide bond formation and
amino acid polymers would start to be made.

SpudCells are so far away from what is needed to be done to recreate
the initial self replicating cells that your whole argument is GIGO.

Perhaps I should have stated this explicitly: I'm not suggesting that
SpudCell itself directly models OOL, or intends to. Rather, the
exercise of creating a synthetic cell illuminates some of the
fundamental problems with OOL. What I am suggesting is that further
advances will deepen these. Actually attempting to construct even a
partially functioning cell will shut down much of the hand waving and
hype that passes for OOL science. Bring it on.

This model does not do that.-a It has nothing to do with the origin of life.-a All these guys did was figure out how to get the needed
components into their "cell" in order to replicate the DNA strand.

They understood what they needed to add to the cell, but they didn't
have a means of getting it all into the cell in one step, so they first created the "cell" containing the DNA, and then they fused other lipid bubbles with that one, and the other lipid bubbles contained the
material needed to start transcribing the DNA and included things like ribosomes so that the mRNA could be translated into protein.-a That is
all that they did.-a It had nothing to do with the origin of life.-a It
was just a way to create a minimal replicating cell, but it wasn't very
good at replicating.-a They just have the minimum number of genes needed
to replicate the DNA.-a They haven't tried to put in the genes needed to insure that the two daughter cells have enough of the cellular
components to maintain replication.-a The first systems to insure that fission produced two functional cells likely evolved before DNA was used
as the genetic material.-a This was before things like ribosomes existed.
-aThe initial system was likely adapted to deal with new functional
units like ribosomes, and could have eventually been replaced by
something that worked better.

All we have to go by are Archaea and Eubacteria and their common
ancestor had already evolved the genetic code and the cellular system
needed to support it and both share the same means of dividing a double membrane cell.-a Archaea started messing with linear DNA molecules and
had to evolve a system to get a functional set into all daughter cells. Eubacteria never evolved such a system, so plasmids are routinely lost
by accident.-a One lineage of Archaea is likely the ancestor of our eukaryotic nucleus and eukaryotes perfected mitosis so that the multiple linear chromosomes could be equally divided between the two new daughter cells.

Your effort is just GIGO.

How could you miss the opportunity to tell him, "Don't reinvent the cell!"

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/26/2026 6:56 PM, MarkE wrote:

On 27/07/2026 9:09 am, RonO wrote:

This model does not do that.-a It has nothing to do with the origin of
life.-a All these guys did was figure out how to get the needed
components into their "cell" in order to replicate the DNA strand.

They understood what they needed to add to the cell, but they didn't
have a means of getting it all into the cell in one step, so they
first created the "cell" containing the DNA, and then they fused other
lipid bubbles with that one, and the other lipid bubbles contained the
material needed to start transcribing the DNA and included things like
ribosomes so that the mRNA could be translated into protein.-a That is
all that they did.-a It had nothing to do with the origin of life.-a It
was just a way to create a minimal replicating cell, but it wasn't
very good at replicating.-a They just have the minimum number of genes
needed to replicate the DNA.-a They haven't tried to put in the genes
needed to insure that the two daughter cells have enough of the
cellular components to maintain replication.-a The first systems to
insure that fission produced two functional cells likely evolved
before DNA was used as the genetic material.-a This was before things
like ribosomes existed. -a-aThe initial system was likely adapted to
deal with new functional units like ribosomes, and could have
eventually been replaced by something that worked better.

All we have to go by are Archaea and Eubacteria and their common
ancestor had already evolved the genetic code and the cellular system
needed to support it and both share the same means of dividing a
double membrane cell.-a Archaea started messing with linear DNA
molecules and had to evolve a system to get a functional set into all
daughter cells. Eubacteria never evolved such a system, so plasmids
are routinely lost by accident.-a One lineage of Archaea is likely the
ancestor of our eukaryotic nucleus and eukaryotes perfected mitosis so
that the multiple linear chromosomes could be equally divided between
the two new daughter cells.

Your effort is just GIGO.

Ron Okimoto

You keep assuming materialistic OOL, which is begging the question, and
head in the sand.

You are wrong about that. I just put up what is known. You are the one
that depends on what we do not know, and that you haven't got a clue
about how your designer could have done anything. I have a starting
point, you have nothing. You are the one that depends on something that
you can't even demonstrate exists.

You have to start dealing with the facts that Denton has come to grips
with. You should know by now that Denton understands that biological evolution is just a fact of nature. He doesn't need his designer to be responsible for the origin of life on earth. Denton just claims that
his designer got the ball rolling with the Big Bang and it all unfolded
into what we have today. Denton has probably written half a dozen
deistic books since he came back to the ID scam after the Dover fiasco.
You never hear about those books because none of the other ID perps
support Denton's Deistic non Biblical notions of intelligent design.

I look forward to the impact of this emerging research on OOL.

It will have just about no impact because it isn't anywhere close to how
life had to have evolved. Probably all the components including the DNA
are additions to the original lifeform. The first replicating cell
didn't have DNA, and probably didn't have RNA, none of the genes existed
that are encoded into the DNA that was used. There wasn't any means to translate the genes into proteins because the first replicating cell did
not have a genetic code. The genetic code likely evolved after
ribozymes had evolved to replace necessary enzymatic functions of the
self replicating molecules that the first cells needed to function.
Ribozymes do not need a genetic code in order to make RNA polymers with specific enzymatic activity. The code likely evolved to make peptides
out of specific amino acids. My guess is that these would have been the
amino acids needed to make nucleotides, and other cellular components.
The RNA world would need a means of maintaining a high concentration of
the amino acids that it needed to make more RNA. Making amino acid
polymers would be a way to reduce the loss of amino acids by diffusion
out of the cell. Part of the protein could be hydrophobic and would
stick in the membrane. It would be like hanging carcasses in a meat
locker. Specific mRNAs and their polypeptides could be selected for if
they had useful functions. Polypeptides are better than ribozymes and eventually they replaced nearly all the ribozymes of the cell.

Ron Okimoto

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or bottom-up (SpudCell) - the clearer our understanding of the challenges facing OOL becomes, including:

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the-a prebiotic assembly of complex molecules and structures needed before Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule affect
the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already encode highly specific functions. These are not merely complex molecules, are functionally specified molecules operating in a coordinated coding
system, i.e. information-bearing and highly specified.

This links to 1. How do you evolve and refine enzymes and other proteins needed by a protocell (like SpudCell) before the first protocell?
Outside this context, an enzymerCOs biological function does not confer reproductive advantage because there is no reproducing protocell to
benefit from it.

Even if they evolved as naked polymers or in some other chemical system (e.g. autocatalytic set), they have not been selected and evolved for
the unrelated context of a protocell. You can only ask so much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation and
to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane lipids, ribosomes, enzymes, polymerases, translation components and small
molecules. [2]

A first protocell would require similar coddling, which seems extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without any proposed solutions (however speculative). However, what SpudCell does is bring into sharper focus the nature and magnitude of the chicken-and-egg paradox at the heart OOL.

May such research continue apace.

Absolutely. This kind of work can yield some real medical benefits IMO.
As far as OOL research, they will never get past the information
problem. I have no issue with them trying and coming up with various theories. Yet, I will not be afforded the same decency when I conclude
this could not have happened naturally and decide to find out how it
could have happened otherwise. That's just how it works.
--
Science DoesnrCOt Support Darwin. Scientists Do

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 28/07/2026 6:42 am, sticks wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the challenges
facing OOL becomes, including:

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already encode
highly specific functions. These are not merely complex molecules, are
functionally specified molecules operating in a coordinated coding
system, i.e. information-bearing and highly specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function does
not confer reproductive advantage because there is no reproducing
protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask so
much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

Absolutely.-a This kind of work can yield some real medical benefits IMO.
-aAs far as OOL research, they will never get past the information problem.-a I have no issue with them trying and coming up with various theories.-a Yet, I will not be afforded the same decency when I conclude this could not have happened naturally and decide to find out how it
could have happened otherwise.-a That's just how it works.

Indeed.

Information content is related to the rarity of functional amino acid sequences within the total sequence space.

E.g., Keefe and Szostak estimated that approximately one in 10^11 random 80-residue sequences possessed their selected ATP-binding activity [1].
Axe estimated that sequences capable of performing a particular enzyme function as low as one in 10^77 [2].

Allowing for multiple functions and for suboptimal functionality will
improve these proportions. Nevertheless, the relative sparsity of
functional polymers means that prebiotic mechanisms will need
significant (though non-exhaustive) search and refine capability. This requires the ability to support many generations with sufficiently high copying fidelity. The circularity here is that this requires the output
at the start, e.g. long and specific enzymes to enable such iterations.

SpudCell is able to do what does only because it is primed with fully functional biological polymers.

_______

[1] Functional proteins from a random-sequence library https://www.nature.com/articles/35070613

[2] Estimating the prevalence of protein sequences adopting functional
enzyme folds
https://pubmed.ncbi.nlm.nih.gov/15321723/

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 27/07/2026 1:48 pm, RonO wrote:

I look forward to the impact of this emerging research on OOL.

It will have just about no impact because it isn't anywhere close to how life had to have evolved.-a Probably all the components including the DNA are additions to the original lifeform.-a The first replicating cell
didn't have DNA, and probably didn't have RNA, none of the genes existed that are encoded into the DNA that was used.-a There wasn't any means to translate the genes into proteins because the first replicating cell did
not have a genetic code.-a The genetic code likely evolved after
ribozymes had evolved to replace necessary enzymatic functions of the
self replicating molecules that the first cells needed to function. Ribozymes do not need a genetic code in order to make RNA polymers with specific enzymatic activity.-a The code likely evolved to make peptides
out of specific amino acids.-a My guess is that these would have been the amino acids needed to make nucleotides, and other cellular components.
The RNA world would need a means of maintaining a high concentration of
the amino acids that it needed to make more RNA.-a Making amino acid polymers would be a way to reduce the loss of amino acids by diffusion
out of the cell.-a Part of the protein could be hydrophobic and would
stick in the membrane.-a It would be like hanging carcasses in a meat locker.-a Specific mRNAs and their polypeptides could be selected for if they had useful functions.-a Polypeptides are better than ribozymes and eventually they replaced nearly all the ribozymes of the cell.

Ron Okimoto

You are essentially substituting one speculative sequence for another,
i.e. an unknown pre-RNA replicator (PNA, TNA etc?)

Ribozymes avoid the need for a genetic code, but not the need for sequence-specific function, replication fidelity, activated monomers and inheritance.

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/28/2026 2:09 AM, MarkE wrote:

On 27/07/2026 1:48 pm, RonO wrote:

I look forward to the impact of this emerging research on OOL.

It will have just about no impact because it isn't anywhere close to
how life had to have evolved.-a Probably all the components including
the DNA are additions to the original lifeform.-a The first replicating
cell didn't have DNA, and probably didn't have RNA, none of the genes
existed that are encoded into the DNA that was used.-a There wasn't any
means to translate the genes into proteins because the first
replicating cell did not have a genetic code.-a The genetic code likely
evolved after ribozymes had evolved to replace necessary enzymatic
functions of the self replicating molecules that the first cells
needed to function. Ribozymes do not need a genetic code in order to
make RNA polymers with specific enzymatic activity.-a The code likely
evolved to make peptides out of specific amino acids.-a My guess is
that these would have been the amino acids needed to make nucleotides,
and other cellular components. The RNA world would need a means of
maintaining a high concentration of the amino acids that it needed to
make more RNA.-a Making amino acid polymers would be a way to reduce
the loss of amino acids by diffusion out of the cell.-a Part of the
protein could be hydrophobic and would stick in the membrane.-a It
would be like hanging carcasses in a meat locker.-a Specific mRNAs and
their polypeptides could be selected for if they had useful
functions.-a Polypeptides are better than ribozymes and eventually they
replaced nearly all the ribozymes of the cell.

Ron Okimoto

You are essentially substituting one speculative sequence for another,
i.e. an unknown pre-RNA replicator (PNA, TNA etc?)

I am just stating what we know about life on earth, and what we know is possible. You have nothing by comparison. No one knows what actually happened, but we do know what still exists. You don't even have
anything that you can determine still exists. That is just a fact. You
don't even know if your designer could have once existed. Remnants of
the RNA world still exists. We still have the RNA peptidase, mRNA and
tRNA. There are still a bunch of structural RNAs in the nucleus. We
can evolve ribozymes that have specific enzymatic functions and we have created ribozymes that can charge specific amino acids onto the correct
tRNA. What do you have by comparison?

Ribozymes avoid the need for a genetic code, but not the need for sequence-specific function, replication fidelity, activated monomers and inheritance.

No one cares about sequence specific function except the IDiotic
creationist types. All that anyone needs to know is that arbitrary
sequence can have enzymatic function. Different sequences can have the
same enzymatic function. So no specification seems to be required.
What you need is evidence that there was a plan, but no such evidence
exists. You've run from Denton's conclusions that his designer could
have gotten the ball rolling with the Big Bang and it all unfolded into
what we have today.

RNAs can be replicated like DNA. Selection can improve the function of ribozymes, and new functions can be selected for. What is needed is a
reason to produce RNA polymers, and my take is that the reason is simply
that nucleotides evolved and were used as energy transfer molecules to
aid the primative cellular metabolism before ribozymes existed and
before the genetic code was even possible. Nucleotides remain the
energy coin of the cell today. Making polymers of excess nucleotides
would maintain a higher concentration of nucleotides inside of the cell
than outside.

Behe has put up Thorton's work on steroid receptors as an example where
a new steroid receptor evolved over half a billion years ago. This
receptor bound a new ligand and the new gene could be used to regulate different aspects of cellular metabolism. The new receptor type evolved
into a major receptor family of it's own by gene duplication before and
during the Cambrian explosion. What Behe doesn't note is that Thorton
did not stop with finding the path taken to evolve the new function.
His lab took the ancestral sequence and randomly mutated it. They
determined that there were multiple paths to evolving the same ligand
binding function. One of those paths required only a single amino acid substitution, but it was not the path taken even though it was the most
likely event that would have evolved the new function. Some of the alternatives would have taken 3 substitutions, but they were not the
ones used. The path taken was one that would be expected to have
occurred routinely among those ancestral eukaryotes, but the 3
substitution paths were not taken likely because they are so unlikely to
occur as a group in nature. ID scam specification has to fight reality.

What do you have by comparison? Your nothing doesn't seem to be a very convincing alternative.

Ron Okimoto

--- Synchronet 3.22a-Linux NewsLink 1.2

From Newsgroup: talk.origins

On 7/28/2026 1:16 AM, MarkE wrote:

On 28/07/2026 6:42 am, sticks wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already
encode highly specific functions. These are not merely complex
molecules, are functionally specified molecules operating in a
coordinated coding system, i.e. information-bearing and highly
specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function does >>> not confer reproductive advantage because there is no reproducing
protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask so
much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the
internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

Absolutely.-a This kind of work can yield some real medical benefits
IMO. -a-aAs far as OOL research, they will never get past the
information problem.-a I have no issue with them trying and coming up
with various theories.-a Yet, I will not be afforded the same decency
when I conclude this could not have happened naturally and decide to
find out how it could have happened otherwise.-a That's just how it works. >>

Indeed.

Information content is related to the rarity of functional amino acid sequences within the total sequence space.

You put up the reason for such a small amount of sequence space to have
been searched to account for the existing proteins. The paper you put
up where you claimed that too many new genes had to evolve to create multicellular animals. It turned out that nearly all the genes used in
the diversification of multicellular animals evolved before the Cambrian explosion. It took around 3 billion years to evolve those genes. Not
only that but the vast majority of new genes evolved by gene
duplication, so that very little new protein space had to be searched in
order to evolve the new gene functions. Very little protein space has
been searched because more searching was not needed.

E.g., Keefe and Szostak estimated that approximately one in 10^11 random 80-residue sequences possessed their selected ATP-binding activity [1].
Axe estimated that sequences capable of performing a particular enzyme function as low as one in 10^77 [2].

ATP binding is common among the polypeptides used by lifeforms, but it
likely evolved de novo only a few times. Most (nearly all) of the genes associated with ATP binding evolved by gene duplication or fusions from progenitors that also had that function. More protein space was not
needed to be searched.

Allowing for multiple functions and for suboptimal functionality will improve these proportions. Nevertheless, the relative sparsity of
functional polymers means that prebiotic mechanisms will need
significant (though non-exhaustive) search and refine capability. This requires the ability to support many generations with sufficiently high copying fidelity. The circularity here is that this requires the output
at the start, e.g. long and specific enzymes to enable such iterations.

SpudCell is able to do what does only because it is primed with fully functional biological polymers.

SpudCells tell you nothing about what was needed to create the first replicating cells. Likely none of the SpudCell components existed in
the first self replicating lifeform. There was likely no RNA nor DNA,
and there was no genetic code, so that if there were polypeptides they
would have been making themselves by some other mechanisms than what
later evolved. No one knows what the first self replicating molecules
were made of. SpudCells tell you nothing about the origin of life on earth.

SpudCells only tell you that you can get replication by getting the
genes to do what you already know that they can do, but with a minimum
number of accessory genes that exist in lifeforms today. SpudCell 36
gene genome is more like a virus than a replicating cell. They need to
add things like functional ribosomes (not encoded among the SpudCell) to
get translation of the 36 genes in the SpudCell genome. Ribosomes need
to have 3 ribosomal RNA genes and over 50 protein genes to be functional.

Ron Okimoto

_______

[1] Functional proteins from a random-sequence library https://www.nature.com/articles/35070613

[2] Estimating the prevalence of protein sequences adopting functional enzyme folds
https://pubmed.ncbi.nlm.nih.gov/15321723/

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From Newsgroup: talk.origins

On 7/28/2026 9:30 AM, RonO wrote:

On 7/28/2026 1:16 AM, MarkE wrote:

On 28/07/2026 6:42 am, sticks wrote:

On 7/26/2026 5:59 AM, MarkE wrote:

ID's best friend may turn out to be research like this. The more we
attempt to construct cells/protocells - either top-down (Venter) or
bottom-up (SpudCell) - the clearer our understanding of the
challenges facing OOL becomes, including:

1. The assembly problem

The ingenuity in the assembly of SpudCell has been recognised and
praised, even by ID proponents [1]. While this does not directly
correlate with presumed natural assembly of protocells and their
precursors, it does give a sense of the difficulties with the
prebiotic assembly of complex molecules and structures needed before
Darwinian evolution can begin.

Darwinian evolution requires heritable variation, differential
reproduction, sufficient replication fidelity, etc. But before those
conditions exist, chemistry must somehow assemble the machinery that
makes heredity and reproduction possible. Natural selection cannot
preserve a molecule merely because it will later become useful in a
future cell. It can operate only once differences in the molecule
affect the reproductive success of an existing replicating system.

2. The information problem

SpudCell incorporates proteins and RNAs whose sequences already
encode highly specific functions. These are not merely complex
molecules, are functionally specified molecules operating in a
coordinated coding system, i.e. information-bearing and highly
specified.

This links to 1. How do you evolve and refine enzymes and other
proteins needed by a protocell (like SpudCell) before the first
protocell? Outside this context, an enzymerCOs biological function
does not confer reproductive advantage because there is no
reproducing protocell to benefit from it.

Even if they evolved as naked polymers or in some other chemical
system (e.g. autocatalytic set), they have not been selected and
evolved for the unrelated context of a protocell. You can only ask
so much of exaption.

3. The environment problem

The researchers optimised the external medium to support translation
and to prevent loss through the +#-haemolysin pores from diluting the >>>> internal contents. Feeder liposomes repeatedly supplied membrane
lipids, ribosomes, enzymes, polymerases, translation components and
small molecules. [2]

A first protocell would require similar coddling, which seems
extremely unlikely on an early-Earth.

Conclusion

I'm not suggesting that these are new arguments, or problems without
any proposed solutions (however speculative). However, what SpudCell
does is bring into sharper focus the nature and magnitude of the
chicken-and-egg paradox at the heart OOL.

May such research continue apace.

Absolutely.-a This kind of work can yield some real medical benefits
IMO. -a-aAs far as OOL research, they will never get past the
information problem.-a I have no issue with them trying and coming up
with various theories.-a Yet, I will not be afforded the same decency
when I conclude this could not have happened naturally and decide to
find out how it could have happened otherwise.-a That's just how it
works.

Indeed.

Information content is related to the rarity of functional amino acid
sequences within the total sequence space.

You put up the reason for such a small amount of sequence space to have
been searched to account for the existing proteins.-a The paper you put
up where you claimed that too many new genes had to evolve to create multicellular animals.-a It turned out that nearly all the genes used in
the diversification of multicellular animals evolved before the Cambrian explosion.-a It took around 3 billion years to evolve those genes.-a Not only that but the vast majority of new genes evolved by gene
duplication, so that very little new protein space had to be searched in order to evolve the new gene functions.-a Very little protein space has
been searched because more searching was not needed.

E.g., Keefe and Szostak estimated that approximately one in 10^11
random 80-residue sequences possessed their selected ATP-binding
activity [1]. Axe estimated that sequences capable of performing a
particular enzyme function as low as one in 10^77 [2].

ATP binding is common among the polypeptides used by lifeforms, but it likely evolved de novo only a few times.-a Most (nearly all) of the genes associated with ATP binding evolved by gene duplication or fusions from progenitors that also had that function.-a More protein space was not
needed to be searched.

Allowing for multiple functions and for suboptimal functionality will
improve these proportions. Nevertheless, the relative sparsity of
functional polymers means that prebiotic mechanisms will need
significant (though non-exhaustive) search and refine capability. This
requires the ability to support many generations with sufficiently
high copying fidelity. The circularity here is that this requires the
output at the start, e.g. long and specific enzymes to enable such
iterations.

SpudCell is able to do what does only because it is primed with fully
functional biological polymers.

SpudCells tell you nothing about what was needed to create the first replicating cells.-a Likely none of the SpudCell components existed in
the first self replicating lifeform.-a There was likely no RNA nor DNA,
and there was no genetic code, so that if there were polypeptides they
would have been making themselves by some other mechanisms than what
later evolved.-a No one knows what the first self replicating molecules
were made of.-a SpudCells tell you nothing about the origin of life on earth.

SpudCells only tell you that you can get replication by getting the
genes to do what you already know that they can do, but with a minimum number of accessory genes that exist in lifeforms today.-a SpudCell 36
gene genome is more like a virus than a replicating cell.-a They need to
add things like functional ribosomes (not encoded among the SpudCell) to
get translation of the 36 genes in the SpudCell genome.-a Ribosomes need
to have 3 ribosomal RNA genes and over 50 protein genes to be functional.

Ron Okimoto

_______

[1] Functional proteins from a random-sequence library
https://www.nature.com/articles/35070613

[2] Estimating the prevalence of protein sequences adopting functional
enzyme folds
https://pubmed.ncbi.nlm.nih.gov/15321723/

The ID perps have an article up that actually demonstrates that they are
just prevaricating about the evolution of information in protein sequences.

https://scienceandculture.com/2026/07/evolution-of-biological-information-the-line-of-descent/

Ewert is prevaricating about increases in information evolving over
time. Dembski admitted that it happens, but Dembski started to claim
that it was "lesser specified complexity". Dembski admitted that new functions could evolve for a sequence by arbitrary changes creating new functions, but he wanted to claim that, that type of increase in
information was not what mattered to the ID scam. Dembski wanted to
claim that it was the specified complexity of the original polypeptide
that had the original function that was what could not be achieved by
natural mechanism, but He could never demonstrate what he claimed. He
was never able to validate the claims, so none of Dembski's junk made it
onto the ID perps list of the 6 best evidences for intelligent design.
Really, what Ewert is in denial of (increased information content of an existing gene) was already claimed to be possible by Dembski, so there
is absolutely no reason for Ewert's attempted denial.

Genes like cytochrome oxidase II (COXII) have a very long history in the evolution of life on earth. Ewert has to run from reality. COXII and Cytochrom c (Cyt c) are part of the oxidative phosphorylation pathway.
Oxygen is burned and ATP is produced in extant lifeforms. There are
lineages of both Archaea and eubacteria that have evolved oxidative phosphorylation because the last common ancestor of both bacterial types
had both COXII and Cyt c. Even though this common ancestor had an
anaerobic metabolism it needed to deal with toxic molecular oxygen, and
these two genes were involved in reduction of oxygen. Oxygen generating photosynthesis had not yet evolved and the environment was poor in
oxygen, but the early cells had to deal with it. Their functions
changed over time as the two genes were co-opted to work in oxidative phosphorylation after oxygen levels rose to a level where that became practical. The genes continued to evolve as the endosymbiotic bacteria
that became our mitochondria evolved it's function of becoming the power
house of the eukaryotic cell.

Very little protein space had to be searched to evolve the new
functions. The genes existed and they just had to be changed a bit to
do something different. Dembski understands that there is nothing here
for Ewert to prevaricate about. There is no restriction on any existing
gene evolving a new function. Dembski claimed that a new law of thermodynamics existed that would prevent the creation of new
information, but you don't see anyone touting any new laws of
thermodynamics as being confirmed to exist. Dembski would have likely
gotten the Nobel Prize by now if he had really inferred a new law of thermodynamics into existence. Dembski first proposed the new law in
the 1990's, but brought it back as a last ditch effort to salvage CSI
(complex specified information) a couple years before he retired from
the ID scam in 2014 as an abject IDiotic failure. Nothing that Dembski
has ever proposed about ID has ever been validated. Change in function
of a gene due to amino acid sequence changes is a well documented fact.

Ron Okimoto

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