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“In the Beginning Were the Particles” – Thoughts on Abiogenesis

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Design inference
Origin Of Life
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Recently we have been discussing Dr. Sewell’s thermodynamics-related paper/video on this thread.  In addition to some excellent discussion on the Second Law, the question of abiogenesis has naturally arisen.  Though related to the Second Law issue (by way of the compensation argument), I would like to move discussion of the abiogenesis question to this new thread, both so we can keep the other thread more focused on the Second Law, and also so we can have a more in-depth discussion here on this most fascinating topic of abiogenesis.

—–

I find posts that go on for dozens of pages to be rather tedious.  Notwithstanding my original intent, this post grew in length as I laid out the various points.  In the spirit of the great statesmen of old: I apologize for the length.  If I had had more time I would have made it shorter.

I. Asking the Right Questions

This topic of abiogenesis came up again on a different thread when AVS asserted that, given the Earth is an open system and receives energy from the Sun, “the generation of life was inevitable.”  Several commenters picked up on this, and I underscored that receipt of energy from the Sun doesn’t get us anywhere near the origin of life:

The compensation argument in regards to OOL and evolution is nonsensical because (i) OOL and evolution are not primarily thermal problems, (ii) even to the extent that energy is needed for OOL and evolution, simply pouring energy into the system isn’t helpful; there needs to be a directing process to channel the energy in useful ways, and (iii) no-one doubts that there is plenty of energy available, whether it be lightning strikes, volcanic vents, the Sun, deep sea vents, or otherwise; energy (at least in terms of raw quantity) has never been the issue.

I have also offered this challenge on more than one occasion, including in the recent discussions:

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, arganine, etc.?). I’ll further give you just the right concentration to encourage optimum reaction. I’m also willing to give you the most benign and hospitable environment you can possibly imagine for your fledgling structures to form (take your pick of the popular ideas: volcanic vents, hydrothermal pools, mud globules, tide pools, deep sea hydrothermal vents, cometary clouds in space . . . whichever environment you want). I’ll even throw in whatever type of energy source you want in true Goldilocks fashion: just the right amount to facilitate the chemical reactions; not too much to destroy the nascent formations. I’ll further spot you that all these critical conditions occur in the same location spatially. And at the same time temporally. Shoot, as a massive bonus I’ll even step in to prevent contaminating cross reactions. I’ll also miraculously make your fledgling chemical structures immune from their natural rate of breakdown so you can keep them around as long as you want.

Every single one of the foregoing items represents a huge challenge and a significant open question to the formation of life, but I’m willing to grant them all.

Now, with all these concessions, what do you think the next step is?

Go ahead, what is your theory about how life forms?

In fairness, AVS has since backed down and said that his comment was just a “thought experiment”.  Later, when queried on the details, he further acknowledged that OOL is “not a simple feat” and “no simple task”.  Eventually, when Upright BiPed pressed on the informational and organizational aspects, AVS accused him of “moving the goalposts” and complained that even if he provided a mechanism for OOL we would “just sneer” and dismiss it.

I don’t mean to pick on AVS in particular.  We have seen this play out with more than one commenter over the years, and AVS’s frustration is understandable.  The abiogenesis story resides at the level of vague generalizations, questionable assumptions, and wild speculations.  It would be frustrating for any of us to have to provide a plausible naturalistic scenario.  Furthermore (and note, I am not saying this is the case with AVS necessarily), when someone thinks that life arose by purely natural processes – convinced even to the point of it forming an important part of their personal belief system – a challenge to that story becomes an attack on that person’s belief system, to their creation story, to their “Where did we come from?” and “Why are we here?” questions.

Finally, as is so often the case, when someone holds a strong belief in abiogenesis, they tend to assume the answers are out there somewhere – certainly at least the broad outlines, with the details soon to be filled in by noble scientists diligently dedicated to the task.  When that individual is forced to actually look into the details, however, it is understandably frustrating for them to discover that the answers aren’t out there and to be confronted by the fact that the abiogenesis story is riddled with holes . . . a dozen haunting questions springing up in the face of each minor issue addressed.  This is not only frustrating, but completely disconcerting – the original confidence giving way to quiet whispers of doubt, and the quiet whispers of doubt slowly building into a cacophony of cognitive dissonance.

billmaz offered a more realistic assessment of origin of life research:

Nobody has figured out abiogenesis. Let’s start with that. But it is also unscientific to immediately turn to deus ex machina to explain it. It is still a work in progress. The issue, as I see it, is not that certain molecules can spontaneously combine to form proteins, or RNA, but how did they “evolve” to actually correspond to information exchange? Which came first, the RNA or the proteins? And how did a code in the RNA come to correspond to a specific protein? And how the heck did all the other proteins evolve that are needed to translate the code from RNA (or later DNA) into proteins without there being an evolutionary advantage in any of the intervening steps? Damn difficult questions, but that doesn’t drive me to design yet. It’s just a challenge to exhaust all the known forces to explain it before I go hunting for an other-wordly one.

billmaz is at least highlighting some of the right questions.  And his comment raises two important issues:

1. What is the inference?  billmaz characterized the inference, essentially as, “We don’t know how life arose.  Therefore God did it.”  This is incorrect.  As I stated:

And the inference is not: “Abiogenesis is hard, so deus ex machina.”

The inference is: (i) naturalistic abiogenesis fails on multiple accounts, based on the current state of knowledge, (ii) there are good scientific reasons to conclude it isn’t possible given the resources of the known universe, furthermore (iii) we do know of a cause that can produce the kinds of effects at issue (the kinds of things you note in your #121). Even then, we can’t conclude that “God dunnit”; but, yes, we can draw a reasonable inference that some intelligent cause was responsible.

2. Can we draw the inference yet?  As to the question of whether we should hold off drawing an inference to design or wait until we have “exhausted” all other avenues of research, I think there can be a fruitful discussion.  I happen to think that there is plenty of evidence to draw a reasonable inference.  Others, I grant, may disagree.  But I fear perhaps some disagree precisely to avoid drawing an inference.

In other words, the following scenario quite often plays out:

If I acknowledge OOL is a hard problem, then I am at least being realistic and looking some of the facts squarely in the face.  Furthermore, if I say that design is a possible explanation, then I manifest my reasonableness in being open to alternative explanations.  But if I then couple my apparent reasonableness with a claim that design can only be seriously considered if and when – at some unspecified distant future, one that, conveniently, is far enough off to not present any present-day implications – all naturalistic possibilities (again, typically vague and unspecified) have been exhausted, then I have essentially foreclosed the realistic possibility of ever inferring design.  Design becomes some distant hypothetical, one that I can acknowledge in the spirit of appearing reasonable, while still keeping myself firmly planted in the “there is likely a natural explanation” camp.

I do not know if billmaz is using the “exhaust” all natural possibilities as a way to avoid drawing an uncomfortable conclusion about OOL.  Surely some are, but let’s assume for a moment that billmaz is truly willing, here and now, to consider design as a reasonable explanation, but just doesn’t think the science supports it.  Only billmaz can answer that question by looking hard in the mirror.  But fine.  I can live with that approach from an integrity standpoint.  I happen to disagree with billmaz and think that the science is quite clear on this issue, and that a reasonable inference can be drawn, but I remain open to the theoretical possibility of some new discovery that would change my mind.

On this issue of whether we know enough now to draw a reasonable inference or need to await future discoveries, Joe sarcastically responded to billmaz:

I’m with billmaz on this.  Science gave up way to[o] soon on Stonehenge.  Heck it’s only rocks and mother nature makes rocks in abundance.  So there isn’t any reason why mother nature, give[n] billions of years, couldn’t have produced many Stonehenge-type formations.

. . . We are just rushing to judgment with our meager “knowledge”.  Obviously the we of today don’t know anything but the we of tomorrow will figure it all out.

The science of today is meaningless and should just stay out of the way of the science of tomorrow.

Joe raises a good point, though.  Why are so many people willing to consider the possibility of design – nay, going so far as to conclude the fact of design – in the case of something like Stonehenge, but refuse to even consider the possibility of design in the origin of life?  It certainly cannot be because natural processes are more likely to have produced a living organism than Stonehenge.  Quite the contrary.

Is it because things like stones are more (no pun intended) concrete and easier to grasp for most people than harder-to-understand concepts like amino acids, homochiralty, interfering chemical reactions, etc.?

Is it because the origin of life resides in such a murky and distant past that the imagination can take over our rational faculties and produce fantasies of the “Who knows?  It might have happened.” variety?

Is it, as some argue, because we know humans exist and understand how humans might have created Stonehenge, but it is less definitive who or what could have created life?

Is it because of the constant propagandistic drumbeat of the truth of abiogenesis that pervades our schools and institutions of higher learning?

Is it because of a commitment to naturalistic explanations, no matter how absurd, and an unwillingness to consider intelligent causes, for fear of the implications?

Or a combination of the above?

I agree with billmaz that there is value in continuing the research and trying to find the answers.  No quibble there.  So perhaps it is more a question of where we are each at on the spectrum (see “Attitudes Toward Abiogenesis” below).

II. The Value of Origin of Live Research?

A fair amount of money is currently spent on origin of life research.  Some view a naturalistic origin of life as one of the great remaining questions that will undoubtedly (eventually) be answered by science.  Others view it as a fool’s errand, a waste of time and money.

Personally, I think there is value in origin of life research.  Certainly in the biochemical bench science aspect.  Even in some of the more intangible research questions – those surrounding how information arises, what protocols and hierarchies exist in the cell, and so on.  Not because I expect any of these efforts to yield a naturalistic explanation for the origin of life (quite the opposite), but because of the additional insights such efforts will yield to help us better understand exactly what we are up against in the creation of initial life.

I also expect origin of life research can be helpful in increasing our understanding of how simple organisms work (if not quite getting to the answer of how they arose), what parameters need to be taken into account, what engineering solutions can be brought to bear.  Finally, origin of life research can also provide insights into specific issues that can have application in biology beyond the strict “where did it come from” question.

Please don’t misunderstand.  I’m talking about real, objective, substantive scientific research.  I give no countenance to “research” or “studies” that consist of career-padding published papers filled with unfounded assumptions, wild speculations, attacks on design or religion, or philosophical propaganda about how life just surely must have arisen by purely natural means.

III. Attitudes Toward Abiogenesis

What then is the appropriate attitude toward naturalistic abiogenesis?

There are many possible approaches, but I believe the following offers a decent spectrum of possible attitudes:

1. Abiogenesis is true and we have a pretty good idea how it happened, just some details remain to be worked out.

2. Abiogenesis is true, but we don’t have a good idea how it happened.  However, with more time and additional study we will no doubt discover the details.

3. Abiogenesis is probably true, but we don’t know how it happened.  Nevertheless, science should focus on naturalistic explanations.

4. Abiogenesis may or may not be true.  There is much that we don’t know.  We should continue to exhaust all possible naturalistic explanations, but if those don’t pan out after a lot more study and research for several more decades, at some future point we may need to consider the possibility of design.

5. Abiogenesis may or may not be true.  We should continue to exhaust all possible naturalistic explanations, but in the meantime we should also be open to the possibility of design.

6. Abiogenesis may or may not be true.  It is too difficult a problem and too distant in the past for us to really study properly.  We’ll never know, and in the absence of specific empirical evidence we shouldn’t draw conclusions one way or another.

7. Abiogenesis is likely false.  There is good evidence that it cannot work within the resources of the known universe.  While we should continue to exhaust all possible naturalistic explanations, we should consider the possibility of design.

8. Abiogenesis is almost certainly false.  There are multiple and compounding problems with the abiogenesis story and strong evidence that it cannot work within the resources of the known universe.  Furthermore, there is good evidence for design and we can draw a reasonable inference to design.  However, we should continue to exhaust all possible naturalistic explanations.

9. Abiogenesis is false, with essentially the same level of certainty that anything can be said to be false.  There are multiple and compounding problems with the abiogenesis story and powerful evidence that it cannot work within the resources of the known universe.  Furthermore, the evidence points strongly to design and we can draw a reasonable inference of design.  However, we should continue to carry out origin of life research, as such research could change our assessment of the evidence and/or provide answers to other important biological questions in the process.

10. Abiogenesis is false, with essentially the same level of certainty that anything can be said to be false.  Furthermore, it is a fool’s errand and we should stop wasting money on origin of life research.

—–

What Do You Think?

A. Which of the above approaches to abiogenesis most closely represents your view, or is there another one you would like to share?

B. In addition to the challenges to a naturalistic abiogenesis that I have outlined in section II above, what other aspects of the abiogenesis story are problematic?

C. If you had a chance to give a 30-second “elevator pitch” to someone, what would you say in those few brief words to help them catch a glimpse of the challenges with the naturalistic abiogenesis story and, potentially, consider the possibility of design in the origin of life?

Comments
AVS: You seem to ignore the difference between "crossing the hydrophobic core of a membrane" and "being highly concentrated into a cell". The synthesis of new RNA macromolecules requires high concentrations of substrates, not just a few random molecules which by chance crossed the membrane. Unless you are imagining a primordial ocean literally repleted with nucleotides, a "nucleotide world"! Is that your idea? And you know, the synthesis of macromolecules requires energy. In cells, it is given by ATP. To show you how the energy problem is realy important, I quote here from a very recent paper: "A ribozyme that triphosphorylates RNA 5?-hydroxyl groups" "The polymerization of RNA is entropically unfavorable in aqueous environments. Strategies to energetically drive RNA polymerization may have been different in two phases of the RNA world. First, in the prebiotic phase and perhaps in an early phase of the RNA world, RNA polymerization may have been driven by the evaporation of water from a solution (20) and from lipid encapsulations (21), or by the activation of the nucleotide's 5?-phosphate with a wide range of leaving groups (22) such as adenine (23), cyanide (24), imidazole (25,26), or 2-methylimidazole (27). Importantly, these activation groups lead to hydrolysis in aqueous environment within hours. Second, in later phases of the RNA world, when lipid vesicles presumably encapsulated aqueous droplets of self-replicating RNA systems (9,28–30), kinetically more stable activation groups would have been important. This requirement is fulfilled by nucleoside triphosphates, the universal energy currency in all known life forms. Nucleoside triphosphates can be generated from nucleosides and cyclic trimetaphosphate (TMP) (31). TMP is a prebiotically plausible compound because it can be generated by volcanic activity (32), by the erosion of phosphide minerals (33) and by heating of phosphate in the presence of urea (34). Additionally, TMP results from the self-reaction of the termini of linear polyphosphates in aqueous medium (35). The prebiotic availability of TMP is supported by the recent finding of abundant, reactive and reduced phosphorus species in sediments of 3.5 billion-year-old marine sediments (36). These phosphorus species can form polyphosphates including TMP if sources such as lightening provide hydroxyl radicals (33). Although TMP is the most reactive polyphosphorylating reagent of alcohols among all polyphosphates (37), the reaction between nucleoside 5?-hydroxyl groups and TMP proceeds efficiently only at pH values >12 (31). At such high pH, RNA world organisms would hydrolyze quickly. Therefore, RNA world organisms would require a catalyst to use TMP as energy source." So, as you can see, the problem of energy is a big problem. We need abundant energetic molecules (such as TMP) in the environment, and concentrated into the cell. And we need ribozymes to catalyze that energy so that it can be used by the ribozyme which polymerazes the concentrated nucleotides. Fairy tales, fairy tales...gpuccio
April 7, 2014
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Don't get your panties in a bunch Upright. I was merely using it as an example of the hydrophobic effect. If you knew how to read, you would have seen the word "today" at the end of my sentence.AVS
April 7, 2014
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Protein folding? There are no proteins in your scenario, remember?Upright BiPed
April 7, 2014
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As I said, prebiotic simulations have generated activated nucleotides and mixing these molecules with minerals has produced nucleotide molecules up to 50 bases in length. More recent work has shown the length can get up to 100 nucleotides even without activated nucleotides. This was done simply by introducing heat and small nonpolar molecules to a solution of nucleotide monomers.AVS
April 7, 2014
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I've already told you guys about the studies done on bicelles and their ability to replicate. The hydrophobic effect is a pretty powerful force, holding the membrane together and driving protein folding in cells today.AVS
April 7, 2014
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AVS: "Yes, gpucc, we have engineered inefficient ribozymes. Is that our point?" Our point, or at least my point, is that the only ribozymes we know that can build other long RNA molecules from nucleotides are: a) Complex b) Engineered c) Could never arise by chance in a prebiotic soup, least of all be selected in a membrane with the resources to do what they can do when they have the resources in a lab. IOWs, the RNA world scenario is completely irrational.gpuccio
April 7, 2014
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Pucc, the use of ribose sugars as a substrate has already been shown to be possible for nucleotide synthesis. Activation of nucleotides has been seen when prebiotic conditions are simulated. Also the sugar and nucleotide base structure are cyclic, meaning they are able to cross the hydrophobic core of a membrane. I'm not sure what your point is about "energy support." And I've already explained the division of the cell contents.AVS
April 7, 2014
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AVS: OK, but these simple cells must have divided regularly and with some order, I suppose. How? Were the membranes simply shaken by forces, like a tornado in the junkyard, and then instead of rupturing they just divide and replicate? OK, OK, you can imagine what you like. As I said, if one is bound to believe something by faith, there is nothing that can be done.gpuccio
April 7, 2014
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AVS: And I have not even mentioned how proteins should enter this scenario, how the ribozyme which replicates itself into a ribozyme should, by RV and NS, start coding for proteins from AAs which have suddenly entered our cell, and find at the same time a symbolic code to connect codons to aminoacids, a new enzymatic system which syntesizes proteins from AAs guided by that nucleotide sequence, and so on... Maybe I am too good. Maybe I just feel compassionate :)gpuccio
April 7, 2014
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Gpucc, mitosis is only such a complex process in today's cells because the cells themselves are so incredibly complex. The first cells obviously were much simpler, not requiring the perfect division of chromosomes or partitioning of organelles or anything like that.AVS
April 7, 2014
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AVS: And I suppose that your "cell" should contain both the complex ribozyme and a sufficient concentration of the substrates (the nucleotides). How do you think that a high concentration of nucleotides (molecules which are extremely difficult to generate) should be contained in the inner space of an inert membrane? Do you really believe that? In living beings, high concentrations of components inside the cell are obtained only at the expense of very complex transport mechanisms, and energy. And yet you imagine a "cell" with a membrane which, I suppose, is not generated by the cell "genome" (which, at this point, would be the complex ribozyme and nothing else), butr coems "naturally" from the environment. Such a natural membrene, however, should be able to: a) Maintain the ribozyme (we will not ask here how it was generated and how it got into the "cell" b) Ensure a high concentration of very rare (is at all existing in the environment) components, the nucleotides. c) Ensure some form of special energy support to the inner environment d) Divide itself intro two daughter cells, each with its own membrane, sharing each the complete resources which will allow the cell is alive and working. Magic? Fairy tales? Imagination? Do you really believe all that, and have faith that science will some day support such a scenario? A simple "yes" will do :)gpuccio
April 7, 2014
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It seemed you thought that I was saying that what arose in the first cell, arose again on its own in the new cell. This is not what I was saying. It is not a matter of chance that what is in the original cell, is also in the new cells. It is a certainty. As I already said, whatever is in the original cell diffuses throughout it and when the cell partitions into two cell, the contents are split between the two new cells. The two new cells have the same or very similar capabilities as the parent cell, so yes I see that as the old cell replicating itself into two cells.AVS
April 7, 2014
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GP, he's not even talking about a biotic membrane under the constraint of the cell. I'm giving him all the room I can and he still can't make a coherent case.Upright BiPed
April 7, 2014
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GP, agreed.Upright BiPed
April 7, 2014
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Yes, gpucc, we have engineered inefficient ribozymes. Is that our point?AVS
April 7, 2014
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AVS: I suppose you are aware of how complex and delicate a process is cell division, with an equal division of cell resources between the two daughter cells. Can you really believe that such a thing would happen by itself, without any complex controlling mechanism?gpuccio
April 7, 2014
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So instead of "No Upright", you actually mean "Yes Upright" If something in the original cell happens to appear by chance in a second cell, you see that as the original cell “replicating” itself.Upright BiPed
April 7, 2014
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UB: I am really amazed at how intelligent people can really believe in the myth of RNA world. I have never seen a more "ad hoc", irrational scientific hypothesis in my whole life. I believe that only the psychological pressure of having to explain what is impossible, but is believed by faith, can explain how a whole generation of scientists is wasting time and resources in the doomed attempt to support a theory which has no rationale.gpuccio
April 7, 2014
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No, upright, I'm saying that whatever molecules are in the original cell when the membrane is partitioned into two new cells, will be split between the two new cells. Both cells will now have the same or very similar capabilities as the original.AVS
April 7, 2014
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So if something in the original cell happens to appear by chance in a second cell, you see that as the original cell "replicating" itself. good griefUpright BiPed
April 7, 2014
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AVS: You stated (#146):
I think there have been RNA molecules that are self-replicating, both carrying out catalytic activity and holding the information for its own synthesis at the same time. And functional protein-like amino acid polymers have already been demonstrated to form on their own under certain conditions and have catalytic activity. Catalytic activity doesn’t even require a complex protein or RNA molecule, are you aware of this?
Well, do you agree that true self replication of a ribozyme from nucleotides (not from appropriately engineered oligonucleotides) has not yet been achieved, not even by intelligent design? And do you agree that all the imperfect examples we have, and that I have cited, are the product of intelligent design, and are not simple? Remember, any self-replicating system should originate by chance alone. No kind of selection, not even NS, is possible until you get self-replication of information. Your thoughts?gpuccio
April 7, 2014
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As I said upright, any molecules in the parent cell partition into the two daughter cells. The metabolic system in my early cell(s) is not based on enzyme-catalyzed reactions, but reactions that are more favorable and less complex. Goodnight.AVS
April 7, 2014
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AVS,
You are trying to get me to commit to the existence of a protein molecule so that you can then ask how that molecule was encoded into an information medium.
No, actually I was interested in you describing how the constituents of the metabolic pathways in your original "living organism" replicate themselves in another.
For the last time, I’m not going there.
goodnightUpright BiPed
April 7, 2014
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I was referring to Ribozymes in general. Some can catalyze peptide bonds, some can catalyze phosphodiester linkages, they can serve numerous functions.AVS
April 7, 2014
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AVS: I suppose you refer to something like this: "Selection of an improved RNA polymerase ribozyme with superior extension and fidelity" http://rnajournal.cshlp.org/content/13/7/1017.full.pdf Well, let's see:
Guided by the catalytic mechanisms utilized by protein polymerases, attempts have focused on isolating ribozymes that are capable of polymerizing a primer in a template-dependent manner as a key first step in the creation of a replicase ribozyme ... No approach has been more successful than the efforts that resulted in the 189 nucleotide (nt)-long Round-18 polymerase, which was selected from a pool built by appending a 76-random-nucleotide accessory sequence to the class I ligase
Emphasis mine. So, to sum up: a) The Round 18 polymerase has been built by intelligent selection (it's not a case that Szostak was part of the team). In no way it arose ib "a prebiotic soup environment", or anything like that. It is the product of intelligent design. b) The Round 18 polymerase is 189 nucleotides long! That means that its total complexity is 6*10^113, IOWs 378 bits! Maybe it is not the most complex RNA molecule we have, but its is certainly not simple. It corresponds to a protein of 63 AAs, and it could well be beyond my threshold of 150 bits for our planet as a biological system. But let's go on. Let's see what this product of human intelligent RNA engineering can do:
This polymerase can extend an RNA primer-template (PT) complex by up to 14 nt in a template-directed manner after 24 h of incubation. Nonetheless, the ability of the Round-18 ribozyme to polymerize more than one RNA helical turn is limited; more typically the Round-18 polymerase adds only a few nucleotides to a given PT complex. This poor polymerization ability has been attributed to weak and highly variable PT recognition
IOWs, we are really, really distant from any chance of "self-replication". Do you agree? These human designers are certainly clever, but not so clever as we would like :) So, what is needed? The answer is simple enough: more design, better design.
Therefore, the efficiency of this polymerase must be greatly improved in order to create an RNA system with true autoreplicative potential. Achieving this goal will require a complex combination of improved PT recognition, processivity, fidelity, and NTP utilization. As these polymerase properties are interdependent, it will be increasingly difficult to optimize these properties simultaneously using standard selection methods. Indeed, recent attempts to isolate superior polymerase ribozymes from the same pool that was used to isolate the Round-18 polymerase using conventional in vitro selection techniques have not yet proven fruitful
Emphasis mine. What an informative paper, would you agree? Good science. But the intelligence is certainly stimulated by the challenge:
Recently, in vitro compartmentalization (IVC) has been used as an alternative for conventional in vitro selection in the direct isolation of trans-ribozymes performing multiple-turnover chemistries ... In this study we have developed a large-scale IVC system to select for an improved RNA polymerase ribozyme from a mutagenized library based on the Round-18 ribozyme and with a diversity of ~ 9 * 10^14 sequences. After six rounds of selection, where ribozyme polymerases were required to act in a completely trans-fashion, we isolated a sequence that had extension properties superior to the Round-18 ribozyme in every assay tested.
Again, emphasis mine. Again, good intelligent engineering. That was really difficult, I suppose. We should really admire those intelligent and motivated scientists :) So, let's see again what the new production can do:
B6.61 incorporates > 20 nt of sequence Although both the WT and the B6.61 polymerases extended the PT(P7:T21) by 14 nt, B6.61 polymerized extension of > 9 nt about threefold faster than the WT (Fig. 7). More interesting was the finding that B6.61 extended PT(P7:T31) beyond the 14-nt limit, reaching a total extension of > 20 nt ... B6.61 is more accurate A clue to B6.61’s superiority was revealed by observing that B6.61 had improved fidelity
OK, we should be satisfied. After years of intelligent design and intelligent application of lab resources and human creativity, our scientists succeeded in creating a molecule that can elongate a template of 20 nt with godd fidelity. We are still very distant from any chance of self-replication (the polymerase is nore than 180 nt long!). But the story goes on. In 2011, we have new results: "Ribozyme-Catalyzed Transcription of an Active Ribozyme" Of this, I can only give the abstract:
A critical event in the origin of life is thought to have been the emergence of an RNA molecule capable of replicating a primordial RNA “genome.” Here we describe the evolution and engineering of an RNA polymerase ribozyme capable of synthesizing RNAs of up to 95 nucleotides in length. To overcome its sequence dependence, we recombined traits evolved separately in different ribozyme lineages. This yielded a more general polymerase ribozyme that was able to synthesize a wider spectrum of RNA sequences, as we demonstrate by the accurate synthesis of an enzymatically active RNA, a hammerhead endonuclease ribozyme. This recapitulates a central aspect of an RNA-based genetic system: the RNA-catalyzed synthesis of an active ribozyme from an RNA template.
Again, emphasis mine. Well, great progress has been done. Our new molecule cannot yet self-replicate, but it can replicate a natural ribozyme :) To sum it up: interesting and complex intelligent research about RNA intelligent engineering has been able, in many years, to demonstrate the following truth: We can intelligently design complex functional molecules, but it's not that easy! Ah, by the way, all that is used as propaganda for a natural origin of those molecules, but I really cannot understand why... :)gpuccio
April 7, 2014
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I haven't even mentioned the existence of proteins in my cell and why would I need to transport energy? I know what you are doing. You are trying to get me to commit to the existence of a protein molecule so that you can then ask how that molecule was encoded into an information medium. For the last time, I'm not going there.AVS
April 6, 2014
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Let me help you out AVS: Proteins A, B, C, and D arose and contribute to the transport of energy in my original cell. They replicate themselves in a new cell by ...Upright BiPed
April 6, 2014
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I already told you Upright, reproduction of the first cell I have proposed is driven by instability of the membrane as it increases in size and/or by outside energy input. The daughter cells may not have the exact same quantity of what was in the original cell, but they are all likely to be present in some amount. Also, as I have just said the metabolic system is based on chemical reactions that occur naturally, producing formaldehyde, which is a good candidate for the formation of more complex molecules through subsequent condensation reactions. The membrane also provides a possible energy storage site in the form of a chemical, electrical, or electrochemical gradient similar to how it does in cells now. Diffusion of these molecules throughout the parent cell ensures that they are relatively evenly distributed in the daughter cells when replication occurs via the the mechanisms I mention above.AVS
April 6, 2014
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AVS, If that is the case, then your "living organism" can neither: reproduce itself nor can its progeny evolve (because there won't be any). If you believe otherwise, then describe whatever metabolic activity you have in mind to sustain your original "living cell" (i.e. the production and/or distribution of energy, for instance) along with the constituents in your original cell related to this activity (to whatever degree you wish to describe them) and then tell us how they reproduce themselves in another membrane.Upright BiPed
April 6, 2014
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EA, I understand your confusion, as I have already said, this confusion stems from a complete lack of knowledge on the topic of experimental biology. If we are "producing molecules in the lab" we are mass producing them and have various ways to look at these molecules. If a scientist were to try to produce the first living cell in an Earth-like environment, how do you suggest he looks for this cell? You do realize how small cells are right? You can't just wade into a prebiotic soup environment and pluck out your first cell. I think there have been RNA molecules that are self-replicating, both carrying out catalytic activity and holding the information for its own synthesis at the same time. And functional protein-like amino acid polymers have already been demonstrated to form on their own under certain conditions and have catalytic activity. Catalytic activity doesn't even require a complex protein or RNA molecule, are you aware of this?AVS
April 6, 2014
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