Chemistry Origin Of Life

Alicia Cartelli on Abiogenesis

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

—–

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.

81 Replies to “Alicia Cartelli on Abiogenesis

  1. 1
    Mung says:

    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.

    So?

    These molecules form simple membrane structures spontaneously due to the hydrophobic effect and provide an environment more suitable for life inside the first protocells.

    From lipids to membranes to protocells with a flick of the magic wand.

    These early cell membranes provide the ability to concentrate reactants and protect products of chemical reactions.

    Sadly, early cell membranes are not produced by the imagination.

    Membrane permeability of small molecules can be altered by simple proteins that span the hydrophobic layer and also by temperature changes.

    Poof a membrane protein into existence. Just one.

    Simple vesicles can join together, in essence “growing” and vibrations of the surrounding media can cause them to replicate.

    Nothing like what happens with a real cell.

    Spin a tale
    A tale of creation
    It cannot fail
    A magic libation

  2. 2
    Mung says:

    Magic up a cell membrane for us Alicia.

    I bet you can do better than the Protocells: Bridging Nonliving and Living Matter book.

    I bet you’ve read this book, you know, what with you being the resident expert and all on cell membranes:

    Membrane Structural Biology: With Biochemical and Biophysical Foundations

  3. 3
    Jim Smith says:

    How about putting some numbers behind the theory?

    What are the rates of all these chemical reactions? What are the total amounts of and concentrations of reactants that would be available? How much time it would take for life to arise? And don’t forget the inhibiting effects of other molecules present on the rates of reactions.

    I realize this is a hard thing to do but someone could take a rough stab by making some assumptions or working out parts that are most open to modeling. It would create a starting point for discussion.

    Anything is probable given enough time and probabilistic resources. But was there enough time and were there enough resources? The intelligent design researchers calculate “No.” Arguing chemistry without considering the rates of reaction is open to the criticism that it is a “just so story”. Why not produce a real theory, a mathematical theory, that can be falsified?

  4. 4
    OldArmy94 says:

    Where is the information?

  5. 5
    RexTugwell says:

    This article showed a certain plausibility of abiogenesis until I read the following:

    “1. Miller-Urey demonstrated”

  6. 6

    Jim Smith @3:

    That it is possible that matter not directed by intelligence could have done a thing they imagine is all that is necessary to satisfy a Darwinist. The probabilities are irrelevant.

  7. 7
    EvilSnack says:

    WJM @ 6:

    And remember that “could have” only means “we’re not aware of any physical law stopping it”.

  8. 8
    Mung says:

    This might be an appropriate thread to discuss this article at ENV.

    An “Exquisitely Designed” Enzyme that Maintains DNA Building Blocks

    Silly me. I guess for some reason I thought that the molecules needed for DNA and RNA just came in across Alicia’s magical membrane already pre-made and also were magically prohibited from leaving back across that membrane.

    Now I read about a system of manufacture and balance within the cell. Perhaps that system pre-existed the cell membrane itself and just magically got enclosed inside it when the first cells were first formed.

  9. 9
    smordecai says:

    All of the elements necessary to build my 1994 Lincoln Mark VIII occur naturally, therefore given enough time…

  10. 10
    Mung says:

    Ribonucleotide reduction is the only pathway for de novo synthesis of deoxyribonucleotides in extant organisms. This chemically demanding reaction, which proceeds via a carbon-centered free radical, is catalyzed by ribonucleotide reductase (RNR). The mechanism has been deemed unlikely to be catalyzed by a ribozyme, creating an enigma regarding how the building blocks for DNA were synthesized at the transition from RNA to DNA-encoded genomes.

    The Origin and Evolution of Ribonucleotide Reduction

    https://en.wikipedia.org/wiki/Ribonucleotide_reductase

  11. 11
    Alicia Cartelli says:

    I did not respond to the challenge so that you could “post it as a head post for discussion,” EA. I simply wanted to lay out some of the basic supporting evidence behind abiogenesis (to clarify that you did not have to allow for most of the concessions that you did) and also to come up with a theoretical “first living thing”, as the challenge asked. All I wanted in return was for you to rebut at least a single thing I had said.
    And here we are, almost two months later, still waiting for your response.

  12. 12
    Mung says:

    What’s the proper way to rebut handwaving, Alicia?

  13. 13
    Eric Anderson says:

    Alicia:

    Thank you for the clarification. So it leads me to wonder what your primary point is. I presume you aren’t suggesting that, even with my many concessions, that an answer for abiogenesis is close at hand. So are you simply trying to show that lots of work has been done on abiogenesis? I certainly agree. Are you suggesting that all the things I’ve listed in my concessions have been worked out already, or just that some progress (conveniently undefined) has been made?

    If all you are saying is that lots of people have been working really hard on abiogenesis and that they have lots of ideas and speculations, then great, we are in agreement.

    On the other hand, if you are suggesting that what you have posted somehow eliminates the need for my concessions, then you need to both read my challenge more carefully and to follow the science a little more closely.

    I’m not going to go through all of these, but just to start at the top, I said “I’m willing to grant you all the amino acids you want. I’ll even give them all to you in a non-racemic mixture. You want them all left-handed? No problem. I’ll also grant you the exact relative mixture of the specific amino acids you want (what percentage do you want of glycine, alanine, arginine, etc.?). I’ll further give you just the right concentration to encourage optimum reaction.”

    Your response in #1 was that amino acids can be produced “by certain conditions,” that amino acids have been found in meteorites, and so on. Agreed. And big deal.

    What I conceded was so far beyond that, that your response barely scratched the surface. You haven’t addressed the racemic question, relative abundance, or favorable concentration levels, just to name three specific concessions I made.

    Then you go on in later paragraphs to talk about hypothetical things like self-replicating molecules and protocells.

    Again, I don’t dispute that researchers have a host of wild ideas and speculations. The question is whether any of them can pan out. And for OOL more specifically, even if all the wild speculations pan out, how does life begin? Thus the thrust of my challenge.

    There is also the elephant in the room about what “fitness” could possibly mean in the prebiotic context. Speed? Fidelity of replication? Likelihood of reaction? Sheer numbers? No-one can say, because the very idea is nonsensical. But I’m willing to add the all-important Darwinian fitness concept to my challenge as well: go ahead and use whatever concept of fitness you want to drive the supposed “evolution” of your fledgling molecules.

    Finally, you mentioned in discussing your theoretical first living thing that because RNA polymers bind tightly to amino acids and tend to show some sequences used by today’s translational system that we are somehow on the road to a “limited genetic code.” Nonsense. The existence of a particular chemical reaction or a particular sequence does not lead to a limited genetic code. Further, your claims that such a system would move “closer to the more efficient system seen today” and that “evolution of this early translational system would make protein synthesis more efficient” are nothing but sheer, utter, unsupported speculation.

    Much of what you wrote demonstrates a failure to clearly think through the difference between necessary and sufficient conditions. The fact that some molecule exists in nature, or that certain reactions take place in certain conditions is interesting, but of little consequence on the road to OOL. Noting these kinds of things is about as relevant to explaining OOL as would be claiming we know how the Space Shuttle formed because we have have observed copper in nature.

    There need to be some serious, concrete proposals, with numbers putting things in perspective. Vague, ill-defined, handwaving “what-if’s” and “maybe’s” and “it-is-hypothesized’s” don’t cut it.

  14. 14
    Mung says:

    The simplest known single-celled organism is light years beyond current OOL efforts.

    The cell membrane is not some simple lipid vesicle that all the resources needed by the cell can simply enter when and as needed. Cell membranes require proteins.

  15. 15
    Zachriel says:

    Mung: The simplest known single-celled organism is light years beyond current OOL efforts.

    That’s immaterial, as more complex membranes are posited to have evolved from simpler structures.

    Mung: The cell membrane is not some simple lipid vesicle that all the resources needed by the cell can simply enter when and as needed.

    One candidate for protocells are single-chain amphiphiles, which are permeable to small molecules, but act to contain complex molecular products. See Chen & Walde, From Self-Assembled Vesicles to Protocells, Cold Spring Harbor Laboratory Press 2010.

  16. 16
    Alicia Cartelli says:

    My first point is that few to none of your concessions are even needed. It has already been demonstrated how all the major biomolecules can be synthesized by a model early earth environment and the racemic question is in reality a non-issue for the origin of life. It’s not me that needs to read more carefully or follow the science more closely.
    “Big deal.”
    The fact that you think what I said is not a big deal, demonstrates your misunderstanding of the chemistry behind abiogenesis. There is no requirement for specific relative abundances. The concentration issue is really the only problem, which there are a number of hypotheses as to how it can be overcome.
    The racemic question is a non-issue for the origin of life, again if you understood the chemistry, you would know this.
    The definition of fitness is really not any different; a molecule has a higher fitness if it increases the ability of the living system to survive the environment.
    And no, not nonsense, RNA structures have been shown to preferentially bind amino acids. This means there is a direct link between nucleotide sequence and amino acid specification and the chemical leftovers can still be seen in the genetic code today.
    There is no failure to clearly think on my part, there is unfortunately a failure to understand on yours though.

    “The fact that some molecule exists in nature, or that certain reactions take place in certain conditions is interesting, but of little consequence on the road to OOL.”
    No, EA, the conditions required for certain reactions to take place are actually incredibly important to OOL, the fact that you think they aren’t is just another example of how completely clueless you are. You have no idea what you are talking about.

  17. 17
    Mung says:

    Understanding the origin of cellular life on Earth requires the discovery of plausible pathways for the transition from complex prebiotic chemistry to simple biology, defined as the emergence of chemical assemblies capable of Darwinian evolution. We have proposed that a simple primitive cell, or protocell, would consist of two key components: a protocell membrane that defines a spatially localized compartment, and an informational polymer that allows for the replication and inheritance of functional information. Recent studies of vesicles composed of fatty-acid membranes have shed considerable light on pathways for protocell growth and division, as well as means by which protocells could take up nutrients from their environment. Additional work with genetic polymers has provided insight into the potential for chemical genome replication and compatibility with membrane encapsulation. The integration of a dynamic fatty-acid compartment with robust, generalized genetic polymer replication would yield a laboratory model of a protocell with the potential for classical Darwinian biological evolution, and may help to evaluate potential pathways for the emergence of life on the early Earth.

    The origins of cellular life

    Note what these authors think is necessary for Darwinian evolution.

  18. 18
    Mung says:

    Zachriel: That’s immaterial, as more complex membranes are posited to have evolved from simpler structures.

    That’s immaterial. Wishful thinking doesn’t count.

  19. 19
    Mung says:

    Zachriel: One candidate for protocells are single-chain amphiphiles, which are permeable to small molecules, but act to contain complex molecular products.

    Amphiphiles are not membranes.

  20. 20
    Virgil Cain says:

    Alicia:

    It has already been demonstrated how all the major biomolecules can be synthesized by a model early earth environment

    That is simply not true but it shows how gullible you are and what little you will accept as long as you think it supports your position.

    And no, not nonsense, RNA structures have been shown to preferentially bind amino acids. This means there is a direct link between nucleotide sequence and amino acid specification and the chemical leftovers can still be seen in the genetic code today.

    As I said, you are so gullible you will accept anything as long as you think it supports your position. Unfortunately there isn’t any evidence tat the genetic code can evolve via physicochemical processes

  21. 21
    RexTugwell says:

    Alicia @ 16: “The racemic question is a non-issue”
    The racemic question?! It’s called the problem of homochirality and I’m calling bullsh-t on your knowledge of abiogenesis. Looking back on what you’ve written, it’s becoming clear that you’re BSing your way through this thread.

  22. 22
    praxeology says:

    Miller-Urey demonstrated that methane, ammonia, and hydrogen gases in a highly favorable early earth model could produce cyanide, formaldehyde, and amino acids.

    True. And as we all know, the experiment was soon criticized for lack of plausibility: the early earth atmosphere was not a reducing one. When Miller repeated his experiment, he found tar, not amino acids.

    Subsequent studies demonstrated similar results in more realistic models.

    The “subsequent studies” phrase refers to the work of Miller’s graduate student, Jeffrey Bada, who repeated the experiment with a “more realistic” combination of gases (i.e., carbon dioxide and nitrogen) which produced nitrites, preventing the amino acids from forming. See:

    http://www.scientificamerican......-repeated/

    “Bada discovered that the reactions were producing chemicals called nitrites, which destroy amino acids as quickly as they form. They were also turning the water acidic—which prevents amino acids from forming.”

    However,

    “…primitive Earth would have contained iron and carbonate minerals that neutralized nitrites and acids. So Bada added chemicals to the experiment to duplicate these functions. When he reran it, he still got the same watery liquid as Miller did in 1983, but this time it was chock-full of amino acids.”

    Problem:

    Carbonates are themselves formed by biological activity:

    http://goldschmidt.info/2009/a.....s/A699.pdf
    How and where on Earth were and are carbonate minerals formed?
    W.E. KRUMBEIN
    Geomicrobiology, ICBM, Carl von Ossietzky Universitaet
    Oldenburg, D-26111 Oldenburg

    “Calcium and magnesium carbonates are formed practically exclusively by microbial decay of organic carbon compounds, by photosynthesis and by Golgi related biochemical activity of macro-organisms.

    “In a nutshell: Carbonate minerals are formed exclusively under the control of biochemical processes. Biochemical processes need life as a prerequisite.”

    Bada’s attempt at rehabilitating the conclusion of Miller’s experiment suffers from question-begging, by using a product of pre-existing biological activity in order to demonstrate the plausibility of abiogenesis.

  23. 23
    Virgil Cain says:

    RE- Membranes-> Bacteria have a different type of membrane from archaea and there isn’t any way to get one from the other nor any evidence they shared a common ancestor.

  24. 24
    Mung says:

    Virgil, they don’t need any stinking evidence. All they need is to say that cell membranes must have been simpler, therefore they were simpler.

  25. 25
    Virgil Cain says:

    Steenking, they don’t need any steenking evidence. For them their steenking word is their steenking evidence. So there

  26. 26
    Zachriel says:

    Mung: That’s immaterial.

    Any reasonable discussion of abiogenesis will presuppose Darwinian evolution. See Mung’s citation @17.

    Mung: Amphiphiles are not membranes.

    Amphiphiles will spontaneously form into vesicles, which are permeable to small molecules, but act to contain complex molecular products. Hence, they act as a membrane.

    praxeology: And as we all know, the experiment was soon criticized for lack of plausibility

    Complex organic compounds have been shown to form in a wide variety of different environments, so the availability of such compounds is not in serious question.

  27. 27
    Mung says:

    Zachriel: Any reasonable discussion of abiogenesis will presuppose Darwinian evolution.

    Any reasonable discussion of abiogenesis will start with the facts.

    Zachriel: Amphiphiles will spontaneously form into vesicles

    The cell is not a vesicle.

    https://en.wikipedia.org/wiki/Vesicle_%28biology_and_chemistry%29

  28. 28
    Zachriel says:

    Mung: Any reasonable discussion of abiogenesis will start with the facts.

    The vast majority of biologists accept the evidence for common descent, which points to a common ancestor of all life, and that this primordial ancestor appeared soon after Earth cooled enough for liquid water to form. That’s the beginning of any reasonable discussion of abiogenesis. Without that, any such discussion is without foundation.

    Mung: The cell is not a vesicle.

    The modern cell is not a vesicle. We’re discussing the posited primordial cell. That’s like saying, when someone proposes a primitive precursor, “It’s not a cat!”

  29. 29
    Virgil Cain says:

    The vast majority of biologists accept the evidence for common descent,

    The same evidence can be used for a common design and there isn’t any way to scientifically test Common Descent.

    And no, we don’t have to assume Common Descent in order to discuss abiogenesis. That is just stupid talk.

  30. 30
    Mung says:

    The vast majority of biologists accept the evidence for common descent

    so?

    which points to a common ancestor of all life

    so?

    and that this primordial ancestor appeared soon after Earth cooled enough for liquid water to form.

    so?

    The vast majority of biologists accept the evidence for a LUCA. Without that, any such discussion is without foundation. And that’s where you are, far away from the LUCA.

    Facts, Zachriel, if you have any. Story time is over.

  31. 31
    Mung says:

    Zachriel: The modern cell is not a vesicle. We’re discussing the posited primordial cell. That’s like saying, when someone proposes a primitive precursor, “It’s not a cat!”

    You can’t possibly be denying that the vesicles in modern cells are actually vesicles. I don’t know what that has to do with cats, but if anyone is screaming not a cat it’s you, not me.

  32. 32
    Eric Anderson says:

    Alicia @16:

    Rarely have I read such bald-faced, unsupported, hand-waving claims. You have no theory, no proposal, nothing that even passes the laugh test for abiogenesis.

    Claiming that very significant hurdles — which have been acknowledged by serious researchers and on which a great deal of time and money has been spent — are non-issues or simple to overcome is too facile and demonstrates a lack of understanding of the issues.

    Also, the hand-waving dismissal of the fitness question in a pre-biotic environment likely stems from the fact that you have never even thought of that important point before. It is the typical vague, Darwinian fantasy: once fitness, whatever that means, comes along, magic does the rest.

    Further:

    RNA structures have been shown to preferentially bind amino acids. This means there is a direct link between nucleotide sequence and amino acid specification and the chemical leftovers can still be seen in the genetic code today.

    It is not at all clear what you are trying to say, but as near as I can figure out what you are getting at, this is pure nonsense. Preferential binding in no way provides a direct link between nucleotide sequence and amino acid specification. Even if there were a link, you can’t get from that paltry observation to the claim that the “chemical leftovers” can be seen in the genetic code today. It doesn’t even make sense.

    Look, I don’t expect everyone to have an keen interest in abiogenesis or to follow the area closely. There is no shame in acknowledging that you are relatively new to the area and are still learning. We would welcome such an honest approach. Your views would be a lot more respectable if you would acknowledge the significant hurdles serious researchers are spending millions of dollars working on, rather than spouting a bunch of bald assertions and trying to give the impression that abiogenesis is pretty much a done deal — just filling in the details folks. There is absolutely no credibility in such an approach.

  33. 33
    Eric Anderson says:

    Any reasonable discussion of abiogenesis will presuppose Darwinian evolution.

    What the . . . !?

    Did someone actually say that!? Good grief. Now we see where things have gone off the rails from the get-go.

  34. 34
    praxeology says:

    @Zachriel: “Complex organic compounds have been shown to form in a wide variety of different environments, so the availability of such compounds is not in serious question.”

    Relevant and brilliant. Thank you! I suggest you immediately inform Jeffrey Bada of your profound insights and exhort him to repeat yet again Stanley Miller’s experiment, but next time NOT to add carbonates as the alkalizing agent (which he did last time, and which require the prior existence of living organisms) but some other “complex organic compounds” in order to undo the destructive effects of nitrites and acids that would otherwise form. And please: don’t feel compelled to be specific about which complex organic compounds, precisely, or in what proportions, would be needed to make the experiment come out the way it “ought to.” The more generic your suggestion to him, the better.

    In any case, I know Jeffrey Bada would appreciate hearing from someone as well-informed as you. In fact, we all appreciate it.

    Honest.

  35. 35
    Virgil Cain says:

    The alleged primordial cell needs either ATP or it’s poor relative acetyl phosphate. Without either of those you cannot manufacture polypeptides in a solution. Acetyl phosphate may be available in the vent pores but it wouldn’t be inside the primordial cell. ATP requires ATP synthase and that is an impossibility for a primordial cell.

  36. 36
    Zachriel says:

    Mung: so?

    Eric Anderson: What the . . . !?

    What we know about the history of life is clearly important to understanding its origin.

    praxeology: carbonates … which require the prior existence of living organisms)

    Carbonates can form abiogenetically in the presence of water.

  37. 37
    Virgil Cain says:

    Zachriel:

    What we know about the history of life is clearly important to understanding its origin.

    That is your opinion and only an opinion. Too bad we will never know the history of life.

  38. 38
    Mung says:

    Zachriel: What we know about the history of life is clearly important to understanding its origin.

    Glad you’re finally on board!

    So we have the LUCA. Now what do we know about the history of life prior to the LUCA and how do we know it?

    Or are you claiming the LUCA was a vesicle?

  39. 39
    Zachriel says:

    Mung: So we have the LUCA. Now what do we know about the history of life prior to the LUCA and how do we know it?

    Little. The evidence indicates that the LUCA was part of a complex ecosystem that had a history of rampant horizontal gene transfer. As with many “singularities”, the reality may be anything but simple.

    Before that, events are obscured. Evidence indicates that complex molecules can form in plausible primordial conditions, including possibly nucleotides. RNA can apparently act as a self-replicator. There is evidence in ribosomes that RNA is the primitive condition, which has led to the hypothesis of RNA World. There is little certainty, however, concerning the origin of life, though once replication began, darwinian evolution would have resulted in continued adaptation.

  40. 40
    Eric Anderson says:

    The evidence indicates that the LUCA was part of a complex ecosystem that had a history of rampant horizontal gene transfer.

    Rampant horizontal gene transfer. Really? Meaning, from other LUCA’s? 🙂 Or presumably you are hypothesizing that horizontal gene transfer occurred after LUCA had already reproduced, split into various populations, various different genes had arisen through some hypothetical and unspecified means, and so on.

    Evidence indicates that complex molecules can form in plausible primordial conditions, including possibly nucleotides.

    Let’s assume this is true. And then the molecules do what? Sit around and wait for the right other molecule to come along so that they can carefully build up the chain of molecules needed for the next step in the process? Or do they promptly start reacting with whatever they can react with in their environment, quickly eliminating their usefulness as individualized building blocks? Thought so.

    RNA can apparently act as a self-replicator.

    Please provide some evidence for this remarkable claim. The hypothetical self-replicating molecule has never been seen or heard from, to my knowledge, but I would love to know where you are getting your claim from.

    . . . though once replication began, darwinian evolution would have resulted in continued adaptation.

    Are you talking about a self-replicating molecule here, or some more advanced form of replicating entity? And what evidence do you have that Darwinian evolution would have resulted in any changes? Look, we understand that this is the theory. But just restating the theory isn’t evidence.

  41. 41
    Zachriel says:

    Eric Anderson: Meaning, from other LUCA’s?

    As noted, with many “singularities”, the reality may be anything but simple. The LUCA is thought to have been an ancestral population, not an individual.

    Eric Anderson: Or presumably you are hypothesizing that horizontal gene transfer occurred after LUCA had already reproduced, split into various populations, various different genes had arisen through some hypothetical and unspecified means, and so on.

    Horizontal gene transfer was probably rampant before the LUCA, and still significant after that period.

    Eric Anderson: Let’s assume this is true.

    You don’t have to assume it, as it has been repeatedly tested.

    Eric Anderson: And then the molecules do what?

    There’s no complete theory of abiogenesis. However, there are a number hypotheses, each of which attempt to explain a part of the process.

    Eric Anderson: Please provide some evidence for this remarkable claim.

    While complete sequence replication hasn’t been achieved, partial replication has been observed, and the evidence indicates that it is within the capability of RNA to self-replicate.

    Does your use of the word “remarkable” imply you don’t think it is possible, rather than a limitation of current scientific knowledge?

    Eric Anderson: Are you talking about a self-replicating molecule here, or some more advanced form of replicating entity?

    Once replication begins, then competition for resources will lead to adaptation.

    Eric Anderson: And what evidence do you have that Darwinian evolution would have resulted in any changes?

    The evolutionary diversification of life from primitive forms.

  42. 42
    Phinehas says:

    Z:

    Does your use of the word “remarkable” imply you don’t think it is possible, rather than a limitation of current scientific knowledge?

    Possible? That’s setting the bar rather low, isn’t it?

    Follow that up with a false dichotomy, and the type of reasoning helpful for believing in abiogenesis starts to become apparent.

  43. 43
    Zachriel says:

    Phinehas: Possible? That’s setting the bar rather low, isn’t it?

    It was a legitimate question. Are you also ruling out the possibility that RNA can self-replicate?

  44. 44
    Phinehas says:

    Z:

    Are you also ruling out the possibility that RNA can self-replicate?

    Nope. But then I recognize that there is a nearly infinite gap between the possible and the mindbogglingly improbable. And I do find it remarkable when folks swallow the mindbogglingly improbable as though it were no great thing. It makes me wonder whether such harbor something very like a religious belief in chance and its god-like capabilities. Such faith is quite remarkable indeed.

  45. 45
    Eric Anderson says:

    As noted, with many “singularities”, the reality may be anything but simple. The LUCA is thought to have been an ancestral population, not an individual.

    We’re talking about abiogenesis, keep in mind. You can call LUCA an ancestral population all you want, but you still have to start with a living organism that somehow reproduces and then diversifies into an ancestral population. Or are you suggesting that abiogenesis occurred multiple times, with the fledgling self-reproducing molecules turning into different organisms, thereby forming a population?

    Horizontal gene transfer was probably rampant before the LUCA . . .

    This is nothing but pure, unadulterated speculation. You have no way of knowing anything of the kind.

    Furthermore, it is completely irrelevant to the questions at hand.

    Does your use of the word “remarkable” imply you don’t think it is possible, rather than a limitation of current scientific knowledge?

    My use of the word underscores the following facts:
    (i) a self-replicating molecule, to my knowledge, has never been seen or identified, notwithstanding its central role to the abiogenesis creation story and the unfailing efforts of numerous researchers over many years to produce such a thing;
    (ii) there are serious theoretical problems with the idea of a self-replicating molecule as the first step in the history of life, as I have detailed in a prior post;
    (iii) from an engineering standpoint it is an open question whether such a thing could actually exist, at least in the alleged “simple” form we are often told; and
    (iv) even if such a thing could be achieved under very carefully-controlled conditions in the lab, there is good reason to think it would not be able to function in the real world.

    Thus, my use of the word is based on what we actually know. Unfortunately, people keep naively throwing out the idea of this self-replicating molecule as though it really exists, as though it answers some questions about how life starts.

    As I said in my prior post, it may be possible to design a self-replicating molecule in the lab. But it will not be as simple as the materialist creation story would like us to believe and it will have little chance of functioning in the real world — not without a lot of additional structures and machinery in place.

    Once replication begins, then competition for resources will lead to adaptation.

    Yes, yes, we know what the theory is (setting aside for a moment the technical problem with your loose statement about how adaptation comes about). You don’t need to keep repeating the vague claims of the theory. You need to show why we should take the theory seriously.

    —–

    Part of what we’re seeing here, and much of what makes up the disconnect in the discussions about abiogenesis is that skeptics want to see some actual evidence, some carefully-thought-through analyses. In contrast, true believers are all too often perfectly content with made-up stories, half-baked ideas, vague assertions, and wild speculations.

  46. 46
    Eric Anderson says:

    It makes me wonder whether such harbor something very like a religious belief in chance and its god-like capabilities. Such faith is quite remarkable indeed.

    Well said.

  47. 47
    Zachriel says:

    Phinehas: Nope. But then I recognize that there is a nearly infinite gap between the possible and the mindbogglingly improbable.

    So it’s possible, though you would presumably say it would have to be contrived. That’s all you had to say. So we have evidence that RNA can act as a replicator (partial replication has been observed) and as a genetic memory.

    Eric Anderson: We’re talking about abiogenesis, keep in mind.

    That’s right. The LUCA is posited to be highly derived from the first life, and the evidence supports horizontal mechanisms at play before the LUCA. Naïve notions of common descent would lead one to posit a singularity; however, nature is rarely so simple.

    Eric Anderson: Or are you suggesting that abiogenesis occurred multiple times, with the fledgling self-reproducing molecules turning into different organisms, thereby forming a population?

    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.

    Eric Anderson: This is nothing but pure, unadulterated speculation.

    It is highly speculative, but not purely so. See Woese, On the evolution of cells, Proceedings of the National Academy of Sciences 2002.

    Eric Anderson: (ii) there are serious theoretical problems with the idea of a self-replicating molecule as the first step in the history of life, as I have detailed in a prior post;

    That’s not the question, but whether it is possible for RNA to self-replicate. We know that RNA can self-catalyze, including partial sequence replication, and also replicate in highly contrived situations. These results are hardly trivial, and are an entailment of the RNA World Hypothesis.

  48. 48
    Mung says:

    Prior to the LUCA is ignorance. Wishful Thinking. Handwaving. Fantasy. Fiction. Zachriels.

    Take the idea of HGT prior to the LUCA. Our reasons for believing in HGT come from looking at organisms that evolved AFTER the LUCA, not from looking at the LUCA or organisms that were hypothetically prior to the LUCA.

    Perhaps Zachriel is proposing something like independent birth of organisms.

  49. 49
    Mung says:

    Once replication begins, then competition for resources will lead to adaptation.

    Handwaving.

  50. 50
    Zachriel says:

    Mung: Prior to the LUCA is ignorance.

    It’s largely obscure, but not completely so.

    Mung: Perhaps Zachriel is proposing something like independent birth of organisms.

    The evidence doesn’t support independent origins.

  51. 51
    praxeology says:

    “Carbonates can form abiogenetically in the presence of water.”

    Calcium carbonate only forms biogenetically. See Krumbein link above (“In a nutshell: Carbonate minerals are formed exclusively under the control of biochemical processes. Biochemical processes need life as a prerequisite.”). Bada added calcium carbonate as a buffer to the acidic product of his neutral gas mixture.

    Bada also added ferrous iron as a reducing agent; thus, instead of Miller’s incorrect reducing atmosphere, Bada designed a speculative reducing ocean that could counter the destructive effects of a neutral atmosphere comprising N2 and CO2.

    Interesting from the standpoint of investigator interference, but hardly worth celebrating as a breakthrough in abiogenesis.

  52. 52
    Mung says:

    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?

  53. 53
    Eric Anderson says:

    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.

  54. 54
    Zachriel says:

    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/scienc.....st04feb_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.

  55. 55
    Virgil Cain says:

    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.

  56. 56
    Eric Anderson says:

    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.

  57. 57
    Virgil Cain says:

    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 RNAs

  58. 58
    Eric Anderson says:

    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.

  59. 59
    Zachriel says:

    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.

  60. 60
    Eric Anderson says:

    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.

  61. 61
    Virgil Cain says:

    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.

  62. 62
    Zachriel says:

    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.

  63. 63
    Virgil Cain says:

    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.

  64. 64
    Eric Anderson says:

    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.

  65. 65
    Zachriel says:

    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.

  66. 66
    Phinehas says:

    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.

  67. 67
    Alicia Cartelli says:

    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.

  68. 68
    Phinehas says:

    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.

  69. 69
    Phinehas says:

    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.

  70. 70
    Virgil Cain says:

    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.

  71. 71
    Virgil Cain says:

    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.

  72. 72
    Mung says:

    Alicia Cartelli: I presented some of the simplest supporting evidence for abiogenesis…

    Soap bubbles therefore cell membranes?

  73. 73
    Mung says:

    Consider a cell capable of producing a like copy of itself.

  74. 74
    Alicia Cartelli says:

    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.

  75. 75
    Mung says:

    Consider a cell capable of producing a like copy of itself. Does it have a membrane? (Yeah, I know, stupid question.)

  76. 76
    Mapou says:

    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.

  77. 77
    Zachriel says:

    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?

  78. 78
    Mung says:

    And RNA can fold on itself, so any linear sequential copying mechanism would require something to cause it to unfold and keep it unfolded.

  79. 79
    Zachriel says:

    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?

  80. 80
    Virgil Cain says:

    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.

  81. 81
    Zachriel says:

    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.

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