Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)

In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.

Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox

Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:

https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)

TRANSCRIPT:

QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?

RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.

On Saturday, December 2, 2023 at 3:51:56 PM UTC+11, MarkE wrote:
> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>
> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>
> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>
> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>
> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>
> TRANSCRIPT:
>
> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>
> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.

List of References [pinned in comments]

1. a. Lindahl T. Instability and decay of the primary structure of DNA. Nature, 1993; 362: 709–715.
b. Lindahl T, Nyberg B. Rate of depurination of native deoxyribonucleic acid. Biochemistry, 1972; 11:3610–3618.
c. Lindahl T. DNA repair enzymes acting on spontaneous lesions in DNA. In: DNA Repair Processes, W. Nichols and D. Murphy, Editors. 1977, Miami: Symposia Specialists. 225–240.
2. Ames BN, Shigenaga MK, Hagen TM. Oxidants, antioxidants, and the degenerative diseases of aging. Proc Natl Acad Sci U S A, 1993; 90:7915–7922.
3. Tice, R. and R. Setlow, DNA repair and replication in aging organisms and cells, in Handbook of the Biology of Aging, E. Finch and E. Schneider, Editors. 1985, New York: Van Nostrand Reinhold. 173–224.
4. Haber, J. E., DNA recombination: the replication connection.Trends in Biochemical Sciences, 1999; 24:271–275.
5. a. Keiler KC, Feaga HA. Resolving nonstop translation complexes is a matter of life or death. Journal of Bacteriology 2014; 196:2123-2130.
b. Ishimura R, Nagy G, Dotu I, Zhou H, Yang XL, Schimmel P, Senju S, Nishimura Y, Chuang JH, Ackerman SL. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science 2014; 345:455–459.
c. Houseley J and Tollervey D. The many pathways of RNA degradation. Cell 2009; 136:763-776.
6. Dianov G and Lindahl T. Reconstitution of the DNA base excision-repair pathway. Current biology 1994; 4:1069-1076. The specific enzymes responsible for Base Excision Repair vary slightly between different forms of life. Some organisms require only 4 enzymes, but the main point stands - thousands of letters of DNA code are required for the repair mechanisms to exist.
7. Gene sizes found on: https://www.ncbi.nlm.nih.gov/gene/947067, taken from E. coli.
ung (uracil DNA glycosylase): 896 nt;
Nfo (endonuclease IV) 858 nt
RecJ exonuclease: 1734 nt https://www.ncbi.nlm.nih.gov/gene/947367.
polymerase A: 2787 nt.
ligase A: 2016 nt.
= 8291 nt total, not including the 100+ genes needed to manufacture proteins.
8.Eigen, M. Self-organization of matter and evolution of biological macromolecules. Naturwissenschaften, 1971; 58:465–523.
9. Yan LL, Zaher HS. How do cells cope with RNA damage and its consequences? J Biol Chem, 2019; 294:15158-15171.
10. And, there are many other required recognition, recycling, and repair mechanisms. We didn’t even touch on the required mechanisms to correct for production of toxic substances through side reactions or spontaneous chemistry. If you’d like to know more, see Haas D. et al. Metabolite damage and damage control in a minimal genome. Computational Biology, 2022; 13:1-16.
11. *Or label all good molecules to protect them from destruction (i.e., methylation of DNA)
12. Ito K, Chadani Y, Nakamori K, Chiba S, Akiyama Y, Abo T. Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS One, 2011; 6:e28413. http://dx.doi.org/10.1371/journal.pone.0028413.
13. Keiler KC, Feaga HA. Resolving nonstop translation complexes is a matter of life or death. Journal of Bacteriology, 2014; 196:2123-2130.
14. a. Keiler KC, Feaga HA. Resolving nonstop translation complexes is a matter of life or death. Journal of Bacteriology, 2014; 196:2123-2130.
b. Ishimura R, Nagy G, Dotu I, Zhou H, Yang XL, Schimmel P, Senju S, Nishimura Y, Chuang JH, Ackerman SL. RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration. Science, 2014; 345:455–459.
c. Houseley J and Tollervey D. The many pathways of RNA degradation. Cell, 2009; 136:763-776.
15. a. Rawlings ND, Barrett AJ, Thomas PD, Huang X, Bateman A, Finn RD. The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database. Nucleic Acids Res, 2018; 46: D624-D632. https://doi.org/10.1093/nar/gkx1134
b. Rawlings ND, Bateman A. How to use the MEROPS database and website to help understand peptidase specificity. Protein Sci, 2021; 30: 83-92. https://doi.org/10.1002/pro.3948.
16. Mackie GA. RNase E: at the interface of bacterial RNA processing and decay. Nature Reviews Microbiology, 2013; 11:45-57.

On 12/1/2023 10:50 PM, MarkE wrote:
> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>
> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>
> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>
> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>
> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>
> TRANSCRIPT:
>
> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>
> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>
My take is that this isn't an issue. RNA gene replication was already
something that was consistently happening in the first RNA systems. The
first proteins to be made were likely just storage units for amino acids
used to make nucleotides. Bits of the genetic code would have evolved
as a means to store the most useful amino acids, and may have accidently
made functional proteins that could be replicated with enough fidelity
to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
that were used to make this RNA based storage protein making system
work. The genetic code would have first began to evolve because
specific amino acids would have been preferred to store in this manner.
You would need specific tRNAs, and mRNAs and some type of acylation
system to charge the tRNAs. The system didn't need a high fidelity,
just as long as enough of the correct amino acids got stored in a
useable form. Once you had a partial genetic code, you could make
proteins of a specific amino acid sequence using storage mRNA. These
mRNA "genes" might be selected for by some accidental function that the
protein might have in addition to it's amino acid storage ability. This
would likely lead to selection for a more complete genetic code (tRNA
anticodons) in order to utilize all of the mRNA sequence.
The real issue is how the system switched from RNA based enzymes to
protein based enzymes. The tRNAs and their amino acid charging system
would have been RNA based. The current genetic code may have evolved
before the proteins used today to make proteins existed. The evidence
is that the genetic code existed before the two families of synthases
(charge tRNAs with a specific amino acid) evolved. There are two types
of synthases and it looks like they evolved from the same DNA sequence.
It has been proposed that one evolved from the sense strand and the
other evolved from the anti-sense strand of the same sequence of DNA.
the genetic code had to exist before these two synthases evolved because
they maintain a conserved sequence of amino acids that indicate that
they were encoded by the same strand of DNA, but one from the sense
strand and one from the anti-sense strand. Apparently both proteins
could charge tRNAs, but they had to duplicate and evolve to charge all
the amino acids of our current genetic code. The evolution of synthases
was likely instrumental in selecting useful tRNAs to be charged with
specific amino acids. If you look at the genetic code it looks like the
tRNAs with similar anticodons were able to be charged with similar amino
acids, and this is just a hold over from the RNA based system. The
protein based system probably adapted to the existing RNA based system.
Eventually proteins became an integral part of the process, augmented
the ribosomes, and took the place of the RNAs that were involved in the
protein making machinery. My guess is that the RNA based system could
have remained functional until the protein based system could take over.
Currently DNA replication has the lowest error rate, RNA transcription
has a higher error rate, and there is an error rate in translation of
the protein sequence. My guess is that there wasn't a
phenotype/genotype dichotomy enough to worry about when the systems were
evolving, and life doesn't have an issue with the way things currently are.
Ron Okimoto

On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> On 12/1/2023 10:50 PM, MarkE wrote:
> > Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >
> > In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >
> > Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >
> > Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >
> > https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >
> > TRANSCRIPT:
> >
> > QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >
> > RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >
> My take is that this isn't an issue. RNA gene replication was already
> something that was consistently happening in the first RNA systems.

You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:

"Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox

It applies to RNA and DNA replication.

> The first proteins to be made were likely just storage units for amino acids
> used to make nucleotides. Bits of the genetic code would have evolved
> as a means to store the most useful amino acids, and may have accidently
> made functional proteins that could be replicated with enough fidelity
> to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
> that were used to make this RNA based storage protein making system
> work. The genetic code would have first began to evolve because
> specific amino acids would have been preferred to store in this manner.
> You would need specific tRNAs, and mRNAs and some type of acylation
> system to charge the tRNAs. The system didn't need a high fidelity,
> just as long as enough of the correct amino acids got stored in a
> useable form. Once you had a partial genetic code, you could make
> proteins of a specific amino acid sequence using storage mRNA. These
> mRNA "genes" might be selected for by some accidental function that the
> protein might have in addition to it's amino acid storage ability. This
> would likely lead to selection for a more complete genetic code (tRNA
> anticodons) in order to utilize all of the mRNA sequence.
>
> The real issue is how the system switched from RNA based enzymes to
> protein based enzymes. The tRNAs and their amino acid charging system
> would have been RNA based. The current genetic code may have evolved
> before the proteins used today to make proteins existed. The evidence
> is that the genetic code existed before the two families of synthases
> (charge tRNAs with a specific amino acid) evolved. There are two types
> of synthases and it looks like they evolved from the same DNA sequence.
> It has been proposed that one evolved from the sense strand and the
> other evolved from the anti-sense strand of the same sequence of DNA.
> the genetic code had to exist before these two synthases evolved because
> they maintain a conserved sequence of amino acids that indicate that
> they were encoded by the same strand of DNA, but one from the sense
> strand and one from the anti-sense strand. Apparently both proteins
> could charge tRNAs, but they had to duplicate and evolve to charge all
> the amino acids of our current genetic code. The evolution of synthases
> was likely instrumental in selecting useful tRNAs to be charged with
> specific amino acids. If you look at the genetic code it looks like the
> tRNAs with similar anticodons were able to be charged with similar amino
> acids, and this is just a hold over from the RNA based system. The
> protein based system probably adapted to the existing RNA based system.
> Eventually proteins became an integral part of the process, augmented
> the ribosomes, and took the place of the RNAs that were involved in the
> protein making machinery. My guess is that the RNA based system could
> have remained functional until the protein based system could take over.
>
> Currently DNA replication has the lowest error rate, RNA transcription
> has a higher error rate, and there is an error rate in translation of
> the protein sequence. My guess is that there wasn't a
> phenotype/genotype dichotomy enough to worry about when the systems were
> evolving, and life doesn't have an issue with the way things currently are.
>
> Ron Okimoto

On 12/3/2023 6:55 AM, MarkE wrote:
> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>> On 12/1/2023 10:50 PM, MarkE wrote:
>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>
>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>
>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>
>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>
>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>
>>> TRANSCRIPT:
>>>
>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>
>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>
>> My take is that this isn't an issue. RNA gene replication was already
>> something that was consistently happening in the first RNA systems.
>
> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>
> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
RNA replication likely evolved after there were simple self replicators,
and we have no pretty much no idea of what they were made of. Just look
at the literature, they are proposing that the first macromolecules were
using mineral surfaces to catalyze the reactions needed to put the
subunits together.
It does look like we had an RNA phase of life because we have the
vestiges of the system in the ribosomes, tRNA, mRNAs and things like
small nuclear RNAs that are all functional RNAs. The RNA phase could
have obviously been less efficient when it first evolved, and that
inefficiency would have likely been beneficial. Something else likely
existed before RNA. My guess is that nucleotides started to be produced
and used just like they still are used today. They are used as energy
transfer molecules. Making polymers of nucleotides would keep them from
defusing out of the cell until you needed them. It turned out that the
polymers were amenable to replication, and could have enzymatic
properties of their own.
This just means that the first polymers of nucleotides did not have to
be replicated. Some part of some existing self replicator could have
just stuck nucleotides together (reverse nuclease activity).
Replication could evolve after the RNA polymers started to have useful
functions, and was likely first used just to make more nucleotide
polymers for storage, and didn't have to have much fidelity at all.
Really, DNA could have evolved to replicate RNA polymers that were used
to store useful energy transfer nucleotides. Higher fidelity would be
selected for once those RNA polymers had useful enzymatic functions.
RNA and DNA were likely not required to be very accurate in their
replication when they first started to be used by lifeforms.

> https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>
> It applies to RNA and DNA replication.
It only applies after the products of the replication are associated
with a lot of essential functions. As noted above the initial
replication may have just been effective enough to keep making storage
polymers. It would not be until the RNAs started to have multiple
essential enzymatic functions like the ribosomal peptidase that the
systems would need to have the level of error management that they have
today. The current error management systems evolved after the genetic
code evolved and likely took over from the RNAs that were doing the same
job before there was a genetic code. You do not need a genetic code to
replicate functional RNAs. The enzymatic functions are due to the
secondary and tertiary structures that the primary sequence can form.
What is this gap denial going to do for you? You don't want to believe
in the designer that created life 3.8 billion years ago and let it
evolve into what we have today over billions of years. Denial that only
allows you to temporarily lie to yourself about the situation isn't much
of anything worth doing. You likely have gone and observed how sad the
Reason to Believe attempts are when they try to reinterpret the Bible
and still have to deny reality in order to maintain their Biblical
beliefs. You likely should be looking into alternatives like Biologos.
They claim to be Christians, but claim that their alternative has
nothing to do with what is in the Bible.
Ron Okimoto
>
>> The first proteins to be made were likely just storage units for amino acids
>> used to make nucleotides. Bits of the genetic code would have evolved
>> as a means to store the most useful amino acids, and may have accidently
>> made functional proteins that could be replicated with enough fidelity
>> to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
>> that were used to make this RNA based storage protein making system
>> work. The genetic code would have first began to evolve because
>> specific amino acids would have been preferred to store in this manner.
>> You would need specific tRNAs, and mRNAs and some type of acylation
>> system to charge the tRNAs. The system didn't need a high fidelity,
>> just as long as enough of the correct amino acids got stored in a
>> useable form. Once you had a partial genetic code, you could make
>> proteins of a specific amino acid sequence using storage mRNA. These
>> mRNA "genes" might be selected for by some accidental function that the
>> protein might have in addition to it's amino acid storage ability. This
>> would likely lead to selection for a more complete genetic code (tRNA
>> anticodons) in order to utilize all of the mRNA sequence.
>>
>> The real issue is how the system switched from RNA based enzymes to
>> protein based enzymes. The tRNAs and their amino acid charging system
>> would have been RNA based. The current genetic code may have evolved
>> before the proteins used today to make proteins existed. The evidence
>> is that the genetic code existed before the two families of synthases
>> (charge tRNAs with a specific amino acid) evolved. There are two types
>> of synthases and it looks like they evolved from the same DNA sequence.
>> It has been proposed that one evolved from the sense strand and the
>> other evolved from the anti-sense strand of the same sequence of DNA.
>> the genetic code had to exist before these two synthases evolved because
>> they maintain a conserved sequence of amino acids that indicate that
>> they were encoded by the same strand of DNA, but one from the sense
>> strand and one from the anti-sense strand. Apparently both proteins
>> could charge tRNAs, but they had to duplicate and evolve to charge all
>> the amino acids of our current genetic code. The evolution of synthases
>> was likely instrumental in selecting useful tRNAs to be charged with
>> specific amino acids. If you look at the genetic code it looks like the
>> tRNAs with similar anticodons were able to be charged with similar amino
>> acids, and this is just a hold over from the RNA based system. The
>> protein based system probably adapted to the existing RNA based system.
>> Eventually proteins became an integral part of the process, augmented
>> the ribosomes, and took the place of the RNAs that were involved in the
>> protein making machinery. My guess is that the RNA based system could
>> have remained functional until the protein based system could take over.
>>
>> Currently DNA replication has the lowest error rate, RNA transcription
>> has a higher error rate, and there is an error rate in translation of
>> the protein sequence. My guess is that there wasn't a
>> phenotype/genotype dichotomy enough to worry about when the systems were
>> evolving, and life doesn't have an issue with the way things currently are.
>>
>> Ron Okimoto
>

On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> On 12/3/2023 6:55 AM, MarkE wrote:
> > On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> >> On 12/1/2023 10:50 PM, MarkE wrote:
> >>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >>>
> >>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >>>
> >>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>
> >>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >>>
> >>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >>>
> >>> TRANSCRIPT:
> >>>
> >>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >>>
> >>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >>>
> >> My take is that this isn't an issue. RNA gene replication was already
> >> something that was consistently happening in the first RNA systems.
> >
> > You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> >
> > "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> RNA replication likely evolved after there were simple self replicators,
> and we have no pretty much no idea of what they were made of. Just look
> at the literature, they are proposing that the first macromolecules were
> using mineral surfaces to catalyze the reactions needed to put the
> subunits together.

What "simple replicators"?

"RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?

This is pure "just so" story-telling, Ron. The fact that you state it without missing a beat points to James Tour's frustration with and accusations of the claims and postering of the OOL project.

>
> It does look like we had an RNA phase of life because we have the
> vestiges of the system in the ribosomes, tRNA, mRNAs and things like
> small nuclear RNAs that are all functional RNAs. The RNA phase could
> have obviously been less efficient when it first evolved, and that
> inefficiency would have likely been beneficial. Something else likely
> existed before RNA. My guess is that nucleotides started to be produced
> and used just like they still are used today. They are used as energy
> transfer molecules. Making polymers of nucleotides would keep them from
> defusing out of the cell until you needed them. It turned out that the
> polymers were amenable to replication, and could have enzymatic
> properties of their own.
>
> This just means that the first polymers of nucleotides did not have to
> be replicated. Some part of some existing self replicator could have
> just stuck nucleotides together (reverse nuclease activity).
> Replication could evolve after the RNA polymers started to have useful
> functions, and was likely first used just to make more nucleotide
> polymers for storage, and didn't have to have much fidelity at all.
> Really, DNA could have evolved to replicate RNA polymers that were used
> to store useful energy transfer nucleotides. Higher fidelity would be
> selected for once those RNA polymers had useful enzymatic functions.
>
> RNA and DNA were likely not required to be very accurate in their
> replication when they first started to be used by lifeforms.
> > https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >
> > It applies to RNA and DNA replication.
> It only applies after the products of the replication are associated
> with a lot of essential functions. As noted above the initial
> replication may have just been effective enough to keep making storage
> polymers. It would not be until the RNAs started to have multiple
> essential enzymatic functions like the ribosomal peptidase that the
> systems would need to have the level of error management that they have
> today. The current error management systems evolved after the genetic
> code evolved and likely took over from the RNAs that were doing the same
> job before there was a genetic code. You do not need a genetic code to
> replicate functional RNAs. The enzymatic functions are due to the
> secondary and tertiary structures that the primary sequence can form.
>
> What is this gap denial going to do for you? You don't want to believe
> in the designer that created life 3.8 billion years ago and let it
> evolve into what we have today over billions of years. Denial that only
> allows you to temporarily lie to yourself about the situation isn't much
> of anything worth doing. You likely have gone and observed how sad the
> Reason to Believe attempts are when they try to reinterpret the Bible
> and still have to deny reality in order to maintain their Biblical
> beliefs. You likely should be looking into alternatives like Biologos.
> They claim to be Christians, but claim that their alternative has
> nothing to do with what is in the Bible.
>
> Ron Okimoto
> >
> >> The first proteins to be made were likely just storage units for amino acids
> >> used to make nucleotides. Bits of the genetic code would have evolved
> >> as a means to store the most useful amino acids, and may have accidently
> >> made functional proteins that could be replicated with enough fidelity
> >> to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
> >> that were used to make this RNA based storage protein making system
> >> work. The genetic code would have first began to evolve because
> >> specific amino acids would have been preferred to store in this manner..
> >> You would need specific tRNAs, and mRNAs and some type of acylation
> >> system to charge the tRNAs. The system didn't need a high fidelity,
> >> just as long as enough of the correct amino acids got stored in a
> >> useable form. Once you had a partial genetic code, you could make
> >> proteins of a specific amino acid sequence using storage mRNA. These
> >> mRNA "genes" might be selected for by some accidental function that the
> >> protein might have in addition to it's amino acid storage ability. This
> >> would likely lead to selection for a more complete genetic code (tRNA
> >> anticodons) in order to utilize all of the mRNA sequence.
> >>
> >> The real issue is how the system switched from RNA based enzymes to
> >> protein based enzymes. The tRNAs and their amino acid charging system
> >> would have been RNA based. The current genetic code may have evolved
> >> before the proteins used today to make proteins existed. The evidence
> >> is that the genetic code existed before the two families of synthases
> >> (charge tRNAs with a specific amino acid) evolved. There are two types
> >> of synthases and it looks like they evolved from the same DNA sequence..
> >> It has been proposed that one evolved from the sense strand and the
> >> other evolved from the anti-sense strand of the same sequence of DNA.
> >> the genetic code had to exist before these two synthases evolved because
> >> they maintain a conserved sequence of amino acids that indicate that
> >> they were encoded by the same strand of DNA, but one from the sense
> >> strand and one from the anti-sense strand. Apparently both proteins
> >> could charge tRNAs, but they had to duplicate and evolve to charge all
> >> the amino acids of our current genetic code. The evolution of synthases
> >> was likely instrumental in selecting useful tRNAs to be charged with
> >> specific amino acids. If you look at the genetic code it looks like the
> >> tRNAs with similar anticodons were able to be charged with similar amino
> >> acids, and this is just a hold over from the RNA based system. The
> >> protein based system probably adapted to the existing RNA based system..
> >> Eventually proteins became an integral part of the process, augmented
> >> the ribosomes, and took the place of the RNAs that were involved in the
> >> protein making machinery. My guess is that the RNA based system could
> >> have remained functional until the protein based system could take over.
> >>
> >> Currently DNA replication has the lowest error rate, RNA transcription
> >> has a higher error rate, and there is an error rate in translation of
> >> the protein sequence. My guess is that there wasn't a
> >> phenotype/genotype dichotomy enough to worry about when the systems were
> >> evolving, and life doesn't have an issue with the way things currently are.
> >>
> >> Ron Okimoto
> >

On 12/3/2023 6:10 PM, MarkE wrote:
> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
>> On 12/3/2023 6:55 AM, MarkE wrote:
>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>>>> On 12/1/2023 10:50 PM, MarkE wrote:
>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>>>
>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>>>
>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>>>
>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>>>
>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>>>
>>>>> TRANSCRIPT:
>>>>>
>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>>>
>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>>>
>>>> My take is that this isn't an issue. RNA gene replication was already
>>>> something that was consistently happening in the first RNA systems.
>>>
>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>>>
>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
>> RNA replication likely evolved after there were simple self replicators,
>> and we have no pretty much no idea of what they were made of. Just look
>> at the literature, they are proposing that the first macromolecules were
>> using mineral surfaces to catalyze the reactions needed to put the
>> subunits together.
>
> What "simple replicators"?
>
> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
RNA polymers are probably pretty unlikely to occur on their own, but
they do not have to have occurred on their own. The initial speculation
is that simple self replicators evolved. They may have required a
mineral surface or the speculation is a clay matrix to catalyze their
synthesis.
No one has figured out what these first self replicators were. We do
not know what they could have been made from, but their replication was
likely not perfect, and as they made more copies of themselves those
self replicators would have been able to evolve. They probably were
some type of macromolecule of some kind. Proteins have been the obvious
choice, but glycosylation of proteins (adding sugars to the peptides) is
something that still occurs today, so my guess is that they were some
type of mix, so such a self replicator would have a peptidase to form
peptide bonds and glycosylation activity to tack on carbohydrates. If
it initially relied on a mineral surface for the initial enzymatic
activity the initial products could have just made further reactions
more frequent. They could have just stabilized the catalytic activity
of the mineral surface. In catalyzing imperfect copies of themselves
replacing the mineral surface would be selected for.
No one has figured it out, yet, but RNA polymers would not need to come
first. We know that they eventually came because we have the vestiges
of the RNA world that still exists in lifeforms today.
>
> This is pure "just so" story-telling, Ron. The fact that you state it without missing a beat points to James Tour's frustration with and accusations of the claims and postering of the OOL project.
Yep, but it is better than what you have. What does that tell you about
what you are doing?
Really, you do not even have a designer to do your designing. The
entire point of the ID scam was to claim that they could do the science
that would detect their designer, but they failed. The origin of life
researchers have catalytic mineral surfaces. They know that peptidases
exist so it is possible to make one from scratch. You just have to have
a system that was making peptides, and they posit that it could have
happened in a clay matrix (you don't need to confine your reactants in a
membrane until the self replicators start making lipids by accident.
The thing about such self replicators is that they would only need one
or two enzymatic activities to make more copies of themselves.
Replication was likely very imperfect, so you would get a variety of
macromolecules in the confined space of a clay matrix. A lot of
different enzymatic activities could have been produced. It is all
speculation, but we know that something like it can happen.
Compared to your empty denial there is no comparison.
Did you ever look up the Abzyme research using antibodies to evolve new
enzymatic function. They can screen less than two trillion antibodies
with random mutations in them and find a protein sequence for a specific
enzymatic function that they are screening for. Can you imagine how
many different enzymatic functions were produced in those 2 trillion
tries, but were not selected out of the mess? Even the ID perps have
noted how small of a fraction of the total protein sequence space is
accounted for in the genes of extant lifeforms. Life has only had to
deal with a very limited portion of that protein space. This is mainly
due to the way most new genes evolve. Genes get duplicated. In
tetraploids like the vertebrate common ancestor the whole genome gets
duplicated. Only one pair of genes is needed to keep things going, and
the others are free to evolve new functions. The new gene paper that
you put up demonstrated that nearly all of the new genes that evolved
before the Cambrian diversification of multicellular animals evolved
from existing genes. Only a few changes to that protein sequence were
needed to create new gene functions. It seems to have worked that way
because it can work that way. You have genes that can already fold
efficiently, but they do one thing. You duplicate them and change some
of the sequence and you can evolve a new function in a protein sequence
that already folds efficiently. It still took billions of years to
evolve those genes so that they would be available to participate in the
diversification of multicellular animals.
Ron Okimoto
>
>>
>> It does look like we had an RNA phase of life because we have the
>> vestiges of the system in the ribosomes, tRNA, mRNAs and things like
>> small nuclear RNAs that are all functional RNAs. The RNA phase could
>> have obviously been less efficient when it first evolved, and that
>> inefficiency would have likely been beneficial. Something else likely
>> existed before RNA. My guess is that nucleotides started to be produced
>> and used just like they still are used today. They are used as energy
>> transfer molecules. Making polymers of nucleotides would keep them from
>> defusing out of the cell until you needed them. It turned out that the
>> polymers were amenable to replication, and could have enzymatic
>> properties of their own.
>>
>> This just means that the first polymers of nucleotides did not have to
>> be replicated. Some part of some existing self replicator could have
>> just stuck nucleotides together (reverse nuclease activity).
>> Replication could evolve after the RNA polymers started to have useful
>> functions, and was likely first used just to make more nucleotide
>> polymers for storage, and didn't have to have much fidelity at all.
>> Really, DNA could have evolved to replicate RNA polymers that were used
>> to store useful energy transfer nucleotides. Higher fidelity would be
>> selected for once those RNA polymers had useful enzymatic functions.
>>
>> RNA and DNA were likely not required to be very accurate in their
>> replication when they first started to be used by lifeforms.
>>> https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>
>>> It applies to RNA and DNA replication.
>> It only applies after the products of the replication are associated
>> with a lot of essential functions. As noted above the initial
>> replication may have just been effective enough to keep making storage
>> polymers. It would not be until the RNAs started to have multiple
>> essential enzymatic functions like the ribosomal peptidase that the
>> systems would need to have the level of error management that they have
>> today. The current error management systems evolved after the genetic
>> code evolved and likely took over from the RNAs that were doing the same
>> job before there was a genetic code. You do not need a genetic code to
>> replicate functional RNAs. The enzymatic functions are due to the
>> secondary and tertiary structures that the primary sequence can form.
>>
>> What is this gap denial going to do for you? You don't want to believe
>> in the designer that created life 3.8 billion years ago and let it
>> evolve into what we have today over billions of years. Denial that only
>> allows you to temporarily lie to yourself about the situation isn't much
>> of anything worth doing. You likely have gone and observed how sad the
>> Reason to Believe attempts are when they try to reinterpret the Bible
>> and still have to deny reality in order to maintain their Biblical
>> beliefs. You likely should be looking into alternatives like Biologos.
>> They claim to be Christians, but claim that their alternative has
>> nothing to do with what is in the Bible.
>>
>> Ron Okimoto
>>>
>>>> The first proteins to be made were likely just storage units for amino acids
>>>> used to make nucleotides. Bits of the genetic code would have evolved
>>>> as a means to store the most useful amino acids, and may have accidently
>>>> made functional proteins that could be replicated with enough fidelity
>>>> to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
>>>> that were used to make this RNA based storage protein making system
>>>> work. The genetic code would have first began to evolve because
>>>> specific amino acids would have been preferred to store in this manner.
>>>> You would need specific tRNAs, and mRNAs and some type of acylation
>>>> system to charge the tRNAs. The system didn't need a high fidelity,
>>>> just as long as enough of the correct amino acids got stored in a
>>>> useable form. Once you had a partial genetic code, you could make
>>>> proteins of a specific amino acid sequence using storage mRNA. These
>>>> mRNA "genes" might be selected for by some accidental function that the
>>>> protein might have in addition to it's amino acid storage ability. This
>>>> would likely lead to selection for a more complete genetic code (tRNA
>>>> anticodons) in order to utilize all of the mRNA sequence.
>>>>
>>>> The real issue is how the system switched from RNA based enzymes to
>>>> protein based enzymes. The tRNAs and their amino acid charging system
>>>> would have been RNA based. The current genetic code may have evolved
>>>> before the proteins used today to make proteins existed. The evidence
>>>> is that the genetic code existed before the two families of synthases
>>>> (charge tRNAs with a specific amino acid) evolved. There are two types
>>>> of synthases and it looks like they evolved from the same DNA sequence.
>>>> It has been proposed that one evolved from the sense strand and the
>>>> other evolved from the anti-sense strand of the same sequence of DNA.
>>>> the genetic code had to exist before these two synthases evolved because
>>>> they maintain a conserved sequence of amino acids that indicate that
>>>> they were encoded by the same strand of DNA, but one from the sense
>>>> strand and one from the anti-sense strand. Apparently both proteins
>>>> could charge tRNAs, but they had to duplicate and evolve to charge all
>>>> the amino acids of our current genetic code. The evolution of synthases
>>>> was likely instrumental in selecting useful tRNAs to be charged with
>>>> specific amino acids. If you look at the genetic code it looks like the
>>>> tRNAs with similar anticodons were able to be charged with similar amino
>>>> acids, and this is just a hold over from the RNA based system. The
>>>> protein based system probably adapted to the existing RNA based system.
>>>> Eventually proteins became an integral part of the process, augmented
>>>> the ribosomes, and took the place of the RNAs that were involved in the
>>>> protein making machinery. My guess is that the RNA based system could
>>>> have remained functional until the protein based system could take over.
>>>>
>>>> Currently DNA replication has the lowest error rate, RNA transcription
>>>> has a higher error rate, and there is an error rate in translation of
>>>> the protein sequence. My guess is that there wasn't a
>>>> phenotype/genotype dichotomy enough to worry about when the systems were
>>>> evolving, and life doesn't have an issue with the way things currently are.
>>>>
>>>> Ron Okimoto
>>>
>

On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> On 12/3/2023 6:10 PM, MarkE wrote:
> > On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> >> On 12/3/2023 6:55 AM, MarkE wrote:
> >>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> >>>> On 12/1/2023 10:50 PM, MarkE wrote:
> >>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >>>>>
> >>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >>>>>
> >>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>>>
> >>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >>>>>
> >>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >>>>>
> >>>>> TRANSCRIPT:
> >>>>>
> >>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >>>>>
> >>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >>>>>
> >>>> My take is that this isn't an issue. RNA gene replication was already
> >>>> something that was consistently happening in the first RNA systems.
> >>>
> >>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> >>>
> >>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> >> RNA replication likely evolved after there were simple self replicators,
> >> and we have no pretty much no idea of what they were made of. Just look
> >> at the literature, they are proposing that the first macromolecules were
> >> using mineral surfaces to catalyze the reactions needed to put the
> >> subunits together.
> >
> > What "simple replicators"?
> >
> > "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> RNA polymers are probably pretty unlikely to occur on their own, but
> they do not have to have occurred on their own. The initial speculation
> is that simple self replicators evolved. They may have required a
> mineral surface or the speculation is a clay matrix to catalyze their
> synthesis.
>
> No one has figured out what these first self replicators were. We do
> not know what they could have been made from, but their replication was
> likely not perfect, and as they made more copies of themselves those
> self replicators would have been able to evolve. They probably were
> some type of macromolecule of some kind. Proteins have been the obvious
> choice, but glycosylation of proteins (adding sugars to the peptides) is
> something that still occurs today, so my guess is that they were some
> type of mix, so such a self replicator would have a peptidase to form
> peptide bonds and glycosylation activity to tack on carbohydrates. If
> it initially relied on a mineral surface for the initial enzymatic
> activity the initial products could have just made further reactions
> more frequent. They could have just stabilized the catalytic activity
> of the mineral surface. In catalyzing imperfect copies of themselves
> replacing the mineral surface would be selected for.
>
> No one has figured it out, yet, but RNA polymers would not need to come
> first. We know that they eventually came because we have the vestiges
> of the RNA world that still exists in lifeforms today.

This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.

However, physics and chemistry present an awkward reality. A replicating molecule requires:
- a substantial amount of information
- replicate that with sufficiently high fidelity
- over many replications have a sustainable supply of sufficiently pure and concentrated substrate
- have energy and mechanical/thermal agitation maintained by its environment
- be resilient to interfering reactions
- preserve thermal chemical physical stability
- etc

Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.

Until then, it is hand waving and story telling. It is the scam.

> >
> > This is pure "just so" story-telling, Ron. The fact that you state it without missing a beat points to James Tour's frustration with and accusations of the claims and postering of the OOL project.
> Yep, but it is better than what you have. What does that tell you about
> what you are doing?
>
> Really, you do not even have a designer to do your designing. The
> entire point of the ID scam was to claim that they could do the science
> that would detect their designer, but they failed. The origin of life
> researchers have catalytic mineral surfaces. They know that peptidases
> exist so it is possible to make one from scratch. You just have to have
> a system that was making peptides, and they posit that it could have
> happened in a clay matrix (you don't need to confine your reactants in a
> membrane until the self replicators start making lipids by accident.
> The thing about such self replicators is that they would only need one
> or two enzymatic activities to make more copies of themselves.
> Replication was likely very imperfect, so you would get a variety of
> macromolecules in the confined space of a clay matrix. A lot of
> different enzymatic activities could have been produced. It is all
> speculation, but we know that something like it can happen.
>
> Compared to your empty denial there is no comparison.
>
> Did you ever look up the Abzyme research using antibodies to evolve new
> enzymatic function. They can screen less than two trillion antibodies
> with random mutations in them and find a protein sequence for a specific
> enzymatic function that they are screening for. Can you imagine how
> many different enzymatic functions were produced in those 2 trillion
> tries, but were not selected out of the mess? Even the ID perps have
> noted how small of a fraction of the total protein sequence space is
> accounted for in the genes of extant lifeforms. Life has only had to
> deal with a very limited portion of that protein space. This is mainly
> due to the way most new genes evolve. Genes get duplicated. In
> tetraploids like the vertebrate common ancestor the whole genome gets
> duplicated. Only one pair of genes is needed to keep things going, and
> the others are free to evolve new functions. The new gene paper that
> you put up demonstrated that nearly all of the new genes that evolved
> before the Cambrian diversification of multicellular animals evolved
> from existing genes. Only a few changes to that protein sequence were
> needed to create new gene functions. It seems to have worked that way
> because it can work that way. You have genes that can already fold
> efficiently, but they do one thing. You duplicate them and change some
> of the sequence and you can evolve a new function in a protein sequence
> that already folds efficiently. It still took billions of years to
> evolve those genes so that they would be available to participate in the
> diversification of multicellular animals.
>
> Ron Okimoto
> >
> >>
> >> It does look like we had an RNA phase of life because we have the
> >> vestiges of the system in the ribosomes, tRNA, mRNAs and things like
> >> small nuclear RNAs that are all functional RNAs. The RNA phase could
> >> have obviously been less efficient when it first evolved, and that
> >> inefficiency would have likely been beneficial. Something else likely
> >> existed before RNA. My guess is that nucleotides started to be produced
> >> and used just like they still are used today. They are used as energy
> >> transfer molecules. Making polymers of nucleotides would keep them from
> >> defusing out of the cell until you needed them. It turned out that the
> >> polymers were amenable to replication, and could have enzymatic
> >> properties of their own.
> >>
> >> This just means that the first polymers of nucleotides did not have to
> >> be replicated. Some part of some existing self replicator could have
> >> just stuck nucleotides together (reverse nuclease activity).
> >> Replication could evolve after the RNA polymers started to have useful
> >> functions, and was likely first used just to make more nucleotide
> >> polymers for storage, and didn't have to have much fidelity at all.
> >> Really, DNA could have evolved to replicate RNA polymers that were used
> >> to store useful energy transfer nucleotides. Higher fidelity would be
> >> selected for once those RNA polymers had useful enzymatic functions.
> >>
> >> RNA and DNA were likely not required to be very accurate in their
> >> replication when they first started to be used by lifeforms.
> >>> https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>
> >>> It applies to RNA and DNA replication.
> >> It only applies after the products of the replication are associated
> >> with a lot of essential functions. As noted above the initial
> >> replication may have just been effective enough to keep making storage
> >> polymers. It would not be until the RNAs started to have multiple
> >> essential enzymatic functions like the ribosomal peptidase that the
> >> systems would need to have the level of error management that they have
> >> today. The current error management systems evolved after the genetic
> >> code evolved and likely took over from the RNAs that were doing the same
> >> job before there was a genetic code. You do not need a genetic code to
> >> replicate functional RNAs. The enzymatic functions are due to the
> >> secondary and tertiary structures that the primary sequence can form.
> >>
> >> What is this gap denial going to do for you? You don't want to believe
> >> in the designer that created life 3.8 billion years ago and let it
> >> evolve into what we have today over billions of years. Denial that only
> >> allows you to temporarily lie to yourself about the situation isn't much
> >> of anything worth doing. You likely have gone and observed how sad the
> >> Reason to Believe attempts are when they try to reinterpret the Bible
> >> and still have to deny reality in order to maintain their Biblical
> >> beliefs. You likely should be looking into alternatives like Biologos.
> >> They claim to be Christians, but claim that their alternative has
> >> nothing to do with what is in the Bible.
> >>
> >> Ron Okimoto
> >>>
> >>>> The first proteins to be made were likely just storage units for amino acids
> >>>> used to make nucleotides. Bits of the genetic code would have evolved
> >>>> as a means to store the most useful amino acids, and may have accidently
> >>>> made functional proteins that could be replicated with enough fidelity
> >>>> to do whatever they did. The RNA peptidase, tRNA and mRNAs still exist
> >>>> that were used to make this RNA based storage protein making system
> >>>> work. The genetic code would have first began to evolve because
> >>>> specific amino acids would have been preferred to store in this manner.
> >>>> You would need specific tRNAs, and mRNAs and some type of acylation
> >>>> system to charge the tRNAs. The system didn't need a high fidelity,
> >>>> just as long as enough of the correct amino acids got stored in a
> >>>> useable form. Once you had a partial genetic code, you could make
> >>>> proteins of a specific amino acid sequence using storage mRNA. These
> >>>> mRNA "genes" might be selected for by some accidental function that the
> >>>> protein might have in addition to it's amino acid storage ability. This
> >>>> would likely lead to selection for a more complete genetic code (tRNA
> >>>> anticodons) in order to utilize all of the mRNA sequence.
> >>>>
> >>>> The real issue is how the system switched from RNA based enzymes to
> >>>> protein based enzymes. The tRNAs and their amino acid charging system
> >>>> would have been RNA based. The current genetic code may have evolved
> >>>> before the proteins used today to make proteins existed. The evidence
> >>>> is that the genetic code existed before the two families of synthases
> >>>> (charge tRNAs with a specific amino acid) evolved. There are two types
> >>>> of synthases and it looks like they evolved from the same DNA sequence.
> >>>> It has been proposed that one evolved from the sense strand and the
> >>>> other evolved from the anti-sense strand of the same sequence of DNA..
> >>>> the genetic code had to exist before these two synthases evolved because
> >>>> they maintain a conserved sequence of amino acids that indicate that
> >>>> they were encoded by the same strand of DNA, but one from the sense
> >>>> strand and one from the anti-sense strand. Apparently both proteins
> >>>> could charge tRNAs, but they had to duplicate and evolve to charge all
> >>>> the amino acids of our current genetic code. The evolution of synthases
> >>>> was likely instrumental in selecting useful tRNAs to be charged with
> >>>> specific amino acids. If you look at the genetic code it looks like the
> >>>> tRNAs with similar anticodons were able to be charged with similar amino
> >>>> acids, and this is just a hold over from the RNA based system. The
> >>>> protein based system probably adapted to the existing RNA based system.
> >>>> Eventually proteins became an integral part of the process, augmented
> >>>> the ribosomes, and took the place of the RNAs that were involved in the
> >>>> protein making machinery. My guess is that the RNA based system could
> >>>> have remained functional until the protein based system could take over.
> >>>>
> >>>> Currently DNA replication has the lowest error rate, RNA transcription
> >>>> has a higher error rate, and there is an error rate in translation of
> >>>> the protein sequence. My guess is that there wasn't a
> >>>> phenotype/genotype dichotomy enough to worry about when the systems were
> >>>> evolving, and life doesn't have an issue with the way things currently are.
> >>>>
> >>>> Ron Okimoto
> >>>
> >

On 12/6/2023 4:57 PM, MarkE wrote:
> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
>> On 12/3/2023 6:10 PM, MarkE wrote:
>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
>>>> On 12/3/2023 6:55 AM, MarkE wrote:
>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>>>>>
>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>>>>>
>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>>>>>
>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>>>>>
>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>>>>>
>>>>>>> TRANSCRIPT:
>>>>>>>
>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>>>>>
>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>>>>>
>>>>>> My take is that this isn't an issue. RNA gene replication was already
>>>>>> something that was consistently happening in the first RNA systems.
>>>>>
>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>>>>>
>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
>>>> RNA replication likely evolved after there were simple self replicators,
>>>> and we have no pretty much no idea of what they were made of. Just look
>>>> at the literature, they are proposing that the first macromolecules were
>>>> using mineral surfaces to catalyze the reactions needed to put the
>>>> subunits together.
>>>
>>> What "simple replicators"?
>>>
>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
>> RNA polymers are probably pretty unlikely to occur on their own, but
>> they do not have to have occurred on their own. The initial speculation
>> is that simple self replicators evolved. They may have required a
>> mineral surface or the speculation is a clay matrix to catalyze their
>> synthesis.
>>
>> No one has figured out what these first self replicators were. We do
>> not know what they could have been made from, but their replication was
>> likely not perfect, and as they made more copies of themselves those
>> self replicators would have been able to evolve. They probably were
>> some type of macromolecule of some kind. Proteins have been the obvious
>> choice, but glycosylation of proteins (adding sugars to the peptides) is
>> something that still occurs today, so my guess is that they were some
>> type of mix, so such a self replicator would have a peptidase to form
>> peptide bonds and glycosylation activity to tack on carbohydrates. If
>> it initially relied on a mineral surface for the initial enzymatic
>> activity the initial products could have just made further reactions
>> more frequent. They could have just stabilized the catalytic activity
>> of the mineral surface. In catalyzing imperfect copies of themselves
>> replacing the mineral surface would be selected for.
>>
>> No one has figured it out, yet, but RNA polymers would not need to come
>> first. We know that they eventually came because we have the vestiges
>> of the RNA world that still exists in lifeforms today.
>
> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
It is what they are looking for. It is a target. That is how science
works. We have found that one of the best ways to investigate an issue
is to propose testable hypotheses, and learn something by testing them.
Some researchers are making self replicating molecules, and what is
amazing is that they have had some success.
By comparison, what do the IDiots and normal creationists like Tour
have? Tour isn't even trying to build anything positive. That is the
difference between real science and what the Biblical anti-evolution
creationists have been doing since they first started to claim to be
able to use science as the scientific creationists who failed just as
spectacularly as the ID perps that came after them. It turned out that
there was no science that the scientific creationists wanted to do, so
it all became gap denial, and the ID perps just continued the gap denial
without any intention of doing any actual science.
You know that any successful ID science would have just been more
science for you to deny. The scientific creationists found that out by
actually trying to do the science. Their flood geology failed, and all
they learned about nature was that there likely was never a global flood
that wiped out life on earth except for a few survivors on an Ark.
Their age of the earth science just kept telling them that the earth was
older than they thought. Their last science project was the RATE
project that they started before the ID scam took over from them on TO.
They had to acknowledge in their first reports that the theory of
radiometric dating was sound and the rocks dated to be older than they
could be by their reckoning. As sad as it may be they had to start
claiming that their creator had made the rocks with that composition,
and they all just fit into some orderly ancient age due to their
creators wishes. That didn't work for all the sedimentary and volcanic
rock that has been produced since the earth came into being, so they
have to claim that the half lives of the isotopes were much shorter a
few thousand years ago and half a billion years worth of radioactive
decay may have occurred since the flood or what ever. One half life of
U238 has occurred since the creation of the earth, so we only have half
the U238 that the earth started with. Just imagine how many atomic
bombs that would make, and U238 is only one isotope out of hundreds that
have been decaying. It turned out that Kelvin was wrong, and the earth
would not have cooled as quickly as he calculated because he didn't know
about radioactive decay. The scientific creationist understood
radioactive decay and all they could come up with was fantasy and denial.
>
> However, physics and chemistry present an awkward reality. A replicating molecule requires:
> - a substantial amount of information
> - replicate that with sufficiently high fidelity
> - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> - have energy and mechanical/thermal agitation maintained by its environment
> - be resilient to interfering reactions
> - preserve thermal chemical physical stability
> - etc

Click here to read the complete article

On Wednesday, December 6, 2023 at 6:02:01 PM UTC-5, MarkE wrote:
<snip old stuff>
> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
>
> However, physics and chemistry present an awkward reality. A replicating molecule requires:
> - a substantial amount of information
> - replicate that with sufficiently high fidelity
> - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> - have energy and mechanical/thermal agitation maintained by its environment
> - be resilient to interfering reactions
> - preserve thermal chemical physical stability
> - etc
>
> Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
>
> Until then, it is hand waving and story telling. It is the scam.

An unspecified designer is just assumed. It's assumed because (your) religion requires it. And if you've decided, a priori, that (your) religion is the only allowable explanation, you not only must assume it, you will also resist challenges to it.

However, real design presents an awkward reality. Real design requires
-a real designer
-a thoughtful, detailed design process
-a detailed manufacturing process
-energy inputs to run the manufacturing process
-waste disposal systems to remove the by-products from the manufacturing process
-etc

Show me evidence of such a designer, detailed design methods, manufacturing process, waste disposal, etc.

Until then, it's just hand-waving and story telling. It is the scam.

Now, I know, you have elsewhere said that (supernatural) design explanations are not like scientific explanations - in a different category entirely - and that they therefore do not require any of the detail or empirical evidence required for scientific explanations. I agree with you - such explanations are compatible with any and all possible empirical evidence and therefore cannot stand in an "either it's one or the other" relationship with scientific explanations. An unspecified designer is entirely compatible with a fully worked out, empirically supported scientific account of the origin of life (or of metazoan body plans or DNA repair systems). Likewise, the existence of gaps in scientific explanations of things is not evidence in favor of (supernatural) design. Supernatural explanations, being a different category of thing than natural explanations, cannot be in competition with them.
<snip old stuff>

On 12/6/23 2:57 PM, MarkE wrote:
> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
>> On 12/3/2023 6:10 PM, MarkE wrote:
>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
>>>> On 12/3/2023 6:55 AM, MarkE wrote:
>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>>>>>
>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>>>>>
>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>>>>>
>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>>>>>
>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>>>>>
>>>>>>> TRANSCRIPT:
>>>>>>>
>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>>>>>
>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>>>>>
>>>>>> My take is that this isn't an issue. RNA gene replication was already
>>>>>> something that was consistently happening in the first RNA systems.
>>>>>
>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>>>>>
>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
>>>> RNA replication likely evolved after there were simple self replicators,
>>>> and we have no pretty much no idea of what they were made of. Just look
>>>> at the literature, they are proposing that the first macromolecules were
>>>> using mineral surfaces to catalyze the reactions needed to put the
>>>> subunits together.
>>>
>>> What "simple replicators"?
>>>
>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
>> RNA polymers are probably pretty unlikely to occur on their own, but
>> they do not have to have occurred on their own. The initial speculation
>> is that simple self replicators evolved. They may have required a
>> mineral surface or the speculation is a clay matrix to catalyze their
>> synthesis.
>>
>> No one has figured out what these first self replicators were. We do
>> not know what they could have been made from, but their replication was
>> likely not perfect, and as they made more copies of themselves those
>> self replicators would have been able to evolve. They probably were
>> some type of macromolecule of some kind. Proteins have been the obvious
>> choice, but glycosylation of proteins (adding sugars to the peptides) is
>> something that still occurs today, so my guess is that they were some
>> type of mix, so such a self replicator would have a peptidase to form
>> peptide bonds and glycosylation activity to tack on carbohydrates. If
>> it initially relied on a mineral surface for the initial enzymatic
>> activity the initial products could have just made further reactions
>> more frequent. They could have just stabilized the catalytic activity
>> of the mineral surface. In catalyzing imperfect copies of themselves
>> replacing the mineral surface would be selected for.
>>
>> No one has figured it out, yet, but RNA polymers would not need to come
>> first. We know that they eventually came because we have the vestiges
>> of the RNA world that still exists in lifeforms today.
>
> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
False. Naturalism is not presented as the only allowable explanation,
but the only pragmatically useful one. Supernaturalism has two problem.
First, it has an perfect record of failure in the past. Second, it is
worse than useless, since it does not point to anything else to look
more closely at; it instead tells you to stop looking and hide your head
in the sand.
> However, physics and chemistry present an awkward reality. A replicating molecule requires:
> - a substantial amount of information
> - replicate that with sufficiently high fidelity
> - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> - have energy and mechanical/thermal agitation maintained by its environment
> - be resilient to interfering reactions
> - preserve thermal chemical physical stability
> - etc
See my .sig.
> Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
>
> Until then, it is hand waving and story telling. It is the scam.
A scam is pointing at one thing and calling it something else.
Scientific researchers on abiogenesis don't say they have the answer;
they say (and show) that they have *possible* explanations for *part* of
the answer.
Intelligent design proponents, on the other hand, say, first, that the
scientists have nothing, and second, that magic is a likely (some say
certain) alternative. Sure looks to me like the ID proponents are the
scammers.
And that's before you get into the theological issues, which ID
proponents, for good (selfish) reasons, work studiously to avoid.
--
Mark Isaak
"Wisdom begins when you discover the difference between 'That
doesn't make sense' and 'I don't understand.'" - Mary Doria Russell

On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> On 12/6/23 2:57 PM, MarkE wrote:
> > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> >> On 12/3/2023 6:10 PM, MarkE wrote:
> >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >>>>>>>
> >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >>>>>>>
> >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>>>>>
> >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >>>>>>>
> >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >>>>>>>
> >>>>>>> TRANSCRIPT:
> >>>>>>>
> >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >>>>>>>
> >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >>>>>>>
> >>>>>> My take is that this isn't an issue. RNA gene replication was already
> >>>>>> something that was consistently happening in the first RNA systems..
> >>>>>
> >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> >>>>>
> >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> >>>> RNA replication likely evolved after there were simple self replicators,
> >>>> and we have no pretty much no idea of what they were made of. Just look
> >>>> at the literature, they are proposing that the first macromolecules were
> >>>> using mineral surfaces to catalyze the reactions needed to put the
> >>>> subunits together.
> >>>
> >>> What "simple replicators"?
> >>>
> >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> >> RNA polymers are probably pretty unlikely to occur on their own, but
> >> they do not have to have occurred on their own. The initial speculation
> >> is that simple self replicators evolved. They may have required a
> >> mineral surface or the speculation is a clay matrix to catalyze their
> >> synthesis.
> >>
> >> No one has figured out what these first self replicators were. We do
> >> not know what they could have been made from, but their replication was
> >> likely not perfect, and as they made more copies of themselves those
> >> self replicators would have been able to evolve. They probably were
> >> some type of macromolecule of some kind. Proteins have been the obvious
> >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> >> something that still occurs today, so my guess is that they were some
> >> type of mix, so such a self replicator would have a peptidase to form
> >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> >> it initially relied on a mineral surface for the initial enzymatic
> >> activity the initial products could have just made further reactions
> >> more frequent. They could have just stabilized the catalytic activity
> >> of the mineral surface. In catalyzing imperfect copies of themselves
> >> replacing the mineral surface would be selected for.
> >>
> >> No one has figured it out, yet, but RNA polymers would not need to come
> >> first. We know that they eventually came because we have the vestiges
> >> of the RNA world that still exists in lifeforms today.
> >
> > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> False. Naturalism is not presented as the only allowable explanation,
> but the only pragmatically useful one. Supernaturalism has two problem.
> First, it has an perfect record of failure in the past. Second, it is
> worse than useless, since it does not point to anything else to look
> more closely at; it instead tells you to stop looking and hide your head
> in the sand.

How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):

Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.

Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”

On Friday 8 December 2023 at 00:37:02 UTC+2, MarkE wrote:
> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > On 12/6/23 2:57 PM, MarkE wrote:
> > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > >>>>>>>
> > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > >>>>>>>
> > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > >>>>>>>
> > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > >>>>>>>
> > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > >>>>>>>
> > >>>>>>> TRANSCRIPT:
> > >>>>>>>
> > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > >>>>>>>
> > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > >>>>>>>
> > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > >>>>>> something that was consistently happening in the first RNA systems.
> > >>>>>
> > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > >>>>>
> > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > >>>> RNA replication likely evolved after there were simple self replicators,
> > >>>> and we have no pretty much no idea of what they were made of. Just look
> > >>>> at the literature, they are proposing that the first macromolecules were
> > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > >>>> subunits together.
> > >>>
> > >>> What "simple replicators"?
> > >>>
> > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > >> they do not have to have occurred on their own. The initial speculation
> > >> is that simple self replicators evolved. They may have required a
> > >> mineral surface or the speculation is a clay matrix to catalyze their
> > >> synthesis.
> > >>
> > >> No one has figured out what these first self replicators were. We do
> > >> not know what they could have been made from, but their replication was
> > >> likely not perfect, and as they made more copies of themselves those
> > >> self replicators would have been able to evolve. They probably were
> > >> some type of macromolecule of some kind. Proteins have been the obvious
> > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > >> something that still occurs today, so my guess is that they were some
> > >> type of mix, so such a self replicator would have a peptidase to form
> > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > >> it initially relied on a mineral surface for the initial enzymatic
> > >> activity the initial products could have just made further reactions
> > >> more frequent. They could have just stabilized the catalytic activity
> > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > >> replacing the mineral surface would be selected for.
> > >>
> > >> No one has figured it out, yet, but RNA polymers would not need to come
> > >> first. We know that they eventually came because we have the vestiges
> > >> of the RNA world that still exists in lifeforms today.
> > >
> > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > False. Naturalism is not presented as the only allowable explanation,
> > but the only pragmatically useful one. Supernaturalism has two problem.
> > First, it has an perfect record of failure in the past. Second, it is
> > worse than useless, since it does not point to anything else to look
> > more closely at; it instead tells you to stop looking and hide your head
> > in the sand.
> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
>
> Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
>
> Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”

On 12/7/23 2:32 PM, MarkE wrote:
> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
>> On 12/6/23 2:57 PM, MarkE wrote:
>>> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
>>>> On 12/3/2023 6:10 PM, MarkE wrote:
>>>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
>>>>>> On 12/3/2023 6:55 AM, MarkE wrote:
>>>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>>>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
>>>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>>>>>>>
>>>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>>>>>>>
>>>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>>>>>>>
>>>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>>>>>>>
>>>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>>>>>>>
>>>>>>>>> TRANSCRIPT:
>>>>>>>>>
>>>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>>>>>>>
>>>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>>>>>>>
>>>>>>>> My take is that this isn't an issue. RNA gene replication was already
>>>>>>>> something that was consistently happening in the first RNA systems.
>>>>>>>
>>>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>>>>>>>
>>>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
>>>>>> RNA replication likely evolved after there were simple self replicators,
>>>>>> and we have no pretty much no idea of what they were made of. Just look
>>>>>> at the literature, they are proposing that the first macromolecules were
>>>>>> using mineral surfaces to catalyze the reactions needed to put the
>>>>>> subunits together.
>>>>>
>>>>> What "simple replicators"?
>>>>>
>>>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
>>>> RNA polymers are probably pretty unlikely to occur on their own, but
>>>> they do not have to have occurred on their own. The initial speculation
>>>> is that simple self replicators evolved. They may have required a
>>>> mineral surface or the speculation is a clay matrix to catalyze their
>>>> synthesis.
>>>>
>>>> No one has figured out what these first self replicators were. We do
>>>> not know what they could have been made from, but their replication was
>>>> likely not perfect, and as they made more copies of themselves those
>>>> self replicators would have been able to evolve. They probably were
>>>> some type of macromolecule of some kind. Proteins have been the obvious
>>>> choice, but glycosylation of proteins (adding sugars to the peptides) is
>>>> something that still occurs today, so my guess is that they were some
>>>> type of mix, so such a self replicator would have a peptidase to form
>>>> peptide bonds and glycosylation activity to tack on carbohydrates. If
>>>> it initially relied on a mineral surface for the initial enzymatic
>>>> activity the initial products could have just made further reactions
>>>> more frequent. They could have just stabilized the catalytic activity
>>>> of the mineral surface. In catalyzing imperfect copies of themselves
>>>> replacing the mineral surface would be selected for.
>>>>
>>>> No one has figured it out, yet, but RNA polymers would not need to come
>>>> first. We know that they eventually came because we have the vestiges
>>>> of the RNA world that still exists in lifeforms today.
>>>
>>> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
>> False. Naturalism is not presented as the only allowable explanation,
>> but the only pragmatically useful one. Supernaturalism has two problem.
>> First, it has an perfect record of failure in the past. Second, it is
>> worse than useless, since it does not point to anything else to look
>> more closely at; it instead tells you to stop looking and hide your head
>> in the sand.
>
> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered.
Good question. I note that you ignored the points I just brought up.
I'll add one more: To consider non-natural explanations, one must first
have some non-natural explanations to consider. Simply saying "a
miracle occurred" explains nothing. An explanation has to say *why*
something is one way rather than another way. ID actively avoids having
explanations, natural *or* non-natural.
> From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
>
> Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
>
> Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”

Click here to read the complete article

On Thursday, December 7, 2023 at 5:37:02 PM UTC-5, MarkE wrote:
> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > On 12/6/23 2:57 PM, MarkE wrote:
> > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > >>>>>>>
> > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > >>>>>>>
> > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > >>>>>>>
> > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > >>>>>>>
> > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > >>>>>>>
> > >>>>>>> TRANSCRIPT:
> > >>>>>>>
> > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > >>>>>>>
> > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > >>>>>>>
> > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > >>>>>> something that was consistently happening in the first RNA systems.
> > >>>>>
> > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > >>>>>
> > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > >>>> RNA replication likely evolved after there were simple self replicators,
> > >>>> and we have no pretty much no idea of what they were made of. Just look
> > >>>> at the literature, they are proposing that the first macromolecules were
> > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > >>>> subunits together.
> > >>>
> > >>> What "simple replicators"?
> > >>>
> > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > >> they do not have to have occurred on their own. The initial speculation
> > >> is that simple self replicators evolved. They may have required a
> > >> mineral surface or the speculation is a clay matrix to catalyze their
> > >> synthesis.
> > >>
> > >> No one has figured out what these first self replicators were. We do
> > >> not know what they could have been made from, but their replication was
> > >> likely not perfect, and as they made more copies of themselves those
> > >> self replicators would have been able to evolve. They probably were
> > >> some type of macromolecule of some kind. Proteins have been the obvious
> > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > >> something that still occurs today, so my guess is that they were some
> > >> type of mix, so such a self replicator would have a peptidase to form
> > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > >> it initially relied on a mineral surface for the initial enzymatic
> > >> activity the initial products could have just made further reactions
> > >> more frequent. They could have just stabilized the catalytic activity
> > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > >> replacing the mineral surface would be selected for.
> > >>
> > >> No one has figured it out, yet, but RNA polymers would not need to come
> > >> first. We know that they eventually came because we have the vestiges
> > >> of the RNA world that still exists in lifeforms today.
> > >
> > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > False. Naturalism is not presented as the only allowable explanation,
> > but the only pragmatically useful one. Supernaturalism has two problem.
> > First, it has an perfect record of failure in the past. Second, it is
> > worse than useless, since it does not point to anything else to look
> > more closely at; it instead tells you to stop looking and hide your head
> > in the sand.
> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
>
> Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
>
> Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”
> > > However, physics and chemistry present an awkward reality. A replicating molecule requires:
> > > - a substantial amount of information
> > > - replicate that with sufficiently high fidelity
> > > - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> > > - have energy and mechanical/thermal agitation maintained by its environment
> > > - be resilient to interfering reactions
> > > - preserve thermal chemical physical stability
> > > - etc
> > See my .sig.
> > > Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
> > >
> > > Until then, it is hand waving and story telling. It is the scam.
> > A scam is pointing at one thing and calling it something else.
> > Scientific researchers on abiogenesis don't say they have the answer;
> > they say (and show) that they have *possible* explanations for *part* of
> > the answer.
> >
> > Intelligent design proponents, on the other hand, say, first, that the
> > scientists have nothing, and second, that magic is a likely (some say
> > certain) alternative. Sure looks to me like the ID proponents are the
> > scammers.
> >
> > And that's before you get into the theological issues, which ID
> > proponents, for good (selfish) reasons, work studiously to avoid.
> >
> > --
> > Mark Isaak
> > "Wisdom begins when you discover the difference between 'That
> > doesn't make sense' and 'I don't understand.'" - Mary Doria Russell
A real "materialism-of-the-gaps", in order to be parallel to "god-of-the-gaps" would have to run something like this......

On Thursday, December 7, 2023 at 11:37:02 PM UTC+1, MarkE wrote:
> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > On 12/6/23 2:57 PM, MarkE wrote:
> > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > >>>>>>>
> > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > >>>>>>>
> > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > >>>>>>>
> > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > >>>>>>>
> > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > >>>>>>>
> > >>>>>>> TRANSCRIPT:
> > >>>>>>>
> > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > >>>>>>>
> > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > >>>>>>>
> > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > >>>>>> something that was consistently happening in the first RNA systems.
> > >>>>>
> > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > >>>>>
> > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > >>>> RNA replication likely evolved after there were simple self replicators,
> > >>>> and we have no pretty much no idea of what they were made of. Just look
> > >>>> at the literature, they are proposing that the first macromolecules were
> > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > >>>> subunits together.
> > >>>
> > >>> What "simple replicators"?
> > >>>
> > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > >> they do not have to have occurred on their own. The initial speculation
> > >> is that simple self replicators evolved. They may have required a
> > >> mineral surface or the speculation is a clay matrix to catalyze their
> > >> synthesis.
> > >>
> > >> No one has figured out what these first self replicators were. We do
> > >> not know what they could have been made from, but their replication was
> > >> likely not perfect, and as they made more copies of themselves those
> > >> self replicators would have been able to evolve. They probably were
> > >> some type of macromolecule of some kind. Proteins have been the obvious
> > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > >> something that still occurs today, so my guess is that they were some
> > >> type of mix, so such a self replicator would have a peptidase to form
> > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > >> it initially relied on a mineral surface for the initial enzymatic
> > >> activity the initial products could have just made further reactions
> > >> more frequent. They could have just stabilized the catalytic activity
> > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > >> replacing the mineral surface would be selected for.
> > >>
> > >> No one has figured it out, yet, but RNA polymers would not need to come
> > >> first. We know that they eventually came because we have the vestiges
> > >> of the RNA world that still exists in lifeforms today.
> > >
> > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > False. Naturalism is not presented as the only allowable explanation,
> > but the only pragmatically useful one. Supernaturalism has two problem.
> > First, it has an perfect record of failure in the past. Second, it is
> > worse than useless, since it does not point to anything else to look
> > more closely at; it instead tells you to stop looking and hide your head
> > in the sand.
> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
>
> Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
>
> Response: The entirety of this book seeks to provide a proper scope to the “gap.”

Or, with other words, it makes no attempt at actually filling the gap - so it remains, by
it's own words, a mere "of the gaps" argument, and therefore sterile and uninteresting
when understood as a scientific theory, borerline blasphemous when read as a
theological position.

> The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail.

That is pretty much what one would expect of any scientific progress, in any field. Research starts with the relatively low
hanging fruits, while the "big picture' remains under-defined. As science progresses, a clearer picture of the complexities
emerges, which will pose tougher and tougher challenges to address (and as a result more and more elaborate
theories, often with more and more bootstrapping assumptions. And because there is at least a kernel of truth in
"falsifiability" as an ingedient of scientific practice, of course we should expect also an increase in
the number of theories that have failed - and a failed scientific theory is not worthless, it typically increases
our knowledge and understanding even if it fails its ultimate objective.

On Saturday, December 9, 2023 at 2:47:03 AM UTC+11, Mark Isaak wrote:
> On 12/7/23 2:32 PM, MarkE wrote:
> > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> >> On 12/6/23 2:57 PM, MarkE wrote:
> >>> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> >>>> On 12/3/2023 6:10 PM, MarkE wrote:
> >>>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> >>>>>> On 12/3/2023 6:55 AM, MarkE wrote:
> >>>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> >>>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> >>>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >>>>>>>>>
> >>>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >>>>>>>>>
> >>>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>>>>>>>
> >>>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >>>>>>>>>
> >>>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >>>>>>>>>
> >>>>>>>>> TRANSCRIPT:
> >>>>>>>>>
> >>>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >>>>>>>>>
> >>>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >>>>>>>>>
> >>>>>>>> My take is that this isn't an issue. RNA gene replication was already
> >>>>>>>> something that was consistently happening in the first RNA systems.
> >>>>>>>
> >>>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> >>>>>>>
> >>>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> >>>>>> RNA replication likely evolved after there were simple self replicators,
> >>>>>> and we have no pretty much no idea of what they were made of. Just look
> >>>>>> at the literature, they are proposing that the first macromolecules were
> >>>>>> using mineral surfaces to catalyze the reactions needed to put the
> >>>>>> subunits together.
> >>>>>
> >>>>> What "simple replicators"?
> >>>>>
> >>>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> >>>> RNA polymers are probably pretty unlikely to occur on their own, but
> >>>> they do not have to have occurred on their own. The initial speculation
> >>>> is that simple self replicators evolved. They may have required a
> >>>> mineral surface or the speculation is a clay matrix to catalyze their
> >>>> synthesis.
> >>>>
> >>>> No one has figured out what these first self replicators were. We do
> >>>> not know what they could have been made from, but their replication was
> >>>> likely not perfect, and as they made more copies of themselves those
> >>>> self replicators would have been able to evolve. They probably were
> >>>> some type of macromolecule of some kind. Proteins have been the obvious
> >>>> choice, but glycosylation of proteins (adding sugars to the peptides) is
> >>>> something that still occurs today, so my guess is that they were some
> >>>> type of mix, so such a self replicator would have a peptidase to form
> >>>> peptide bonds and glycosylation activity to tack on carbohydrates. If
> >>>> it initially relied on a mineral surface for the initial enzymatic
> >>>> activity the initial products could have just made further reactions
> >>>> more frequent. They could have just stabilized the catalytic activity
> >>>> of the mineral surface. In catalyzing imperfect copies of themselves
> >>>> replacing the mineral surface would be selected for.
> >>>>
> >>>> No one has figured it out, yet, but RNA polymers would not need to come
> >>>> first. We know that they eventually came because we have the vestiges
> >>>> of the RNA world that still exists in lifeforms today.
> >>>
> >>> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> >> False. Naturalism is not presented as the only allowable explanation,
> >> but the only pragmatically useful one. Supernaturalism has two problem..
> >> First, it has an perfect record of failure in the past. Second, it is
> >> worse than useless, since it does not point to anything else to look
> >> more closely at; it instead tells you to stop looking and hide your head
> >> in the sand.
> >
> > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered.
> Good question. I note that you ignored the points I just brought up.

Let's deal with the fundamental issue first. If we have no agreement on the terms of engagement, meaningful discussion is not possible.

Would you describe your own position as ontological/metaphysical naturalism or similar?

"Metaphysical naturalism (also called ontological naturalism, philosophical naturalism and antisupernaturalism) is a philosophical worldview which holds that there is nothing but natural elements, principles, and relations of the kind studied by the natural sciences." https://en.wikipedia.org/wiki/Metaphysical_naturalism#:~:text=Metaphysical%20naturalism%20(also%20called%20ontological,studied%20by%20the%20natural%20sciences.

>
> I'll add one more: To consider non-natural explanations, one must first
> have some non-natural explanations to consider. Simply saying "a
> miracle occurred" explains nothing. An explanation has to say *why*
> something is one way rather than another way. ID actively avoids having
> explanations, natural *or* non-natural.

ID's explanation: an intelligent agent brought space and time into existence, and created information and embodied it in organisms by some combination of direct "supernatural" intervention (e.g. OoL) and indirect "natural" processes (e.g. microevolution).

On Saturday, December 9, 2023 at 5:07:03 AM UTC+11, broger...@gmail..com wrote:
> On Thursday, December 7, 2023 at 5:37:02 PM UTC-5, MarkE wrote:
> > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > >>>>>>>
> > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > >>>>>>>
> > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > >>>>>>>
> > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > >>>>>>>
> > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > >>>>>>>
> > > >>>>>>> TRANSCRIPT:
> > > >>>>>>>
> > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > >>>>>>>
> > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > >>>>>>>
> > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > >>>>>> something that was consistently happening in the first RNA systems.
> > > >>>>>
> > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > >>>>>
> > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > >>>> and we have no pretty much no idea of what they were made of. Just look
> > > >>>> at the literature, they are proposing that the first macromolecules were
> > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > >>>> subunits together.
> > > >>>
> > > >>> What "simple replicators"?
> > > >>>
> > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > >> they do not have to have occurred on their own. The initial speculation
> > > >> is that simple self replicators evolved. They may have required a
> > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > >> synthesis.
> > > >>
> > > >> No one has figured out what these first self replicators were. We do
> > > >> not know what they could have been made from, but their replication was
> > > >> likely not perfect, and as they made more copies of themselves those
> > > >> self replicators would have been able to evolve. They probably were
> > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > >> something that still occurs today, so my guess is that they were some
> > > >> type of mix, so such a self replicator would have a peptidase to form
> > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > >> it initially relied on a mineral surface for the initial enzymatic
> > > >> activity the initial products could have just made further reactions
> > > >> more frequent. They could have just stabilized the catalytic activity
> > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > >> replacing the mineral surface would be selected for.
> > > >>
> > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > >> first. We know that they eventually came because we have the vestiges
> > > >> of the RNA world that still exists in lifeforms today.
> > > >
> > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > False. Naturalism is not presented as the only allowable explanation,
> > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > First, it has an perfect record of failure in the past. Second, it is
> > > worse than useless, since it does not point to anything else to look
> > > more closely at; it instead tells you to stop looking and hide your head
> > > in the sand.
> > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> >
> > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> >
> > Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”
> > > > However, physics and chemistry present an awkward reality. A replicating molecule requires:
> > > > - a substantial amount of information
> > > > - replicate that with sufficiently high fidelity
> > > > - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> > > > - have energy and mechanical/thermal agitation maintained by its environment
> > > > - be resilient to interfering reactions
> > > > - preserve thermal chemical physical stability
> > > > - etc
> > > See my .sig.
> > > > Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
> > > >
> > > > Until then, it is hand waving and story telling. It is the scam.
> > > A scam is pointing at one thing and calling it something else.
> > > Scientific researchers on abiogenesis don't say they have the answer;
> > > they say (and show) that they have *possible* explanations for *part* of
> > > the answer.
> > >
> > > Intelligent design proponents, on the other hand, say, first, that the
> > > scientists have nothing, and second, that magic is a likely (some say
> > > certain) alternative. Sure looks to me like the ID proponents are the
> > > scammers.
> > >
> > > And that's before you get into the theological issues, which ID
> > > proponents, for good (selfish) reasons, work studiously to avoid.
> > >
> > > --
> > > Mark Isaak
> > > "Wisdom begins when you discover the difference between 'That
> > > doesn't make sense' and 'I don't understand.'" - Mary Doria Russell
> A real "materialism-of-the-gaps", in order to be parallel to "god-of-the-gaps" would have to run something like this......
>
> "Religious people have been trying to explain the origin of life for millennia, and yet they are no closer to doing so than when they began. They cannot even agree among themselves about how did it, how and when it happened, and why it happened. They have provided no evidence for any actual "designer" of life, no design plans, no proposed and empirically supported models of what actually happened when life was created. Nothing whatsoever. Given the utter failure of supernaturalists to explain the origin of life, or even to provide a detailed, testable model of what happened, the only conclusion is that naturalism created life. DOn't ask how or why, no need to do any research on possible mechanisms or biochemistries. The failure of the religious to provide a detailed model of what actually happened means that the only alternative is naturalism. Therefore, there's no further work to be done. All those guys in the labs can go on sabbatical."

On Saturday, December 9, 2023 at 5:32:03 AM UTC+11, Burkhard wrote:
> On Thursday, December 7, 2023 at 11:37:02 PM UTC+1, MarkE wrote:
> > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > >>>>>>>
> > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > >>>>>>>
> > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > >>>>>>>
> > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > >>>>>>>
> > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > >>>>>>>
> > > >>>>>>> TRANSCRIPT:
> > > >>>>>>>
> > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > >>>>>>>
> > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > >>>>>>>
> > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > >>>>>> something that was consistently happening in the first RNA systems.
> > > >>>>>
> > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > >>>>>
> > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > >>>> and we have no pretty much no idea of what they were made of. Just look
> > > >>>> at the literature, they are proposing that the first macromolecules were
> > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > >>>> subunits together.
> > > >>>
> > > >>> What "simple replicators"?
> > > >>>
> > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > >> they do not have to have occurred on their own. The initial speculation
> > > >> is that simple self replicators evolved. They may have required a
> > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > >> synthesis.
> > > >>
> > > >> No one has figured out what these first self replicators were. We do
> > > >> not know what they could have been made from, but their replication was
> > > >> likely not perfect, and as they made more copies of themselves those
> > > >> self replicators would have been able to evolve. They probably were
> > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > >> something that still occurs today, so my guess is that they were some
> > > >> type of mix, so such a self replicator would have a peptidase to form
> > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > >> it initially relied on a mineral surface for the initial enzymatic
> > > >> activity the initial products could have just made further reactions
> > > >> more frequent. They could have just stabilized the catalytic activity
> > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > >> replacing the mineral surface would be selected for.
> > > >>
> > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > >> first. We know that they eventually came because we have the vestiges
> > > >> of the RNA world that still exists in lifeforms today.
> > > >
> > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > False. Naturalism is not presented as the only allowable explanation,
> > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > First, it has an perfect record of failure in the past. Second, it is
> > > worse than useless, since it does not point to anything else to look
> > > more closely at; it instead tells you to stop looking and hide your head
> > > in the sand.
> > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> >
> > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> >
> > Response: The entirety of this book seeks to provide a proper scope to the “gap.”
> Or, with other words, it makes no attempt at actually filling the gap - so it remains, by
> it's own words, a mere "of the gaps" argument, and therefore sterile and uninteresting
> when understood as a scientific theory, borerline blasphemous when read as a
> theological position.

What material evidence, if any, would cause you to consider supernatural agency in the origin of life?

> > The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail.
> That is pretty much what one would expect of any scientific progress, in any field. Research starts with the relatively low
> hanging fruits, while the "big picture' remains under-defined. As science progresses, a clearer picture of the complexities
> emerges, which will pose tougher and tougher challenges to address (and as a result more and more elaborate
> theories, often with more and more bootstrapping assumptions. And because there is at least a kernel of truth in
> "falsifiability" as an ingedient of scientific practice, of course we should expect also an increase in
> the number of theories that have failed - and a failed scientific theory is not worthless, it typically increases
> our knowledge and understanding even if it fails its ultimate objective.
> >As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology.
> That is still a mere gap argument, however much he stomps his foot on the ground and
> yells "it ain't so".
>
> It would stop being a gap argument only if he now started to fill the gap with testable claims
> about the designer that are at least as testable, and productive (in the sense of leading to new
> observations and insights) as those OOL theories that he rejects
> > Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”
> Even if this were true and OOL had nothing more to say than this,
> , it would score at least as high as the "designer did it" inference.
> But with the crucial difference that of course, people do not
> stop at this level. Rather, they do form theories, and test them, which
> leads to new insights. All the hard work and experiments that he
> references, and on which his entire work is parasitic upon.
> > > > However, physics and chemistry present an awkward reality. A replicating molecule requires:
> > > > - a substantial amount of information
> > > > - replicate that with sufficiently high fidelity
> > > > - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> > > > - have energy and mechanical/thermal agitation maintained by its environment
> > > > - be resilient to interfering reactions
> > > > - preserve thermal chemical physical stability
> > > > - etc
> > > See my .sig.
> > > > Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
> > > >
> > > > Until then, it is hand waving and story telling. It is the scam.
> > > A scam is pointing at one thing and calling it something else.
> > > Scientific researchers on abiogenesis don't say they have the answer;
> > > they say (and show) that they have *possible* explanations for *part* of
> > > the answer.
> > >
> > > Intelligent design proponents, on the other hand, say, first, that the
> > > scientists have nothing, and second, that magic is a likely (some say
> > > certain) alternative. Sure looks to me like the ID proponents are the
> > > scammers.
> > >
> > > And that's before you get into the theological issues, which ID
> > > proponents, for good (selfish) reasons, work studiously to avoid.
> > >
> > > --
> > > Mark Isaak
> > > "Wisdom begins when you discover the difference between 'That
> > > doesn't make sense' and 'I don't understand.'" - Mary Doria Russell

On Friday, December 8, 2023 at 11:07:03 PM UTC-5, MarkE wrote:
> On Saturday, December 9, 2023 at 5:07:03 AM UTC+11, broger...@gmail.com wrote:
> > On Thursday, December 7, 2023 at 5:37:02 PM UTC-5, MarkE wrote:
> > > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > > >>>>>>>
> > > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > > >>>>>>>
> > > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > > >>>>>>>
> > > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > > >>>>>>>
> > > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > > >>>>>>>
> > > > >>>>>>> TRANSCRIPT:
> > > > >>>>>>>
> > > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > > >>>>>>>
> > > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information.. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > > >>>>>>>
> > > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > > >>>>>> something that was consistently happening in the first RNA systems.
> > > > >>>>>
> > > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > > >>>>>
> > > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > > >>>> and we have no pretty much no idea of what they were made of. Just look
> > > > >>>> at the literature, they are proposing that the first macromolecules were
> > > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > > >>>> subunits together.
> > > > >>>
> > > > >>> What "simple replicators"?
> > > > >>>
> > > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > > >> they do not have to have occurred on their own. The initial speculation
> > > > >> is that simple self replicators evolved. They may have required a
> > > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > > >> synthesis.
> > > > >>
> > > > >> No one has figured out what these first self replicators were. We do
> > > > >> not know what they could have been made from, but their replication was
> > > > >> likely not perfect, and as they made more copies of themselves those
> > > > >> self replicators would have been able to evolve. They probably were
> > > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > > >> something that still occurs today, so my guess is that they were some
> > > > >> type of mix, so such a self replicator would have a peptidase to form
> > > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > > >> it initially relied on a mineral surface for the initial enzymatic
> > > > >> activity the initial products could have just made further reactions
> > > > >> more frequent. They could have just stabilized the catalytic activity
> > > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > > >> replacing the mineral surface would be selected for.
> > > > >>
> > > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > > >> first. We know that they eventually came because we have the vestiges
> > > > >> of the RNA world that still exists in lifeforms today.
> > > > >
> > > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > > False. Naturalism is not presented as the only allowable explanation,
> > > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > > First, it has an perfect record of failure in the past. Second, it is
> > > > worse than useless, since it does not point to anything else to look
> > > > more closely at; it instead tells you to stop looking and hide your head
> > > > in the sand.
> > > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> > >
> > > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> > >
> > > Response: The entirety of this book seeks to provide a proper scope to the “gap.” The Stairway to Life clarifies that the gap is not simply a missing puzzle piece or a set of unclear details. The gap is, in fact, the entirety of the origin of life. And the gap is growing over time as we learn more about the complexity of cells and as efforts to produce components of life via realistic prebiotic approaches fail. As we have mentioned, additional steps will be added to the Stairway to Life over time. These steps will come from previously unexplored processes that are required for life. For example, we mentioned in Chapter 17 that the current best approximation of a minimal cell that can reproduce autonomously includes 493 genes [201]. This same report specifies that 91 of the 493 genes perform unknown functions. Therefore, about 20% of the minimal genome codes for functions that we have not yet explored. Further, the genome is not the only information contained in life. We are just beginning to explore other forms of information found in living organisms, such as the sugar code that encapsulates cells [226]. Future exploration in these areas will result in new steps in the Stairway to Life and an ever-increasing “gap.” The emperor is not simply missing a lapel pin; the emperor has no clothes. Our conclusion that creative intelligence was essential to start life is based on what we do know, not on what we don’t know. The arguments in this book do not take the following form: “No one knows how life began; therefore, God did it.” Rather, the inference to the need for intelligence in the origin of life follows directly from what we do know about the requirements for life and what we do know about chemistry, physics, thermodynamics, and biology. Turning this objection around, choosing to maintain a belief in abiogenesis despite the absence of a reasonable approach to the Stairway to Life is a “materialism-of-the-gaps” approach—i.e., “we don’t know how life began, but we know that only natural processes were involved.”
> > > > > However, physics and chemistry present an awkward reality. A replicating molecule requires:
> > > > > - a substantial amount of information
> > > > > - replicate that with sufficiently high fidelity
> > > > > - over many replications have a sustainable supply of sufficiently pure and concentrated substrate
> > > > > - have energy and mechanical/thermal agitation maintained by its environment
> > > > > - be resilient to interfering reactions
> > > > > - preserve thermal chemical physical stability
> > > > > - etc
> > > > See my .sig.
> > > > > Show me a demonstration of such a localised, entropy-reversing, sustained, information-increasing prebiotically plausible process.
> > > > >
> > > > > Until then, it is hand waving and story telling. It is the scam.
> > > > A scam is pointing at one thing and calling it something else.
> > > > Scientific researchers on abiogenesis don't say they have the answer;
> > > > they say (and show) that they have *possible* explanations for *part* of
> > > > the answer.
> > > >
> > > > Intelligent design proponents, on the other hand, say, first, that the
> > > > scientists have nothing, and second, that magic is a likely (some say
> > > > certain) alternative. Sure looks to me like the ID proponents are the
> > > > scammers.
> > > >
> > > > And that's before you get into the theological issues, which ID
> > > > proponents, for good (selfish) reasons, work studiously to avoid.
> > > >
> > > > --
> > > > Mark Isaak
> > > > "Wisdom begins when you discover the difference between 'That
> > > > doesn't make sense' and 'I don't understand.'" - Mary Doria Russell
> > A real "materialism-of-the-gaps", in order to be parallel to "god-of-the-gaps" would have to run something like this......
> >
> > "Religious people have been trying to explain the origin of life for millennia, and yet they are no closer to doing so than when they began. They cannot even agree among themselves about how did it, how and when it happened, and why it happened. They have provided no evidence for any actual "designer" of life, no design plans, no proposed and empirically supported models of what actually happened when life was created. Nothing whatsoever. Given the utter failure of supernaturalists to explain the origin of life, or even to provide a detailed, testable model of what happened, the only conclusion is that naturalism created life. DOn't ask how or why, no need to do any research on possible mechanisms or biochemistries. The failure of the religious to provide a detailed model of what actually happened means that the only alternative is naturalism. Therefore, there's no further work to be done. All those guys in the labs can go on sabbatical."
.......
> Insisting that supernatural creation be subject methodological naturalism and the scientific method is a category error.

On Saturday, December 9, 2023 at 5:22:03 AM UTC+1, MarkE wrote:
> On Saturday, December 9, 2023 at 5:32:03 AM UTC+11, Burkhard wrote:
> > On Thursday, December 7, 2023 at 11:37:02 PM UTC+1, MarkE wrote:
> > > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > > >>>>>>>
> > > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > > >>>>>>>
> > > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > > >>>>>>>
> > > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > > >>>>>>>
> > > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > > >>>>>>>
> > > > >>>>>>> TRANSCRIPT:
> > > > >>>>>>>
> > > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > > >>>>>>>
> > > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information.. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > > >>>>>>>
> > > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > > >>>>>> something that was consistently happening in the first RNA systems.
> > > > >>>>>
> > > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > > >>>>>
> > > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > > >>>> and we have no pretty much no idea of what they were made of. Just look
> > > > >>>> at the literature, they are proposing that the first macromolecules were
> > > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > > >>>> subunits together.
> > > > >>>
> > > > >>> What "simple replicators"?
> > > > >>>
> > > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > > >> they do not have to have occurred on their own. The initial speculation
> > > > >> is that simple self replicators evolved. They may have required a
> > > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > > >> synthesis.
> > > > >>
> > > > >> No one has figured out what these first self replicators were. We do
> > > > >> not know what they could have been made from, but their replication was
> > > > >> likely not perfect, and as they made more copies of themselves those
> > > > >> self replicators would have been able to evolve. They probably were
> > > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > > >> something that still occurs today, so my guess is that they were some
> > > > >> type of mix, so such a self replicator would have a peptidase to form
> > > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > > >> it initially relied on a mineral surface for the initial enzymatic
> > > > >> activity the initial products could have just made further reactions
> > > > >> more frequent. They could have just stabilized the catalytic activity
> > > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > > >> replacing the mineral surface would be selected for.
> > > > >>
> > > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > > >> first. We know that they eventually came because we have the vestiges
> > > > >> of the RNA world that still exists in lifeforms today.
> > > > >
> > > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > > False. Naturalism is not presented as the only allowable explanation,
> > > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > > First, it has an perfect record of failure in the past. Second, it is
> > > > worse than useless, since it does not point to anything else to look
> > > > more closely at; it instead tells you to stop looking and hide your head
> > > > in the sand.
> > > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> > >
> > > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> > >
> > > Response: The entirety of this book seeks to provide a proper scope to the “gap.”
> > Or, with other words, it makes no attempt at actually filling the gap - so it remains, by
> > it's own words, a mere "of the gaps" argument, and therefore sterile and uninteresting
> > when understood as a scientific theory, borderline blasphemous when read as a
> > theological position.
> What material evidence, if any, would cause you to consider supernatural agency in the origin of life?

On 12/8/23 7:52 PM, MarkE wrote:
> On Saturday, December 9, 2023 at 2:47:03 AM UTC+11, Mark Isaak wrote:
>> On 12/7/23 2:32 PM, MarkE wrote:
>>> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
>>>> On 12/6/23 2:57 PM, MarkE wrote:
>>>>> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
>>>>>> On 12/3/2023 6:10 PM, MarkE wrote:
>>>>>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
>>>>>>>> On 12/3/2023 6:55 AM, MarkE wrote:
>>>>>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
>>>>>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
>>>>>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
>>>>>>>>>>>
>>>>>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
>>>>>>>>>>>
>>>>>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
>>>>>>>>>>>
>>>>>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
>>>>>>>>>>>
>>>>>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
>>>>>>>>>>>
>>>>>>>>>>> TRANSCRIPT:
>>>>>>>>>>>
>>>>>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
>>>>>>>>>>>
>>>>>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
>>>>>>>>>>>
>>>>>>>>>> My take is that this isn't an issue. RNA gene replication was already
>>>>>>>>>> something that was consistently happening in the first RNA systems.
>>>>>>>>>
>>>>>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
>>>>>>>>>
>>>>>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
>>>>>>>> RNA replication likely evolved after there were simple self replicators,
>>>>>>>> and we have no pretty much no idea of what they were made of. Just look
>>>>>>>> at the literature, they are proposing that the first macromolecules were
>>>>>>>> using mineral surfaces to catalyze the reactions needed to put the
>>>>>>>> subunits together.
>>>>>>>
>>>>>>> What "simple replicators"?
>>>>>>>
>>>>>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
>>>>>> RNA polymers are probably pretty unlikely to occur on their own, but
>>>>>> they do not have to have occurred on their own. The initial speculation
>>>>>> is that simple self replicators evolved. They may have required a
>>>>>> mineral surface or the speculation is a clay matrix to catalyze their
>>>>>> synthesis.
>>>>>>
>>>>>> No one has figured out what these first self replicators were. We do
>>>>>> not know what they could have been made from, but their replication was
>>>>>> likely not perfect, and as they made more copies of themselves those
>>>>>> self replicators would have been able to evolve. They probably were
>>>>>> some type of macromolecule of some kind. Proteins have been the obvious
>>>>>> choice, but glycosylation of proteins (adding sugars to the peptides) is
>>>>>> something that still occurs today, so my guess is that they were some
>>>>>> type of mix, so such a self replicator would have a peptidase to form
>>>>>> peptide bonds and glycosylation activity to tack on carbohydrates. If
>>>>>> it initially relied on a mineral surface for the initial enzymatic
>>>>>> activity the initial products could have just made further reactions
>>>>>> more frequent. They could have just stabilized the catalytic activity
>>>>>> of the mineral surface. In catalyzing imperfect copies of themselves
>>>>>> replacing the mineral surface would be selected for.
>>>>>>
>>>>>> No one has figured it out, yet, but RNA polymers would not need to come
>>>>>> first. We know that they eventually came because we have the vestiges
>>>>>> of the RNA world that still exists in lifeforms today.
>>>>>
>>>>> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
>>>> False. Naturalism is not presented as the only allowable explanation,
>>>> but the only pragmatically useful one. Supernaturalism has two problem.
>>>> First, it has an perfect record of failure in the past. Second, it is
>>>> worse than useless, since it does not point to anything else to look
>>>> more closely at; it instead tells you to stop looking and hide your head
>>>> in the sand.
>>>
>>> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered.
>> Good question. I note that you ignored the points I just brought up.
>
> Let's deal with the fundamental issue first. If we have no agreement on the terms of engagement, meaningful discussion is not possible.
>
> Would you describe your own position as ontological/metaphysical naturalism or similar?
>
> "Metaphysical naturalism (also called ontological naturalism, philosophical naturalism and antisupernaturalism) is a philosophical worldview which holds that there is nothing but natural elements, principles, and relations of the kind studied by the natural sciences." https://en.wikipedia.org/wiki/Metaphysical_naturalism#:~:text=Metaphysical%20naturalism%20(also%20called%20ontological,studied%20by%20the%20natural%20sciences.
Yes, and I hold that that is your position, too. My position is that
the supernatural does not exist *by definition*. "Supernatural" means
outside nature, and "nature", in this context, means all that exists.
If it exists enough for you to talk about it, it cannot be supernatural.
Your claim that an intelligent agent used supernatural intervention is
part of metaphysical naturalism, differing only from what you would call
materialism in its nomenclature. Your metaphysical outlook is basically
the same as mine, but what you call "supernatural", I call, "unknown,
and possibly exceptional to known laws."

Click here to read the complete article

On Saturday, December 9, 2023 at 10:22:03 PM UTC+11, Burkhard wrote:
> On Saturday, December 9, 2023 at 5:22:03 AM UTC+1, MarkE wrote:
> > On Saturday, December 9, 2023 at 5:32:03 AM UTC+11, Burkhard wrote:
> > > On Thursday, December 7, 2023 at 11:37:02 PM UTC+1, MarkE wrote:
> > > > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > > > >>>>>>>
> > > > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > > > >>>>>>>
> > > > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > > > >>>>>>>
> > > > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > > > >>>>>>>
> > > > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > > > >>>>>>>
> > > > > >>>>>>> TRANSCRIPT:
> > > > > >>>>>>>
> > > > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > > > >>>>>>>
> > > > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > > > >>>>>>>
> > > > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > > > >>>>>> something that was consistently happening in the first RNA systems.
> > > > > >>>>>
> > > > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > > > >>>>>
> > > > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > > > >>>> and we have no pretty much no idea of what they were made of.. Just look
> > > > > >>>> at the literature, they are proposing that the first macromolecules were
> > > > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > > > >>>> subunits together.
> > > > > >>>
> > > > > >>> What "simple replicators"?
> > > > > >>>
> > > > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > > > >> they do not have to have occurred on their own. The initial speculation
> > > > > >> is that simple self replicators evolved. They may have required a
> > > > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > > > >> synthesis.
> > > > > >>
> > > > > >> No one has figured out what these first self replicators were. We do
> > > > > >> not know what they could have been made from, but their replication was
> > > > > >> likely not perfect, and as they made more copies of themselves those
> > > > > >> self replicators would have been able to evolve. They probably were
> > > > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > > > >> something that still occurs today, so my guess is that they were some
> > > > > >> type of mix, so such a self replicator would have a peptidase to form
> > > > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > > > >> it initially relied on a mineral surface for the initial enzymatic
> > > > > >> activity the initial products could have just made further reactions
> > > > > >> more frequent. They could have just stabilized the catalytic activity
> > > > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > > > >> replacing the mineral surface would be selected for.
> > > > > >>
> > > > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > > > >> first. We know that they eventually came because we have the vestiges
> > > > > >> of the RNA world that still exists in lifeforms today.
> > > > > >
> > > > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > > > False. Naturalism is not presented as the only allowable explanation,
> > > > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > > > First, it has an perfect record of failure in the past. Second, it is
> > > > > worse than useless, since it does not point to anything else to look
> > > > > more closely at; it instead tells you to stop looking and hide your head
> > > > > in the sand.
> > > > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> > > >
> > > > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> > > >
> > > > Response: The entirety of this book seeks to provide a proper scope to the “gap.”
> > > Or, with other words, it makes no attempt at actually filling the gap - so it remains, by
> > > it's own words, a mere "of the gaps" argument, and therefore sterile and uninteresting
> > > when understood as a scientific theory, borderline blasphemous when read as a
> > > theological position.
> > What material evidence, if any, would cause you to consider supernatural agency in the origin of life?
> Didn't we go over this before?
>
> Already the way you formulate the question points to the main problem:
> why would one expect a supernatural agent to produce "material" (your
> word) evidence? And what would that even mean? For me it already has
> all the hallmarks of a category error: My reasons to accept supernatural
> entities are in turn supernatural, or spiritual, in nature, the momemt
> something material is evidence for X, X more or less becomes by definition
> also material
>
> And by the same token, "explaining" a material fact by recourse to a
> supernatural entity seems to me to be a contradiction in terms. It looks
> superficially like a meaningful sentence, but on closer inspection is
> more akin to "sleepy triangle" - it looks only superficially like a meaningful
> sentence, but is ultimately a category error

On Sunday, December 10, 2023 at 6:57:04 AM UTC-5, MarkE wrote:
> On Saturday, December 9, 2023 at 10:22:03 PM UTC+11, Burkhard wrote:
> > On Saturday, December 9, 2023 at 5:22:03 AM UTC+1, MarkE wrote:
> > > On Saturday, December 9, 2023 at 5:32:03 AM UTC+11, Burkhard wrote:
> > > > On Thursday, December 7, 2023 at 11:37:02 PM UTC+1, MarkE wrote:
> > > > > On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> > > > > > On 12/6/23 2:57 PM, MarkE wrote:
> > > > > > > On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> > > > > > >> On 12/3/2023 6:10 PM, MarkE wrote:
> > > > > > >>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> > > > > > >>>> On 12/3/2023 6:55 AM, MarkE wrote:
> > > > > > >>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> > > > > > >>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> > > > > > >>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> > > > > > >>>>>>>
> > > > > > >>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> > > > > > >>>>>>>
> > > > > > >>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> > > > > > >>>>>>>
> > > > > > >>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> > > > > > >>>>>>>
> > > > > > >>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> > > > > > >>>>>>>
> > > > > > >>>>>>> TRANSCRIPT:
> > > > > > >>>>>>>
> > > > > > >>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> > > > > > >>>>>>>
> > > > > > >>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> > > > > > >>>>>>>
> > > > > > >>>>>> My take is that this isn't an issue. RNA gene replication was already
> > > > > > >>>>>> something that was consistently happening in the first RNA systems.
> > > > > > >>>>>
> > > > > > >>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> > > > > > >>>>>
> > > > > > >>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> > > > > > >>>> RNA replication likely evolved after there were simple self replicators,
> > > > > > >>>> and we have no pretty much no idea of what they were made of. Just look
> > > > > > >>>> at the literature, they are proposing that the first macromolecules were
> > > > > > >>>> using mineral surfaces to catalyze the reactions needed to put the
> > > > > > >>>> subunits together.
> > > > > > >>>
> > > > > > >>> What "simple replicators"?
> > > > > > >>>
> > > > > > >>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> > > > > > >> RNA polymers are probably pretty unlikely to occur on their own, but
> > > > > > >> they do not have to have occurred on their own. The initial speculation
> > > > > > >> is that simple self replicators evolved. They may have required a
> > > > > > >> mineral surface or the speculation is a clay matrix to catalyze their
> > > > > > >> synthesis.
> > > > > > >>
> > > > > > >> No one has figured out what these first self replicators were. We do
> > > > > > >> not know what they could have been made from, but their replication was
> > > > > > >> likely not perfect, and as they made more copies of themselves those
> > > > > > >> self replicators would have been able to evolve. They probably were
> > > > > > >> some type of macromolecule of some kind. Proteins have been the obvious
> > > > > > >> choice, but glycosylation of proteins (adding sugars to the peptides) is
> > > > > > >> something that still occurs today, so my guess is that they were some
> > > > > > >> type of mix, so such a self replicator would have a peptidase to form
> > > > > > >> peptide bonds and glycosylation activity to tack on carbohydrates. If
> > > > > > >> it initially relied on a mineral surface for the initial enzymatic
> > > > > > >> activity the initial products could have just made further reactions
> > > > > > >> more frequent. They could have just stabilized the catalytic activity
> > > > > > >> of the mineral surface. In catalyzing imperfect copies of themselves
> > > > > > >> replacing the mineral surface would be selected for.
> > > > > > >>
> > > > > > >> No one has figured it out, yet, but RNA polymers would not need to come
> > > > > > >> first. We know that they eventually came because we have the vestiges
> > > > > > >> of the RNA world that still exists in lifeforms today.
> > > > > > >
> > > > > > > This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> > > > > > False. Naturalism is not presented as the only allowable explanation,
> > > > > > but the only pragmatically useful one. Supernaturalism has two problem.
> > > > > > First, it has an perfect record of failure in the past. Second, it is
> > > > > > worse than useless, since it does not point to anything else to look
> > > > > > more closely at; it instead tells you to stop looking and hide your head
> > > > > > in the sand.
> > > > > How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered. From "The Stairway To Life: An Origin-Of-Life Reality Check" (pp. 187-189):
> > > > >
> > > > > Objection: Your argument is a plea to the “God of the gaps.” Just because science doesn’t have all the answers doesn’t mean that we have to invoke God to fill the gaps.
> > > > >
> > > > > Response: The entirety of this book seeks to provide a proper scope to the “gap.”
> > > > Or, with other words, it makes no attempt at actually filling the gap - so it remains, by
> > > > it's own words, a mere "of the gaps" argument, and therefore sterile and uninteresting
> > > > when understood as a scientific theory, borderline blasphemous when read as a
> > > > theological position.
> > > What material evidence, if any, would cause you to consider supernatural agency in the origin of life?
> > Didn't we go over this before?
> >
> > Already the way you formulate the question points to the main problem:
> > why would one expect a supernatural agent to produce "material" (your
> > word) evidence? And what would that even mean? For me it already has
> > all the hallmarks of a category error: My reasons to accept supernatural
> > entities are in turn supernatural, or spiritual, in nature, the momemt
> > something material is evidence for X, X more or less becomes by definition
> > also material
> >
> > And by the same token, "explaining" a material fact by recourse to a
> > supernatural entity seems to me to be a contradiction in terms. It looks
> > superficially like a meaningful sentence, but on closer inspection is
> > more akin to "sleepy triangle" - it looks only superficially like a meaningful
> > sentence, but is ultimately a category error
> Here's why I think you're mistaken.
>
> Gould's NOMA attempted to cast "natural" and "supernatural" as disjoint sets. But on what basis? A superset of X, by definition, contains X. The supernatural may contain the natural, and interact with it. Christianity, for example, proclaims a supernatural being who transcends the material universe, but nevertheless brought it into existence, and continues to have dominion over it.
>
> To be sure, the supernatural and natural are different, but talk of detectable interaction between them is not automatically a category error. In fact, God (in the fullest sense) has the ability do anything at will with the material world. Therefore, to categorically rule out supernatural action in the natural, you would need to disprove God's existence.
>
> Let's define "natural" as pertaining to "nature", i.e. the material world whose phenomena obey the "laws of nature", and fundamentally, causality (notwithstanding quantum randomness). Therefore, naturalistic explanations consist of unbroken cause and effect. Methodological naturalism assumes causality, i.e. "the 'causal closure of the physical', the doctrine that all physical effects can be accounted for by physical causes." https://en.wikipedia.org/wiki/Naturalism_(philosophy)
>
> Assume for a moment that we definitively observe a break in causality. What then? Either nature is noncausal (with the implications that follow), or supernatural action has been detected. An example of the latter would be Jesus' miracles: the witnesses of these intuitively recognised them to spectacularly override causality and therefore supernatural, which was their main purpose. (Just to be clear, my point here does not depend on belief in Jesus or miracles.)

On Sunday, December 10, 2023 at 3:52:04 AM UTC+11, Mark Isaak wrote:
> On 12/8/23 7:52 PM, MarkE wrote:
> > On Saturday, December 9, 2023 at 2:47:03 AM UTC+11, Mark Isaak wrote:
> >> On 12/7/23 2:32 PM, MarkE wrote:
> >>> On Friday, December 8, 2023 at 3:17:02 AM UTC+11, Mark Isaak wrote:
> >>>> On 12/6/23 2:57 PM, MarkE wrote:
> >>>>> On Monday, December 4, 2023 at 12:01:58 PM UTC+11, RonO wrote:
> >>>>>> On 12/3/2023 6:10 PM, MarkE wrote:
> >>>>>>> On Monday, December 4, 2023 at 1:31:58 AM UTC+11, RonO wrote:
> >>>>>>>> On 12/3/2023 6:55 AM, MarkE wrote:
> >>>>>>>>> On Sunday, December 3, 2023 at 4:21:58 AM UTC+11, RonO wrote:
> >>>>>>>>>> On 12/1/2023 10:50 PM, MarkE wrote:
> >>>>>>>>>>> Here's a new LSS video primer on DNA repair and the error threshold problem: https://www.youtube.com/watch?v=hQm8vmtM8CI (12:22)
> >>>>>>>>>>>
> >>>>>>>>>>> In relation to recent discussion of "junk DNA", this is another cost to maintaining junk DNA -- the energy and recourses needed for constant repair, though not sure how much this amounts to in practice.
> >>>>>>>>>>>
> >>>>>>>>>>> Incidentally, Wikipedia makes this statement about Eigen's paradox: "Eigen's paradox is one of the most intractable puzzles in the study of the origins of life." https://en.wikipedia.org/wiki/Error_threshold_(evolution)#Eigen's_paradox
> >>>>>>>>>>>
> >>>>>>>>>>> Manfred Eigen himself proposes hypercyles to overcome the error threshold problem:
> >>>>>>>>>>>
> >>>>>>>>>>> https://www.youtube.com/watch?v=qfOtzjdR_A0 (1:47)
> >>>>>>>>>>>
> >>>>>>>>>>> TRANSCRIPT:
> >>>>>>>>>>>
> >>>>>>>>>>> QUESTION: What was the necessity of your theory for hypercycles? There were experiments or facts which made it necessary that you make a theory which has got the name hypercycles?
> >>>>>>>>>>>
> >>>>>>>>>>> RESPONSE: As I said genotype/phenotype dichotomy. I said first of all a theory without this translation, and that would get stuck with the error threshold. In order to overcome the error threshold you have to make good proteins. But in order to make proteins you need more information. So you got stuck somehow. So you needed something to overcome this. And the other is the fact that once you do translation you have to test your translation products, your phenotypes, but you have to store your information in the genotype and you have to make sure that you don't lose that, because otherwise everything is gone. So there was a necessity to... and there could well have been a different model. For instance, one model which we later on found and combined with the hypercycle, was that you have to make compartmentation. In other words, you know that all life is not in homogeneous solution, it's always in cells or in organism and so forth. So you'd have to compartmentalise your system of nucleic acids and proteins, but you might immediately ask: isn't it sufficient to compartment them, why then a hypercycle, now you keep protein and nucleic acids together in your compartment? Well, if you only would put them into a compartment, the nucleic acids would start to compete with one another, so you must fit them into a reaction network and that has to be cyclic.
> >>>>>>>>>>>
> >>>>>>>>>> My take is that this isn't an issue. RNA gene replication was already
> >>>>>>>>>> something that was consistently happening in the first RNA systems.
> >>>>>>>>>
> >>>>>>>>> You're begging the question with the assertion that "RNA gene replication was already something that was consistently happening in the first RNA systems". The paradox disallows such assumptions:
> >>>>>>>>>
> >>>>>>>>> "Without error correction enzymes, the maximum size of a replicating molecule is about 100 base pairs. For a replicating molecule to encode error correction enzymes, it must be substantially larger than 100 bases."
> >>>>>>>> RNA replication likely evolved after there were simple self replicators,
> >>>>>>>> and we have no pretty much no idea of what they were made of. Just look
> >>>>>>>> at the literature, they are proposing that the first macromolecules were
> >>>>>>>> using mineral surfaces to catalyze the reactions needed to put the
> >>>>>>>> subunits together.
> >>>>>>>
> >>>>>>> What "simple replicators"?
> >>>>>>>
> >>>>>>> "RNA replication likely evolved after these". So you're saying that some unspecified non-RNA replicators were somehow replaced by RNA replicators?
> >>>>>> RNA polymers are probably pretty unlikely to occur on their own, but
> >>>>>> they do not have to have occurred on their own. The initial speculation
> >>>>>> is that simple self replicators evolved. They may have required a
> >>>>>> mineral surface or the speculation is a clay matrix to catalyze their
> >>>>>> synthesis.
> >>>>>>
> >>>>>> No one has figured out what these first self replicators were. We do
> >>>>>> not know what they could have been made from, but their replication was
> >>>>>> likely not perfect, and as they made more copies of themselves those
> >>>>>> self replicators would have been able to evolve. They probably were
> >>>>>> some type of macromolecule of some kind. Proteins have been the obvious
> >>>>>> choice, but glycosylation of proteins (adding sugars to the peptides) is
> >>>>>> something that still occurs today, so my guess is that they were some
> >>>>>> type of mix, so such a self replicator would have a peptidase to form
> >>>>>> peptide bonds and glycosylation activity to tack on carbohydrates. If
> >>>>>> it initially relied on a mineral surface for the initial enzymatic
> >>>>>> activity the initial products could have just made further reactions
> >>>>>> more frequent. They could have just stabilized the catalytic activity
> >>>>>> of the mineral surface. In catalyzing imperfect copies of themselves
> >>>>>> replacing the mineral surface would be selected for.
> >>>>>>
> >>>>>> No one has figured it out, yet, but RNA polymers would not need to come
> >>>>>> first. We know that they eventually came because we have the vestiges
> >>>>>> of the RNA world that still exists in lifeforms today.
> >>>>>
> >>>>> This is a key issue I think. An unspecified "replicating molecule" is just assumed. Case in point - that's what you've done. It's assumed because naturalism requires it. And if you have decided a priori that naturalism is the only allowable explanation, you not only must assume it, you will also resist challenges to it.
> >>>> False. Naturalism is not presented as the only allowable explanation,
> >>>> but the only pragmatically useful one. Supernaturalism has two problem.
> >>>> First, it has an perfect record of failure in the past. Second, it is
> >>>> worse than useless, since it does not point to anything else to look
> >>>> more closely at; it instead tells you to stop looking and hide your head
> >>>> in the sand.
> >>>
> >>> How many times have we all been around the block on this fundamental question? A common position here is functionally ontological/metaphysical naturalism. No matter how wide the "gap" may become, non-natural explanations will not be considered.
> >> Good question. I note that you ignored the points I just brought up.
> >
> > Let's deal with the fundamental issue first. If we have no agreement on the terms of engagement, meaningful discussion is not possible.
> >
> > Would you describe your own position as ontological/metaphysical naturalism or similar?
> >
> > "Metaphysical naturalism (also called ontological naturalism, philosophical naturalism and antisupernaturalism) is a philosophical worldview which holds that there is nothing but natural elements, principles, and relations of the kind studied by the natural sciences." https://en.wikipedia.org/wiki/Metaphysical_naturalism#:~:text=Metaphysical%20naturalism%20(also%20called%20ontological,studied%20by%20the%20natural%20sciences.
> Yes, and I hold that that is your position, too. My position is that
> the supernatural does not exist *by definition*. "Supernatural" means
> outside nature, and "nature", in this context, means all that exists.
> If it exists enough for you to talk about it, it cannot be supernatural.
> Your claim that an intelligent agent used supernatural intervention is
> part of metaphysical naturalism, differing only from what you would call
> materialism in its nomenclature. Your metaphysical outlook is basically
> the same as mine, but what you call "supernatural", I call, "unknown,
> and possibly exceptional to known laws."