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DNA errors are scanned electrically

arg-fallbackName="Elshamah"/>
SpecialFrog said:
Do you understand what an argument from ignorance is?

Claiming that your argument lacks evidence doesn't require that I can prove a different argument. I'm happy to accept that there are things that no human currently knows.

A poor explanation with no evidence to support it is not more compelling than no explanation.


Is intelligent design merely an "argument from ignorance?"

http://elshamah.heavenforum.org/t1720-is-intelligent-design-merely-an-argument-from-ignorance?highlight=ignorance

God of the gaps


is a comfortable way to try to criticize and reject a argument and avoid to address actually the issues raised. Atheists resort to it all the time, even when a robust case is made, with clear and detailed observation , and logical inference and conclusion.

http://www.evolutionnews.org/2013/01/why_intelligent068151.html

" In all of our experience of cause and effect, we know that complex and sequence-specific information, when it is traced back to its source, uniformly originates with an intelligent cause. Therefore, when we find complex and sequence-specific digital information encoded in the hereditary molecules of DNA and RNA, the most plausible candidate explanation -- given what we do know about the nature of information -- is that it also originated with a source of intelligent agency.


http://www.ideacenter.org/contentmgr/showdetails.php/id/1186

Is intelligent design merely an "argument from ignorance?"

No. Some critics have misunderstood intelligent design and claimed that it is merely claims that because we can't figure out how some biological structures could have arisen, therefore they were probably designed. The argument for design is not like this. In reality, the argument notes that intelligent design theory is a sufficient causal explanation for the origin of specified (or irreducibly) complex information, and thus argues from positive predictions of design. The lack of detailed step-by-step evolutionary explanations for the origin of irreducible complexity is the result of the fact that irreducible complexity is fundamentally not evolvable by Darwinian evolution.

Misrepresenting the Definition of Intelligent Design

http://www.evolutionnews.org/2009/11/misrepresenting_the_definition028051.html

Behe at the Dover trial : (Day 10 AM Testimony, p. 110.)
"This argument for design is an entirely positive argument. This is how we recognize design by the purposeful arrangement of parts."

Behe also made this clear in the afterward to Darwin's Black Box:

rreducibly complex systems such as mousetraps and flagella serve both as negative arguments against gradualistic explanations like Darwin's and as positive arguments for design. The negative argument is that such interactive systems resist explanation by the tiny steps that a Darwinian path would be expected to take. The positive argument is that their parts appear arranged to serve a purpose, which is exactly how we detect design. (Darwin's Black Box, pp. 263-264 (2006).)

Scott Minnich and Stephen Meyer also explain the positive argument for design:
Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system ... in any other context we would immediately recognize such systems as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes. ("Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic Bacteria," in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (2004).)

This specified complexity, also called complex and specified information (CSI), is a tell-tale indicator that intelligence was at work. Meyer explains why this makes for a positive -- not negative -- argument for design:

by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation. (Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004).)
 
arg-fallbackName="Elshamah"/>
Dragan Glas said:
Greetings,


If you really don't know this, I'll be happy to provide evidence - all you need do is ask.

Kindest regards,

James

Go ahead......
 
arg-fallbackName="SpecialFrog"/>
Elshamah said:
SpecialFrog said:
Do you understand what an argument from ignorance is?

Claiming that your argument lacks evidence doesn't require that I can prove a different argument. I'm happy to accept that there are things that no human currently knows.

A poor explanation with no evidence to support it is not more compelling than no explanation.


Is intelligent design merely an "argument from ignorance?"

Pretty much. Certainly all claims that something is "irreducibly complex" are only supported by arguments from ignorance.

Besides, you have made a number of specific claims, such as DNA and DNA repair having to appear at the same time, and literally your only "evidence" is to demand that people questioning this provide evidence otherwise.

How is that not an argument from ignorance?

Also, it is funny that you quote some Behe where he talks about the flagella as being irreducibly complex since that particular claim has been actually falsified.

Here is a good summary article explaining some of the issues with any "irriducibly complex" claim:

http://scienceblogs.com/pharyngula/2014/04/25/irreducible-complexity-again/
 
arg-fallbackName="DutchLiam84"/>
Elshamah said:
The lack of detailed step-by-step evolutionary explanations for the origin of irreducible complexity is the result of the fact that irreducible complexity is fundamentally not evolvable by Darwinian evolution.
Isn't this almost exactly what the "God of the gaps-argument" is? Practically all examples that I know of that ID-ers call Irreducibly Complex have intermediate stages that can be perfectly explained by Evolutionary Theory. What you call "fundamentally not evolvable" is the mere definition of an argument from ignorance and thus a God of the Gaps-argument by invoking the ID "hypothesis" (don't you dare call it a theory, at least not a scientific one).

Anyway, do you know the difference between bottom-up and top-down design? If not, look it up. Nature is perfectly capable of bottom-up design and fine-tuning of this design, the end result would almost be exactly the same as top-down.
 
arg-fallbackName="Elshamah"/>
Dragan Glas said:

I doubt you did read and understand the paper. Otherwise, you would not have posted it.

but, lets see what it says.

The transition from the RNA to the DNA world was a major event in the history of life.

cool. So they start with evolution, to end with evolution. Nice bias. Beside a baseless assertion which cannot be verified. So its unjustified to make a absolute claim , as the author does.

The invention of DNA

the use of this terminology it not permitted. Invention is something only minds can do.

Recent data from comparative genomics, structural biology and traditional biochemistry have revealed that several of these enzymatic activities have been invented independently more than once

thats called convergent evolution, which is evidence against evolution.

“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

Paleontologist J. William Schopf, one of the world’s leading authorities on early life on Earth, has made this very point in the book Life’s Origin.

Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendents.

The distribution of the different protein families corresponding to these activities in the three domains of life (Archaea, Eukarya, and Bacteria) is puzzling.

they don't say..... LOL....

Several hypotheses have been proposed to explain these observations, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss

how could gene transfer have happened, if there were no genes yet ?? I thought the make of genes depends DNA replication.....
 
arg-fallbackName="Deleted member 619"/>
Jireh said:
The lack of detailed step-by-step evolutionary explanations for the origin of irreducible complexity is the result of the fact that irreducible complexity is fundamentally not evolvable by Darwinian evolution.

Umm, Müller still disagrees with you, and he demonstrated that this is bollocks even before any cretinist fuckwit got hold of the term 'irreducible complexity'. IC is a fucking result of evolution, you moron.

Oh, and only people with shit for brains talk about Darwinian evolution any more. We've moved on in the last 160 years. ;)
 
arg-fallbackName="Dragan Glas"/>
Greetings,
Elshamah said:
Dragan Glas said:
I doubt you did read and understand the paper. Otherwise, you would not have posted it.
I did read it, as I do all papers - whether posted by others or by myself - and I did understand it, thank you.
Elshamah said:
but, lets see what it says.

The transition from the RNA to the DNA world was a major event in the history of life.

cool. So they start with evolution, to end with evolution. Nice bias. Beside a baseless assertion which cannot be verified. So its unjustified to make a absolute claim , as the author does.
The paper is about the evolution of DNA - not RNA - for which is what you asked.
Elshamah said:
The invention of DNA

the use of this terminology it not permitted. Invention is something only minds can do.
Now who is making an "absolute claim"?

Although the term is usually used in that context, it can be used in the context of a process "inventing" something - this may be an unusual usage but is not "prohibited".
Elshamah said:
Recent data from comparative genomics, structural biology and traditional biochemistry have revealed that several of these enzymatic activities have been invented independently more than once

thats called convergent evolution, which is evidence against evolution.
Would you kindly explain how convergent evolution is evidence against evolution?!

And I'm ignoring the contradiction in the sentence per se.
Elshamah said:
“…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.1

Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History (New York, NY: W.W. Norton & Company, 1989), 51.

Paleontologist J. William Schopf, one of the world’s leading authorities on early life on Earth, has made this very point in the book Life’s Origin.

Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendents.

[...]
I'm not sure what point you're trying to make here?!
Elshamah said:
Several hypotheses have been proposed to explain these observations, including independent invention of DNA and DNA replication proteins, ancient gene transfer and gene loss

how could gene transfer have happened, if there were no genes yet ?? I thought the make of genes depends DNA replication.....
You are misinformed:
[url=https://en.wikipedia.org/wiki/Gene said:
Gene[/url]"]The concept of a gene continues to be refined as new phenomena are discovered.[3] Regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a modern working definition is "a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions, and/or other functional sequence regions".[4][5]
As Rumraket has pointed out several times to you already: viruses store their genome as RNA - they could not do this if they were reliant on DNA.

Kindest regards,

James
 
arg-fallbackName="Elshamah"/>
hackenslash said:
Jireh said:
The lack of detailed step-by-step evolutionary explanations for the origin of irreducible complexity is the result of the fact that irreducible complexity is fundamentally not evolvable by Darwinian evolution.

Umm, Müller still disagrees with you, and he demonstrated that this is bollocks even before any cretinist fuckwit got hold of the term 'irreducible complexity'. IC is a fucking result of evolution, you moron.

Oh, and only people with shit for brains talk about Darwinian evolution any more. We've moved on in the last 160 years. ;)


http://creationwiki.org/(Talk.Origins)_Some_systems_are_irreducibly_complex

and please show how multistep synthesis pathways could evolve, where multiple enzymes cannot be co-opted from other places, since they are used exclusively in given pathway, as for example the last 8 enzymes used in the chlorophyll biosynthesis pathway.
 
arg-fallbackName="Elshamah"/>
Dragan Glas said:
viruses store their genome as RNA - they could not do this if they were reliant on DNA.



James

Viruses are not alive, and cannot survive without a host cell. since they do not reproduce in the normal way, its hard to see how they could have gotten started.So they cannot preced living cells, upon which they depend.......Where they came from, is a enduring mystery for evolution. As many other things. I'd say , most things, since the whole concept of grandual change of all life, and living beings, is nonsense.
 
arg-fallbackName="Dragan Glas"/>
Greetings,
Elshamah said:
Dragan Glas said:
viruses store their genome as RNA - they could not do this if they were reliant on DNA.
Viruses are not alive, and cannot survive without a host cell. since they do not reproduce in the normal way, its hard to see how they could have gotten started.So they cannot preced living cells, upon which they depend.......Where they came from, is a enduring mystery for evolution. As many other things. I'd say , most things, since the whole concept of grandual change of all life, and living beings, is nonsense.
Viruses are "life" since they are organic in nature. Also, they can survive in the environment for very long periods of time until a suitable host arrives. The fact that RNA preceded DNA in evolutionary development is why viruses "got started" - they are a simpler form of life. You claim that they couldn't precede living cells, yet they did - through RNA.

Again, your dismissal of evolution is based on nothing more than a argument from ignorance/incredulity.

Have you nothing else to say about the rest of my post - or should I assume that you accept what I've said?!

Kindest regards,

James
 
arg-fallbackName="Rumraket"/>
Elshamah said:
Dragan Glas said:
viruses store their genome as RNA - they could not do this if they were reliant on DNA.

James
Viruses are not alive, and cannot survive without a host cell. since they do not reproduce in the normal way, its hard to see how they could have gotten started.
Completely and utterly irrelevant to what we are discussing, whether viruses should be considered alive or not, or how viruses came to exist in the first place.

We are arguing about whether RNA could serve as the information storage molecule of a cell. To do that it has to be stable enough that it doesn't spontaneously degrade at a higher rate than replication. Since viruses use RNA for their genomes, we know it is stable enough, since in viruses it DOES act as the genetic information storage molecule. It does not degrade in viruses, they manage to pass on their genes to their offspring, still in RNA form, without the information being degraded or lost.

So the problem is solved, we know that RNA can do DNA's job. Not as well as DNA does(which is why DNA evolved), but it is GOOD ENOUGH. Good enough to get the job done. That's it, that's all we need to know. We have concrete real-world evidence that RNA is capable of doing what is being hypothesized: Carry genetic information without degrading.

Additionally we have hard evidence from phylogenetics that the DNA synthesis and replication machineries are evolutionary additions to the basic ribonucleotide anabolism of the cell.
 
arg-fallbackName="Rumraket"/>
Elshamah said:
hackenslash said:
Umm, Müller still disagrees with you, and he demonstrated that this is bollocks even before any cretinist fuckwit got hold of the term 'irreducible complexity'. IC is a fucking result of evolution, you moron.

Oh, and only people with shit for brains talk about Darwinian evolution any more. We've moved on in the last 160 years. ;)


http://creationwiki.org/(Talk.Origins)_Some_systems_are_irreducibly_complex

and please show how multistep synthesis pathways could evolve, where multiple enzymes cannot be co-opted from other places, since they are used exclusively in given pathway, as for example the last 8 enzymes used in the chlorophyll biosynthesis pathway.
Gene duplication. Duplicate an already existing gene, then mutate it.

That's how the vitamin-C biosynthesis pathway evolved. It's a 10-step pathway, with 10 different enzymes catalyzing each step. But they all evolved from the same primordial protein that acted on Glucose, through gene-duplication. Multiple consecutive duplications over evolutionary time. Today the pathway has 10 steps, but it still starts with the enzyme that converts glucose, then it progrsesses through 10 steps that gradually evolved.

Today the pathway is irreducibly complex. Remove any single enzyme from the 10-step pathway and the host organism loses the ability to fully convert Glucose into Vitamin-C. Guess which organism has lost the 10th enzyme? That's right, you buddy.
 
arg-fallbackName="Elshamah"/>
Dragan Glas said:
Viruses are "life" since they are organic in nature. Also, they can survive in the environment for very long periods of time until a suitable host arrives. The fact that RNA preceded DNA in evolutionary development is why viruses "got started" - they are a simpler form of life.

James

A new chicken-and-egg paradox relating to the origin of life

http://www.uncommondescent.com/intelligent-design/do-viruses-help-explain-the-origin-of-life/

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

“In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?”

https://en.wikipedia.org/wiki/Reverse_transcriptase#In_eukaryotes

Creation of double-stranded DNA occurs in the cytosol as a series of these steps:

A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS
Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
A domain on the reverse transcriptase enzyme called RNAse H degrades the 5’ end of the RNA which removes the U5 and R region
The primer then ‘jumps’ to the 3’ end of the viral genome and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA
The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H
Once the strand is completed, second strand synthesis is initiated from the viral RNA
There is then another ‘jump’ where the PBS from the second strand hybridizes with the complementary PBS on the first strand
Both strands are extended further and can be incorporated into the hosts genome by the enzyme integrase

Creation of double-stranded DNA also involves strand transfer, in which there is a translocation of short DNA product from initial RNA dependent DNA synthesis to acceptor template regions at the other end of the genome, which are later reached and processed by the reverse transcriptase for its DNA-dependent DNA activity
 
arg-fallbackName="Rumraket"/>
Elshamah said:
Dragan Glas said:
Viruses are "life" since they are organic in nature. Also, they can survive in the environment for very long periods of time until a suitable host arrives. The fact that RNA preceded DNA in evolutionary development is why viruses "got started" - they are a simpler form of life.

James

A new chicken-and-egg paradox relating to the origin of life

http://www.uncommondescent.com/intelligent-design/do-viruses-help-explain-the-origin-of-life/

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.
... once again I'm speechless. There's so much wrong with this already at your first sentence.

Extant theory goes that cells coevoled with viruses right from the beginning, and that at first there were probably nothing like cells as we know them, genetics started as a host of selfish genetic elements being driven by a geochemical metabolic cycle. Also, since the first bona-fide genomes were probably based on RNA(and no, that RNA was not miraculously synthesized in some lucky organic soup), they didn't need reverse transcriptase to begin with. Reverse transcriptase is basically another polymerase, so it most probably evolved from an RNA polymerase.
 
arg-fallbackName="Dragan Glas"/>
Greetings,

Elshamah, would you kindly use the QUOTE feature so as to distinguish between your quoting of others and your own words - it's confusing and irritating to have to identify them ourselves.
Elshamah said:
Dragan Glas said:
Viruses are "life" since they are organic in nature. Also, they can survive in the environment for very long periods of time until a suitable host arrives. The fact that RNA preceded DNA in evolutionary development is why viruses "got started" - they are a simpler form of life.

James
A new chicken-and-egg paradox relating to the origin of life

http://www.uncommondescent.com/intelligent-design/do-viruses-help-explain-the-origin-of-life/

Cells could not have evolved without viruses, as they need reverse transcriptase (which is found only in viruses) in order to move from RNA to DNA.

In other words, instead of helping to solve the problem of the origin of life on Earth, recent research has only served to highlight one of its central paradoxes. And yet the science media reports the latest discoveries as if the solution is just around the corner. Don’t you find that just a little strange?

“In order to move from RNA to DNA, you need an enzyme called reverse transcriptase,” Dolja said. “It’s only found in viruses like HIV, not in cells. So how could cells begin to use DNA without the help of a virus?”
What, at first glance, appears to be your thoughts/words, are in fact a selective copy/paste from the article, which makes it look as if these separate groups of sentences are contiguous, giving a false impression. They're not.

Viruses are what we call RNA-based genomes that invade DNA-based genomes - if they don't invade DNA-based genomes, they're just RNA-based genomes.

As the article notes:
In a 2012 study in the journal BMC Evolutionary Biology (12:156, doi:10.1186/1471-2148-12-156), Gustavo Caetano-Anolles, a bioinformatics specialist at the University of Illinois, Urbana-Champaign, traced the evolutionary history of proteins occurring in several giant viruses and concluded that these viruses “represent a form of life that either predated or coexisted with the last universal common ancestor,” an organism which is estimated to have lived some 3.5 to 3.8 billion years ago.

[...]

Harvard biochemist Jack Szostak offers a more cautious interpretation of the evidence: although he is willing to accept that parasitic genetic elements (bits of genetic material that use other bits in order to make copies of themselves) may have existed on Earth before cells, he nonetheless insists that true viruses only emerged after cellular organisms did. In her report for Quanta magazine, Carrie Arnold highlights the disagreement between the two camps:

"Whenever you mix a bunch of small RNA molecules together, you get a bunch of parasitic sequences that aren’t good at anything except making copies of themselves faster than anything else,” Szostak said. For these sequences to become similar to modern viruses, they need to parasitize a living cell, not just another strand of RNA."
Your quoting of Dolja's reference to HIV is misleading, as the virus which causes it comes from our relatives - chimpanzees (through contact with infected blood whilst butchering them for "bushmeat") - who contracted SIV from species of monkeys upon which they, in their turn, predated. In other words. from other DNA-based genomes - not directly from independent RNA-based organisms.

You could read The evolution of HIV-1 and the origin of AIDS or, if you prefer, watch the following video by C0nc0rdance, who summarises the relevant research:



[We also have the usual abuse/misuse of probability based on a argument from ignorance/incredulity where Koonin tosses out a vastly improbable number for the evolution of RNA - confusing this with biogenesis.]
Elshamah said:
https://en.wikipedia.org/wiki/Reverse_transcriptase#In_eukaryotes

Creation of double-stranded DNA occurs in the cytosol as a series of these steps:

A specific cellular tRNA acts as a primer and hybridizes to a complementary part of the virus RNA genome called the primer binding site or PBS
Complementary DNA then binds to the U5 (non-coding region) and R region (a direct repeat found at both ends of the RNA molecule) of the viral RNA
A domain on the reverse transcriptase enzyme called RNAse H degrades the 5’ end of the RNA which removes the U5 and R region
The primer then ‘jumps’ to the 3’ end of the viral genome and the newly synthesised DNA strands hybridizes to the complementary R region on the RNA
The first strand of complementary DNA (cDNA) is extended and the majority of viral RNA is degraded by RNAse H
Once the strand is completed, second strand synthesis is initiated from the viral RNA
There is then another ‘jump’ where the PBS from the second strand hybridizes with the complementary PBS on the first strand
Both strands are extended further and can be incorporated into the hosts genome by the enzyme integrase

Creation of double-stranded DNA also involves strand transfer, in which there is a translocation of short DNA product from initial RNA dependent DNA synthesis to acceptor template regions at the other end of the genome, which are later reached and processed by the reverse transcriptase for its DNA-dependent DNA activity
Again, I'm not sure what you intend with this copy/paste?!

Kindest regards,

James
 
arg-fallbackName="Elshamah"/>
Rumraket said:
genetics started as a host of selfish genetic elements being driven by a geochemical metabolic cycle..

please explain this geochemical metabolic cycle. How did that happen ?
 
arg-fallbackName="Rumraket"/>
Elshamah said:
Rumraket said:
genetics started as a host of selfish genetic elements being driven by a geochemical metabolic cycle..

please explain this geochemical metabolic cycle. How did that happen ?
Well as I said, this is speculation so it's not like this is really known to any great degree of certainty. But here's the model:

http://www.nick-lane.net/Sousa et al Phil Trans.pdf
Early bioenergetic evolution
Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO[sub]2[/sub] reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.
 
arg-fallbackName="Elshamah"/>
Rumraket said:
Well as I said, this is speculation so it's not like this is really known to any great degree of certainty. But here's the model:


Abstract
Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood-Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent-ocean interface via the ATP synthase, (iii) harnessing of Na(+) gradients generated by H(+)/Na(+) antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO[sub]2[/sub] reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type 'reduced iron → reduced carbon' at the beginning of bioenergetic evolution.


well, Nick Lane deals with the main issue of how energy was provided to the cell. I have shown already, that the approach is interesting, but antiporters are far from simple. And the recruitment of RNA to make the antiportes is a impossible task.

and there are further problems :

http://www.csj.jp/journals/bcsj/bc-cont/b12may/85_20110349.html

Submarine hydrothermal systems (SHSs) have been thought of as a suitable environment for the origin of life subsequent to the abiotic synthesis of organic molecules. However, it has been pointed out that bioorganic molecules, such as amino acids, are easily degraded at a high temperature, and thus not likely to survive for the next step of chemical evolution in a SHS environment.

and even if you like his proposal, you are arguing that RNA came before DNA, so, i think you dont even know that you propose a RNA world scenario as well.
 
arg-fallbackName="Dragan Glas"/>
Greetings,
Elshamah said:
Rumraket said:
Well as I said, this is speculation so it's not like this is really known to any great degree of certainty. But here's the model:
well, Nick Lane deals with the main issue of how energy was provided to the cell. I have shown already, that the approach is interesting, but antiporters are far from simple. And the recruitment of RNA to make the antiportes is a impossible task.
Would you kindly explain how it's "a impossible task"?
Elshamah said:
and there are further problems :

http://www.csj.jp/journals/bcsj/bc-cont/b12may/85_20110349.html

Submarine hydrothermal systems (SHSs) have been thought of as a suitable environment for the origin of life subsequent to the abiotic synthesis of organic molecules. However, it has been pointed out that bioorganic molecules, such as amino acids, are easily degraded at a high temperature, and thus not likely to survive for the next step of chemical evolution in a SHS environment.
Only for "black smokers", not other SHS where temperatures are at acceptable levels for amino acids to form/survive.
Elshamah said:
and even if you like his proposal, you are arguing that RNA came before DNA, so, i think you dont even know that you propose a RNA world scenario as well.
RNA came before DNA - that's the scientific position.

If you'd read the paper I posted for you earlier, as well as Lane's paper, you wouldn't be arguing against this.

Kindest regards,

James
 
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