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Alicia Cartelli on Abiogenesis

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Please see the note and apology at the end of this post.

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Over on a recent thread Alicia Cartelli responded to my request that if she had “an idea how abiogenesis works” I would post it as a head post for discussion.

I have not yet had time to parse through all this, other than to note that most of what Alicia discusses below was already granted for discussion purposes in my Abiogenesis Challenge. Thus, even if we were to grant the very questionable and optimistic claims, it still does not address the central issues needed for the origin of life, including the issue of information content.

That said, I appreciate Alicia taking time to put together the below and would invite commenters to weigh in, both with respect to the evidentiary claims made, as well as the relevance to a materialistic origins scenario.

The language below is directly from Alicia, although I have added paragraph numbers to allow comments to focus on particular claims and to facilitate discussion.

—–

Alicia Cartelli:

Here’s a very brief overview of the basic supporting work done on abiogenesis and I have taken it a step further for EA at the end and talk briefly about a simplified example of the evolution of the first living organism. Enjoy.

1. Miller-Urey demonstrated that methane, ammonia, and hydrogen gases in a highly favorable early earth model could produce cyanide, formaldehyde, and amino acids. Subsequent studies demonstrated similar results in more realistic models. Amino acids are repeatedly produced by early earth models and have also been found in meteorites. Mimicking volcanic gases flowing through rock crevices produces amino acids and in fact, it tends to produce some of the natural amino acids over the other, unnatural residues. UV light in early earth models produce aldehydes, which are still important intermediates in amino acid synthesis. Polymerization of amino acids, although unfavorable, can be driven by certain conditions. Simply through energy input in the presence of minerals, researchers have demonstrated the formation of protein polymers. We have also observed amino acid polymerization at hydrothermal vents. Amino acids in cooler water have been shown to polymerize when carbon and sulfur-containing gases (commonly ejected by hydrothermal vents) are also present.

2. Important reactants have been hypothesized to accumulate on layers of mineral deposits in the early earth environment; dissolved gases are attracted to these minerals which helps to concentrate them to drive chemical reactions. The minerals function as catalysts as they are reactive in solution and their importance can still be seen at the active site of many enzymes today.

3. The production of acetic acid from dissolved carbon dioxide and hydrogen is spontaneous and still used today by bacteria. Acetic acid is also an important intermediate in the pathway that produces acetyl-CoA, a molecule still used by all living organisms. Recent research has shown that a variety of larger organic molecules can be produced by early earth models, including those important to the eventual synthesis of nucleotides.

4. Free radical production is much more likely in the early earth atmosphere, where there is no ozone layer. Free radicals are highly reactive and computer models have demonstrated the formation of formaldehyde through these types of reactions. In the presence of heat or UV radiation, formaldehyde molecules are able to link together, forming more complicated organic molecules such as sugars. Both 5- and 6-carbon sugars are produced in these models and other studies have shown that enrichment of the 5-carbon sugars occurs on minerals outside of hydrothermal vents. 3-carbon ketoses and other molecules related to sugars have also been found in meteorites.

5. Hydrogen cyanide was also likely produced in the early earth atmosphere as shown in Miller-Urey, and it is an important precursor for nucleic base production. Early earth atmospheric models eventually led to the production of all five nucleic bases. Prebiotic simulations have demonstrated activation of nucleotides through addition of phosphate groups, and further studies have shown that these nucleotides can polymerize in the presence of minerals. Even without nucleotide activation, polymerization of nucleic acids over 90 bases long has been demonstrated to occur when both heat and small lipids are included.

6. Recent studies have shown that, starting with a ribozyme capable of joining two ribonucleotides together, random mutations and copying produces ribozymes capable of replication activity. This enzyme is now capable of using itself as a template, to copy fragments of itself. Other studies have demonstrated molecular evolution by starting with random pools of nucleic acids and selection of nucleic acids that connect uracil base to ribose sugar. After 11 rounds of selection, the ribozyme population was 1,000,000x better at catalyzing the reaction in comparison to the uncatalyzed reaction. Numerous other studies have produced ribozymes with a host of different catalytic activities.

7. Simple lipids have been produced through early earth model systems using hydrogen, carbon dioxide and mineral catalysts. Lipids with amphipathic properties have also been discovered in meteorites. These molecules form simple membrane structures spontaneously due to the hydrophobic effect and provide an environment more suitable for life inside the first protocells. These early cell membranes provide the ability to concentrate reactants and protect products of chemical reactions. Membrane permeability of small molecules can be altered by simple proteins that span the hydrophobic layer and also by temperature changes. Simple vesicles can join together, in essence “growing” and vibrations of the surrounding media can cause them to replicate. Ions and ribonucleotides are known to diffuse through fatty acid membranes and the formation of these membranes is facilitated by minerals as well.

8. It is hypothesized that the first replicating molecule did not consist of RNA, but instead was made up of simpler nucleic acids, which consisted of simpler nucleotide molecules. Nucleic acid-polypeptide hybrid molecules have been proposed, in which nucleic bases are connected by peptide bonds instead of phosphodiester bonds. These simpler molecules are capable of both catalytic activity and acting as a template; and their ability to direct synthesis of RNA as we know it today has been demonstrated, as they have similar 3D geometries. This would allow for evolution from a pre-RNA world to an RNA world. The catalytic repertoire of ribozymes seen in nature today is quite small, however synthetic ribozymes have demonstrated a wide variety of reactions, even rivaling proteins. The distinction between proteinaceous enzymes and ribozymes seems to be the efficiency with which they catalyze reactions, not the range of possible reactions. The ability of ribozymes to catalyze their own replication has been demonstrated, but only in fragments. Ribozymes able to ligate short nucleotide strands, which has already been demonstrated, would piece these fragments together, producing more replicating ribozymes. The efficiency of this ligation reaction would be increased by containing the replicating ribozyme and nucleic acid fragments within a membrane consisting of fatty acids or some derivative of these amphipathic molecules. This would be the first living cell.

9. Sealing these ribozymes into protocells allows for evolution of these first organisms based on not just structure of subcellular components, but also how these components interact with each other. Replication of these protocells would be driven by physical agitation, unevenly splitting the intracellular components into new protocells and providing more variation for selection to act on.

10. Experiments have demonstrated that selection from pools of random RNA molecules can produce RNA polymers that bind tightly to amino acids. These RNA molecules tend to have sequences identical to the codons still used by today’s translational system. This shows the potential for a limited genetic code, of which the remnants cans still be seen today. Synthetic ribozymes have been shown to catalyze tRNA charging, moving the early translational system closer to the more efficient system seen today. Evolution of this early translational system would make protein synthesis more efficient and eventually lead to a protein-dominated world.

—–

EA Note for Readers:

I was away from UD for several weeks and just this week realized that the above post was still in my “Drafts” section in my UD Dashboard, with a date stamp of November 24, 2015. I did not get time to review Alicia’s discussion as I had hoped, and then forgot I hadn’t published this, in between the Thanksgiving trip with the in-laws, various obligations in early December and then Christmas and New Year’s.

My sincere apologies to Alicia for the long delay. Alicia, if there is anything you would like to add to your description, having had a few additional weeks to think about it, please let me know and I will add it to your above description.

Comments
Eric Anderson: [EA] We missed your comments, and have no idea when you made them. Should we monitor edits to our own posts? Eric Anderson: [EA: No, they cannot, at least it has never been demonstrated. This is a false claim.] We presume you will call for the retraction of Robertson & Joyce, Highly Efficient Self-Replicating RNA Enzymes, Cell Chemical Biology 2014? The environment is highly contrived, but nonetheless, they do self-replicate, and furthermore, they experience darwinian evolution. Eric Anderson: [EA: Note comments 57 and 58.] @57 is on our ignore list. As for @58 and the Timmer article you quote from, the fact that RNA can transcribe other RNA sequences is an entailment of RNA World theory, though short of being an actual self-replicator. Eric Anderson: [EA: This is a false claim, based on false premises and a questionable conclusion.] Waving your hands doesn't make the evidence go away. That RNA can transcribe RNA sequences is an entailment of RNA World. While insufficient to "prove" self-replication, it is an entailment. And notably, the reason why abiogenesis is taken seriously is because scientists can propose and test just these sorts of hypotheses — unlike ID, which neither proposes nor tests any entailments that derive from the proposition of intelligent design.Zachriel
January 25, 2016
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Abiogenetic research has found experimental support, such as the discovery of ribozymes, complex molecules can spontaneously form, random RNA sequences having catalytic function, molecular evolution, and evidence of RNA replication.
That's like saying that a natural origin for Stonehenge has found experimental support in the natural formation of different types of stone, floods and glaciers carrying and depositing heavy stones, erosion, etc.Virgil Cain
January 23, 2016
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Mung: And RNA can fold on itself, so any linear sequential copying mechanism would require something to cause it to unfold and keep it unfolded. That seems to be the current limitation of RNA transcription. Do you think a companion ribozyme might be capable disrupting the folding process?Zachriel
January 23, 2016
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And RNA can fold on itself, so any linear sequential copying mechanism would require something to cause it to unfold and keep it unfolded.Mung
January 23, 2016
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Phinehas: I only said I wouldn’t rule out that it’s possible. That’s hardly the same thing as ruling it in. Frankly, I don’t know whether it is possible or not. RNA can self-replicate in contrived situations [EA: No, they cannot, at least it has never been demonstrated. This is a false claim.], and can partially transcribe long sequences from nucleoside triphosphate substrates [EA: Note comments 57 and 58.], so the evidence indicates that RNA or an RNA network can self-replicate under some conditions.[EA: This is a false claim, based on false premises and a questionable conclusion.] Whether this is consistent with plausible primordial conditions is another question. [EA: This statement, at least, is quite correct. And any rational view of primordial conditions says "no."] Phinehas: They might just as well study how water can turn into wine through natural processes. Abiogenetic research has found experimental support, such as the discovery of ribozymes, complex molecules can spontaneously form, random RNA sequences having catalytic function, molecular evolution, and evidence of RNA replication. Lucky guesses?Zachriel
January 23, 2016
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All materialists are math challenged. They have a hard time understanding very simple math. The combinatorial explosion kills any stochastic search mechanism dead. End of debate. Liddle and the rest are obviously clueless. They either need to take a remedial math class or they are blinded by their blind faith in their stupid religion.Mapou
January 22, 2016
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Consider a cell capable of producing a like copy of itself. Does it have a membrane? (Yeah, I know, stupid question.)Mung
January 22, 2016
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A bubble would be the opposite of a cell membrane, Mungy. But it's funny you mention soap because lipids and soap are actually very closely related. Google saponification. Class dismissed.Alicia Cartelli
January 22, 2016
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Consider a cell capable of producing a like copy of itself.Mung
January 22, 2016
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Alicia Cartelli: I presented some of the simplest supporting evidence for abiogenesis... Soap bubbles therefore cell membranes?Mung
January 22, 2016
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Alicia
I presented some of the simplest supporting evidence for abiogenesis and proposed a very basic system for “how life began,” as your original challenge asked for.
Except for being untestable and evidence-free, you did good.
We are all still learning, but I’d put money on the fact that I have a much better understanding of abiogenesis, it’s problems, and biology in general than you and most people here.
I will take that bet.Virgil Cain
January 22, 2016
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Zachriel:
It was self-replicating RNA,
LIAR. Joyce and Lincoln showed a self-sustained replication of RNAs. They did not show self-replicating RNAs. The experiment required two RNAs one for a template and one for a catalyst, along with many other smaller RNAs that just needed to have one bond created to complete the replication.Virgil Cain
January 22, 2016
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1 In the beginning Chance created the heavens and the earth. 3 And Chance said, “Let there be light,” and there was light...
I don't present the above as parody. I really think if you just did a search and replace on Genesis 1, some of the posters here would end up having no issue with it. Clearly, Chance can do whatever God can, or so the belief would appear to claim.Phinehas
January 22, 2016
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Z:
Mung: You may as well say the origin of the first self-replicator was a miracle. Z: Researchers are studying how such an event could have occurred through natural processes.
They might just as well study how water can turn into wine through natural processes. At some point, the highly improbable is indistinguishable from a miracle (aside from the supernatural vs. natural red herring). Mung has it exactly right. Those who believe in abiogenesis appear to be demonstrating at least as much faith as those who believe in God. This starts to become so strikingly apparent in exchanges like the above that I really can't fathom why you don't just go ahead and have done with it and re-label "chance" as "god." I honestly can't see a difference.Phinehas
January 22, 2016
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EA, I presented some of the simplest supporting evidence for abiogenesis and proposed a very basic system for “how life began,” as your original challenge asked for. If you have specific problems with what I said, then tell me. Specifically. The racemic question is not a problem at this stage in abiogenesis. When early ribosome-like molecules began to evolve is when I would assume the selection of L-amino acids was fixed in our molecular ancestors. Fitness doesn’t change. It’s still the ability to survive and reproduce. Preferential binding of amino acids by certain RNA sequences/structures is certainly a direct link between nucleic acid sequence and amino acid sequence. The evolution of the translational system would then build on this and we can still see it in the system today. We are all still learning, but I’d put money on the fact that I have a much better understanding of abiogenesis, it’s problems, and biology in general than you and most people here.Alicia Cartelli
January 22, 2016
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Z:
So it’s possible...
Whoa there Nellie. I only said I wouldn't rule out that it's possible. That's hardly the same thing as ruling it in. Frankly, I don't know whether it is possible or not.Phinehas
January 22, 2016
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Eric Anderson: You have been going on and on about this alleged self-replicating molecule and I have repeatedly asked for evidence, even going so far as to warn you that Joyce doesn’t cut it. That's called handwaving. To refute Joyce, you have to point to specifics. That the enzyme and its substrates are contrived is important to note, but doesn't undermine the claim that it constitutes evidence that self-replication is possible. EA: Joyce did not demonstrate a self-replicating molecule. Please stop posting false claims and insinuations. I would also note that it is you who is claiming evidence for your theory. You need to provide evidence, with explanations. Literature bluffs do not cut it. Eric Anderson: Joyce did not demonstrate a self-replicating RNA molecule, not even in the lab, and certainly nothing that would have any chance of working in the real world. It was self-replicating RNA, though the substrates were contrived. Transcription of long sequences from more basic nucleoside triphosphate substrates is demonstrated by Wochner et al., Ribozyme-Catalyzed Transcription of an Active Ribozyme, Science 2011. EA: By "contrived" you presumably mean pre-made, pre-selected, place in close proximity without significant risk of interfering cross reactions. In other words most definitely not self-replicating. Furthermore, as I have pointed out several times, even if they had been able to produce a self-replicating molecule in the lab, which they didn't, it would have essentially no chance of functioning in the real world. Eric Anderson: Either ... or Or you might try to actually respond rather than flailing your hands.Zachriel
January 22, 2016
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Zachriel: Fair warning: I am close to the end of my patience here. I have never, to my recollection, ever SNIPed or censored anyone's comments on any of my OP's, but you are very close to the line. You have been going on and on about this alleged self-replicating molecule and I have repeatedly asked for evidence, even going so far as to warn you that Joyce doesn't cut it. What do you do? Throw out a citation to Joyce, without any further explanation or discussion. Citation bluffs are not welcome and are a sign of dishonest debate. Joyce did not demonstrate a self-replicating RNA molecule, not even in the lab, and certainly nothing that would have any chance of working in the real world. Either you don't know what his studies showed or you are being intellectually dishonest. You have two options: Either come up with some actual evidence: with a description of the study, what was performed, how it was done, and how the results demonstrate the existence of a self-replicating molecule supportive of abiogenesis. or Stop posting about this topic on this thread.Eric Anderson
January 21, 2016
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however, the evidence, such as from ribosomes, supports some sort of RNA World preceding DNA World.
Neither ribosomes nor ribozymes support a RNA world. You are either gullible or dishonest and the record already has you being dishonest.
You asked for specifics
And you FAILed to provide any.Virgil Cain
January 21, 2016
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Eric Anderson: The question is whether materialistic abiogenesis holds water. So far you haven’t given us any reason to think it can. Well, there's no workable theory of abiogenesis, if that is what you mean; however, the evidence, such as from ribosomes, supports some sort of RNA World preceding DNA World. Eric Anderson: you don’t have any evidence that RNA can self-replicate. You asked for specifics, then wave your hands in reply.Zachriel
January 21, 2016
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There is no evidence of Intelligent Design with regards to abiogenesis,
Intelligent Design: Required by Biological Life? and then there is the fact that basic biological reproduction is irreducibly complex: The cell division processes required for bacterial life. And that level of IC is as good of evidence for the Intelligent Design of life as Eddington's work circa 1919 was for Einstein's theory.
Lincoln & Joyce, Self-Sustained Replication of an RNA Enzyme, Science 2009.
That was not evidence for a self-replicating RNA. Obviously you have something wrong with your integrity file. But thank you as you are a fine example of the dishonesty of our opponents.Virgil Cain
January 21, 2016
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Why are you bringing up intelligent design? The question is whether materialistic abiogenesis holds water. So far you haven't given us any reason to think it can. We can discuss evidence for intelligent design at another time in another thread. ----- Oh, boy. You really need to read the Joyce work more carefully. As I thought, you don't have any evidence that RNA can self-replicate. Please stop referring to made-up hypothetical entities as though they are some kind of a step along the way toward your creation story. Until you have some evidence that such a thing can exist and function in the real world, don't keep trotting it out. You might as well ask us to believe in pixies and fairy dust. Your "entailment" you keep referring to is dead. So is your theory.Eric Anderson
January 21, 2016
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Eric Anderson: No, it refers to people, including you, who reject a priori an answer outside of purely material causes. We are not a materialist, nor do we reject a priori non-material causes. However, for a claim to have scientific validity, it must be a coherent hypothesis with entailments that can be tested. There is no evidence of Intelligent Design with regards to abiogenesis, nor is there any proposed research program to understand how such an event could have occurred. Eric Anderson: Can you provide any evidence showing that RNA can self-replicate in a real world environment such as might be required for abiogenesis? The immediate entailment, can RNA self-replicate?, includes contrived situations. See Sczepanski & Joyce, A cross-chiral RNA polymerase ribozyme, Nature 2014; Lincoln & Joyce, Self-Sustained Replication of an RNA Enzyme, Science 2009.Zachriel
January 21, 2016
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Thanks, Virgil. This part of the article you cited is worth noting:
It's great progress, but the result still comes far short of a molecule that can copy itself. For one thing, the ribozyme tended to stop short of the end of the molecule it was copying, mostly because the two fell out of contact. The authors could tether the two RNA molecules (the ribozyme and the template it was copying) together, which improved matters but didn't solve the problem entirely. The second problem was the fact that the molecule being copied folded over and formed base pairs with itself, which prevented the ribozyme from copying through the folded structure. This creates a serious problem since the activity of the ribozyme depends on it being able to fold into a three-dimensional structure—which creates a bit of a chicken-and-egg problem for making a self-replicating ribozyme.
A chicken-and-egg problem. You'd better believe it. At multiple levels. The conceptual problem for true believers, like Zachriel, is they see some research that is making "progress" and think it shows that a solution to this or that abiogenesis stumbling block is right around the corner. In fact, a more objective reading of the literature and a more careful view of the science is that researchers are continuing to confirm just how difficult and unlikely it is that something like a self-replicating molecule would form and be able to exist in the real world. The true believers read the "it's great progress" part of the articles and don't critically think through the realities.Eric Anderson
January 21, 2016
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Methinks Zachriel is confusing the Lincoln/ Joyce of experiment that showed a self-sustained replication of RNAs that involved a RNA template and a RNA catalyst with self-replication. See also: RNA can't copy itself, but can copy over 200 bases of other RNAsVirgil Cain
January 21, 2016
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First, you use the term “materialists” to refer to biologists who are studying abiogenesis. Second, of course they have looked very skeptically at every proposed theory, including RNA-first.
No, it refers to people, including you, who reject a priori an answer outside of purely material causes. And those who have looked at RNA World objectively have found it very wanting.
There have been many experiments showing the feasibility of RNA self-replication.
You keep saying this -- over and over. Can you provide any evidence showing that RNA can self-replicate in a real world environment such as might be required for abiogenesis? Note, for the umpteenth time: you just saying it does not count.Eric Anderson
January 21, 2016
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The primary evidence comes from molecular phylogeny, as well as the microbiology of ribosomes.
Molecular phylogeny assumes common descent is true. It does not and cannot demonstrate it is. The same goes for the microbiology of ribosomes.
RNA self-replication is an entailment of RNA World.
Of course it is. However there isn't any evidence for a RNA world and no way to test the claim that purely physicochemical processes can produce replicating RNAs capable of evolution.Virgil Cain
January 21, 2016
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praxeology: Calcium carbonate only forms biogenetically. NASA would disagree. "Carbonate rocks on Earth are formed in two ways: through a purely chemical process or via the action of living things. Both means require liquid water." http://science.nasa.gov/science-news/science-at-nasa/2001/ast04feb_1/ As would most chemists. See Morse, Arvidson & Lüttge, Calcium Carbonate Formation and Dissolution, Chemical Reviews 2007: "Over the history of the Earth, the primary source of marine carbonate minerals has shifted from abiotic precipitation to biogenic sources." Furthermore, carbonates have been discovered on Mars. Per your view, this would mean life has been discovered; however, scientists consider carbonate formation to be a natural occurrence in the presence of water. praxeology: Bada also added ferrous iron as a reducing agent So? Ferrous iron (Fe2+) is naturally occurring. It's even found in meteorites. praxeology: Interesting from the standpoint of investigator interference, but hardly worth celebrating as a breakthrough in abiogenesis. The natural genesis of complex molecules is an entailment of abiogenetic theory, but alone is hardly conclusive evidence. Mung: You may as well say the origin of the first self-replicator was a miracle. Researchers are studying how such an event could have occurred through natural processes. Mung: How is your theory of the origin of the one and only self-replicator any different from magic or goddidit? At this point, there is no complete theory, just a speculative hypothesis with some tentative evidence pointing the way. Mung: If scientists manage to create a self-replicator in the lab will this falsify your one and only one theory, or will you just claim that the scientifically designed replicator could never have happened in the natural world? It would be a confirmation of an entailment of RNA World, but alone would hardly be conclusive evidence. Eric Anderson: How can you possibly know, or even have “evidence that supports” what came before LUCA? The primary evidence comes from molecular phylogeny, as well as the microbiology of ribosomes. Eric Anderson: Just one that most materialists have never even thought to ask because it goes against the very heart of their creation story. That's silly. First, you use the term "materialists" to refer to biologists who are studying abiogenesis. Second, of course they have looked very skeptically at every proposed theory, including RNA-first. Eric Anderson: And yes, the results to date are indeed trivial — certainly in the context of what is required for abiogenesis. You have a very strange definition of "trivial". RNA self-replication is an entailment of RNA World. There is evidence that RNA can self-replicate, so that is support for the theory. There have been many experiments showing the feasibility of RNA self-replication.Zachriel
January 21, 2016
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The LUCA is posited to be highly derived from the first life, and the evidence supports horizontal mechanisms at play before the LUCA.
This is pure nonsense. How can you possibly know, or even have "evidence that supports" what came before LUCA? What you probably mean is that some theorists speculate such-and-such.
The most likely case, based on current understanding, is that life arose once, but that it diversified rapidly into an ecosystem of many different types of organisms that had low thresholds for individual identity.
This is just a made-up story.
That’s not the question, but whether it is possible for RNA to self-replicate.
Actually, it is an additional important question. Just one that most materialists have never even thought to ask because it goes against the very heart of their creation story. Many can't even get their head around the possibility that their creation story might be mistaken, so these kinds of foundational questions don't even enter their minds.
We know that RNA can self-catalyze, including partial sequence replication, and also replicate in highly contrived situations. These results are hardly trivial . . .
I hope you're not referring to Joyce et al. Please let me know what evidence you have for this alleged self-replication. And yes, the results to date are indeed trivial -- certainly in the context of what is required for abiogenesis. This despite decades of concerted effort and millions of dollars spent.Eric Anderson
January 20, 2016
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Zachriel: The evidence doesn’t support independent origins. Ah. So now you want to talk evidence, or the lack thereof. You may as well say the origin of the first self-replicator was a miracle. THE ONE. How is your theory of the origin of the one and only self-replicator any different from magic or goddidit? If scientists manage to create a self-replicator in the lab will this falsify your one and only one theory, or will you just claim that the scientifically designed replicator could never have happened in the natural world?Mung
January 20, 2016
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