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

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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
I also want to add my thanks to Eric's for all the terrific posts. I guess I also have to say that AVS did us a favor by volunteering to becoming a pinata for gpuccio, Upright BiPed, and the others here. In fact I haven't seen a beating this bad since I saw the Rodney King beating by the LAPD on TV. ;-) But seriously, this has really been informative. Thank you all. -QQuerius
April 7, 2014
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It seems like AVS is living in his own hypocritical fantasy land where he nitpick a saying that people should be more consice when he is all over the place . A classic troll in action lolwallstreeter43
April 7, 2014
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What is being taught? Definitely nothing with actual evidence...Joe
April 7, 2014
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Pucc, apparently you are unaware that nucleotide synthesis in today's cells is derived from amino acids, as is many other molecules. The other two articles I cited are about oligonucleotide polymerization and those two are about amino acid oligomerization. You asked for references, I gave them. And now all you do is point out how half of them don't talk about nucleotides, but talk about amino acids instead. I'm not sure how that helps your case, not only did I provide references for my claim but also for amino acid oligomerization. As I said, this conversation is pointless because you refuse to learn. Seems to be a common theme here at UD. I guess you can't fix stupid. Mung I'm sorry we couldn't talk about that book, maybe we could have if you actually read it. Joe, you're my favorite and don't you forget it! Just know that despite all your efforts on here, both abiogenesis and evolution is increasingly being taught at the college level. Sorry, guys. Have a nice day! <3AVS
April 7, 2014
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Have I understood well what AVS is saying in post #190? That the polymerization of aminoacids would generate nucleosides? No comment. Regarding his severe accusation: "You obviously just read the titles of the paper and drew conclusions about what they said, no surprise there." I read the abstracts of papers #1 and #4 (I could not find the full text online). Here they are: #1: Polymerization on the rocks: negatively-charged alpha-amino acids. (1998) "Oligomers of the negatively-charged amino acids, glutamic acid, aspartic acid, and O-phospho-L-serine are adsorbed by hydroxylapatite and illite with affinities that increase with oligomer length. In the case of oligo-glutamic acids adsorbed on hydroxylapatite, addition of an extra residue results in an approximately four-fold increase in the strength of adsorption. Oligomers much longer than the 7-mer are retained tenaciously by the mineral. Repeated incubation of short oligo-glutamic acids adsorbed on hydroxylapatite or illite with activated monomer leads to the accumulation of oligomers at least 45 units long. The corresponding reactions of aspartic acid and O-phospho-L-serine on hydroxylapatite are less effective in generating long oligomers, while illite fails to accumulate substantial amounts of long oligomers of aspartic acid or of O-phospho-L-serine." #2: Polymerization of beta-amino acids in aqueous solution. (1998) "We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged alpha- and beta-amino acids in homogeneous aqueous solution. alpha-Amino acids can be oligomerized efficiently using CDI, but not by EDAC. beta-Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an alpha- and beta-dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed." I could not find any reference to nucleotides in them. Can anyone here? I think that's enough with AVS. Calling the rest of that post "fairy tales" would be to do him a favor (that I am not sure he deserves), and offending the noble tradition of fairy tales.gpuccio
April 7, 2014
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Upright Biped- AVS is a joke of a first year biology student who thinks he knows everything.Joe
April 7, 2014
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I haven’t gotten a decent response out of anyone.
yawn. who'da guessed complete denial from the guy afraid to add a protein to a cell.Upright BiPed
April 7, 2014
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Cleaned my clock? I'm not even sure who you are referring to. I haven't gotten a decent response out of anyone. Maybe you're referring to Joe. ;-) See ya.AVS
April 7, 2014
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One last thing...
Especially since you present it to the scientifically illiterate community here at UD.
I'm merely a second stringer around here AVS. There are supremely well-educated and experienced contributors who post here. Your self-serving bigotry be damned. As for me, I'm a Research Director in the major media. I am content to be a reader from all sorts of sources, a fairly successful judge of content, and intelligent enough to see through fog like yours. But hey!! ...that thing that happened to you last night. That was a UD first stringer who came in and cleaned your clock. Don't fool yourself otherwise (famous last words, of course).Upright BiPed
April 7, 2014
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You should strive to present science in the most clear and effective manner possible, Upright. In doing this, it is extremely important to spell out every detail, and allow for as little room for misunderstanding as possible.
Frankly AVS, I thought we were in a mode of more relaxed phraseology anyway – particularly given the fact that you call a “common” unspecified chemical reaction taking place inside a non-biotic membrane a “living organism” … or … that a non-biotic membrane containing such a reaction which happens to become agitated and forms an adjacent membrane and by luck of the draw captures some undetermined portion of the constituents of the origin cell is referred to you as “self-replication”.
Yes even scientists can be ineffective at presenting science, in fact some of them are terrible at it. I’ve read some pretty terribly written papers.
I'm sure the authors of those papers will be glad to heed your advice. I'll post a note.
I’m so glad our conversation has devolved to this point.
The moment you traded science for political posturing (*I won't talk about proteins because I'll have to explain how they get replicated*) there was little else for it to do. cheersUpright BiPed
April 7, 2014
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AVS, if you consider yourself to be scientifically literate then I am glad to be scientifically illiterate because you don't know jack about science. First year biology student AVS. JokeJoe
April 7, 2014
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You should strive to present science in the most clear and effective manner possible, Upright. Especially since you present it to the scientifically illiterate community here at UD. In doing this, it is extremely important to spell out every detail, and allow for as little room for misunderstanding as possible. I was only trying to help. =) Yes even scientists can be ineffective at presenting science, in fact some of them are terrible at it. I've read some pretty terribly written papers. The bottom line is, when presenting science to someone not in the field, and especially when they're not in any scientific field you should be precise as precise with your words as possible. Just a suggestion. I'm so glad our conversation has devolved to this point. Have a nice day. Mung, let me know if you ever read that book, I'm still waiting to hear from you. Bye ladies. <3AVS
April 7, 2014
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Ahh. AVS, I certainly didn't mean to offend your vast intellect by using the common phrase "produce energy from light". Please accept my deepest apologies, I thought the obvious transformation of light to a useful form of cellular energy was abundantly clear, since that's what cyanobacteria are famous for. ... but wait ?!?!
From Google Scholar (biological sciences): “It is well known that an ability to produce energy from light is expected to lower…” “but their ability to produce energy from light provides them with a significant survival advantage” “Proteorhodopsin is associated with processes that produce energy from light (but not via” “They produce energy from light and are named for their green pigment” “photochemical reactions that produce energy from light, and the carbon-fixation” “Chloroplasts produce energy from light by photosynthesis, and were also originally symbiotic” “photosynthetic bacteria in order to 4 Page 23 produce energy from light. In both cases”
How is it even possible that these people cummunicate? :) - - - - - - - - - - (note to AVS, when you are reduced to being a pedantic ass, it really really really shows. It's never a good look).Upright BiPed
April 7, 2014
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Again with the word twisting. I didn't say they don't need the ability to CONVERT light energy. I said that they are not actually "producing" energy, as you stated. I'm sure you are familiar with the law of conservation of energy. Thank you for correcting your word choice, and I suggest you be more careful in the future. At least when dealing with someone who knows what they are talking about. I'm sure you will continue to incorrectly present science to your friends here, bending it as you see fit. I wouldn't expect anything less from UD. =)AVS
April 7, 2014
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There is no need to “produce” energy from light
Well lets rip that capacity from the cyanobacteria and tell our oldest fossils they really didn't need to convert sunlight into a useable form of energy. There's a brilliant first-year biology student from 4 billion years in your future, says you don't need it. ;)Upright BiPed
April 7, 2014
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Gpucc, nucleosides are activated by the addition of phosphate moieties. You don’t realize that amino acids, especially those negatively charged as in articles 1 and 4 that I posted, are not only very similar in structure, but they are directly linked to salvage pathways of nucleotides in cells today. These amino acids consist simply of carbon chains, amino/carboxyl groups, and OH groups. They are reactive and their ability to aggregate on mineral-rich sediments suggests a mechanism by which they can oligomerize to form nucleotides similar to those we see today. You obviously just read the titles of the paper and drew conclusions about what they said, no surprise there. Also, you are assuming that these oligonucleotides being formed had to be as complicated and serve the same function as the self-replicating ribozyme with extremely high fidelity that you mention. They did not. The nucleotide oligomers at this stage are only providing basic catalytic activity, whether its peptide bond formation, phosphodiester bond formation, or a different reaction. The experiment that you have brought up is an example of scientists trying to come up with a ribozyme that almost perfectly replicates itself; I would argue that at early stages, this perfect replication is not required. In fact, duplication with slight differences allows molecules to explore different shapes and functions and would be an integral part of molecular evolution. These early cells that arise can be selected and evolve through their ability to catalyze certain reactions in different combinations, providing the cell with more complex molecules that have various functions. You guys don’t realize how similar the basic biomolecules of life are and how simple their monomer units are, they are all based on carbon chains of varying lengths with different functional groups. The complexity comes from the shapes formed when they are combined into oligomers. “The production of energy from light,” Upright? There is no need to “produce” energy from light, light IS energy and can directly catalyze chemical reactions. You guys simply do not have the science background to talk about this stuff, sorry.AVS
April 7, 2014
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All, thanks for the many comments and the valuable discussion. As promised, I've started another thread to delve in detail into the self-replication issue: https://uncommondescent.com/origin-of-life/thinking-upside-down-the-abiogenesis-paradigm/Eric Anderson
April 7, 2014
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A short oligonucleotide sequence that catalyzes the phosphodiester bonds of more oligonucleotide sequences would be allow the cell to explore various sequences for various functions.
AVS, just so you understand, an RNA script that can catalyze other RNA scripts does nothing to achieve translation. One result is based upon purely deterministic forces and the other bridges a discontinuity between the medium and its physical effect (while preserving that discontinuity). The organization of the translation system requires it in order to function.Upright BiPed
April 7, 2014
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Stephen Meyer - Functional Proteins And Information For Body Plans https://vimeo.com/91289076bornagain77
April 7, 2014
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GP... its worse than just a bad story. He started with an inorganic membrane and light energy, which may now be a hydrovent instead. Perhaps his cell starts in one place and ends in another? Of course, the production of energy from light will be achieved without proteins. Perhaps he envisions some proto-chlorophyll complex made strictly from nucleotides. :) And of course, as he himself has indicated, the only real reason he is avoiding proteins in this "living organism" is not because it makes any biological sense, but because he doesn't want to have to explain how he reproduces a protein without information and translation.Upright BiPed
April 7, 2014
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AVS: Papers #1 and #4 are about aminoacids, they have nothing to do with RNA. Paper #2 and #3 just show the possibility of clay or similar to polymerize nucleotides. I really can't see how that kind of experiments may give support to your statement: "I don’t think that oligonucleotide synthesis had to occur billions of times to get a functional sequence." How do you think that the supposed self-replicating ribozyme was found (189 nt long, remember!) without testing sequences? By sheer luck? And how would a cell which is not even a cell, which has no self-replicating activity, which has no information to be replicated, but only mechanical membranes which are shaken and ruptured by vents, and can undergo no selection process, how would such strange entity "be allowed to explore various sequences for various functions"? That's really beyond my comprehension. So yes, it's really a just so story. Not even a good one.gpuccio
April 7, 2014
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AVS: And how would nucleosides be activated inside the cell? Please, explain. Moreover, I call just so stories those stories which are really just so stories. I have great respect for reasonable stories.gpuccio
April 7, 2014
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AVS:
The environment of hydrothermal vents has already been shown to be conducive to the formation of nucleotides.
A watery environment is the wrong environment for the OoL. Too much water will disperse the chemicals. Does AVS really think things just hang around? Really? How about cytosine which has a short deanimation time especially with high temps?Joe
April 7, 2014
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OK if engineered ribosomes have the same exact parts as ribosomes that are in living cells, and yet dod not function like them, that should be evidence that there is more to ribosomes than their chemical/ physical make-up.Joe
April 7, 2014
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Billmaz said:
If there are billions of planets in the “goldilocks” zone of planetary distance from suns, the “evidence,” such as it is for now, is that there is a very high probability of intelligent life forms on many other planets.
Bill, there could be billions of planets in the goldilocks zone and it might very possibly not mean anything for the existence of life. The problem is that you do not know yet whether life evolved from chemicals without any intelligence involved. You don’t know if it is even possible. If it is possible, then yes that could be interpreted as you have done, but we just don’t know that. And, being in the goldilocks zone is not near enough anyway. There are at least 11 conditions that have to be met by a planet to be able to support life. Please read this article! http://crev.info/2012/01/tilt-a-world-another-constraint-on-habitability/ Here they are: Galactic Habitable Zone, where a star must be located (09/29/2009) Circumstellar Habitable Zone, the right radius from the star where liquid water can exist (10/08/2010) Continuously Habitable Zone, because too much variety can be lethal (7/21/2007) Temporal Habitable Zone, because habitable zones do not last forever (10/27/2008) Chemical and Thermodynamic Habitable Zone, where water can be liquid (12/30/2003) Ultraviolet Habitable Zone, free from deadly radiation (8/15/2006) Tidal Habitable Zone, which rules out most stars that are small (02/26/2011) Stable Obliquity Habitable Zone (1/12/2012) Stellar Chemistry Habitable Zone (9/08/12) Stellar Wind Habitable Zone (9/19/13) Cosmic Ray Habitable Zone, protected by magnetic field and atmosphere (11/23/13) See more at: http://crev.info/2013/11/cosmic-lottery-how-many-habitable-planets/#sthash.lICbTNqQ.dpuftjguy
April 7, 2014
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Eric Anderson at #113:
I’m not sure that life, in and of itself, requires self-replication/reproduction. We could certainly conceive of an organism that does not reproduce itself (for sterility reasons or otherwise) that would still be considered alive. That said, I understand your broader point about the challenging requirements for self-replication — the self-replication that is a characteristic of essentially every life form we study.
The Hypothetical First Cell (HFC) created through abiogenesis must have been a successful self-replicator.
I’m currently in the process of putting together a related follow-on post, which I hope to have up in a few days, and would love your thoughts on it. Also, thank you for the reference to your excellent page on a minimum cell model. I’ve spent a lot of time thinking about this issue as well the past few years and it is an exceedingly interesting issue. I’ll definitely try to read through your essay in more detail (I know we discussed it a while back, but I want to refresh my memory of the issues you brought up).
I am glad that you liked my Minimum Cell Model. And also I am looking forward to your future post on this topic. I would like to add that the Minimum Cell Model was a simplified and more focused version of my presentation on the Simplest Self Replicator at the Engineering and Metaphysics conference in 2012 in Tulsa, OK. The conference presentation (you can see both the video of the presentation and the slides on the above link) was farther developed and extended into the last three chapters of the recently published book Engineering and the Ultimate edited by Jonathan Bartlett, Dominic Halsmer, and Mark R. Hall The Minimum Cell Model (MCM) demonstrates that natural laws and random circumstances are absolutely incapable to produce all required elements of the Hypothetical First Cell (HFC) in the same place, at the same time, arranged in highly specified ways, satisfying particular interfaces and interacting rules and having their behavior very well coordinated and being fundamentally information-driven. The analysis performed in the MCM essay leads to the conclusion that any hope that current or future research in abiogenesis is going to be successful is not founded on reason but has fundamentally a religious and superstition motivation. We talk here about the superstition hold dear by materialists and evolutionists that inanimate matter created life. This is just a plain ridiculous superstition, an absurd faith in in the gods of the matter, a religion worshiping chance, inanimate matter and going against reason, against clear thinking and against objective realities. Life is for many practical purposes a miracle – even in its simplest forms. It is a miracle because we understand that life has many elements that are much beyond our understanding and reach. Self-replication is being revealed at an attentive analysis to be a very sophisticated and complex capability that is observed for material, concrete entities only in the living world. The same analysis concludes that any attempt by scientific, nanotechnology labs to implement, real concrete self-replicators will be destined to failure because such a project poses insolvable technical difficulties. In light of this hard to contest realities, after considering the analysis in the Minimum Cell Model essay, the belief that inanimate matter and happenstance can create a self-replicator and life is just absurd, devoid of any sane reasoning or balanced evaluation of what is feasible or not. Let’s step backwards and have a look at this picture. The scientists, molecular biologists, Nobel laureates are using clever means, techniques and devices trying to achieve only limited mechanisms that are supposed to support abiogenesis – like an RNA that contains an information template and is a self-replicator at the same time. They made some progress on only partial objectives but failure is the general refrain that is heard from the OOL research labs. And then our Martian thinkers like AVS have an unshaken belief that inanimate matter did the job. Failures in lab, failures on a logical analysis – like that done in the MCM assays, DO NOT MATTER. Their belief is unshaken. Have you heard of any more dedicated religious zealots than these poor souls? And some of them have the arrogance to insult and blaspheme anybody that has beliefs solidly confirmed by untainted reason, by real science and by the miracles around us that tell that there is a supreme Designer. Do we really need to support the insults, arrogance and blasphemies of this AVS character? Is there any way to sanitize this blog?InVivoVeritas
April 7, 2014
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I don't think that oligonucleotide synthesis had to occur billions of times to get a functional sequence. A short oligonucleotide sequence that catalyzes the phosphodiester bonds of more oligonucleotide sequences would be allow the cell to explore various sequences for various functions. Here's a couple articles on the abiotic synthesis of oligonucleotide chains, enjoy. A.R. Hill, C. Böhler, L.E. Orgel Polymerization on the rocks: negatively charged ?-amino acids Orig. Life Evol. Biosph., 28 (2001), pp. 235–243 J.P. Ferris Montmorillonite catalysis of 30–50 mer oligonucleotides: laboratory demonstration of potential steps in the origin of the RNA World Orig. Life Evol. Biosph., 32 (2002), pp. 311–332 S.J. Sowerby, C.-M. Mörth, N.G. Holm Effect of temperature on the adsorption of adenine Astrobiology, 1 (2001), pp. 481–487 R. Liu, L.E. Orgel Polymerization of ?-amino acids in aqueous solution Orig. Life Evol. Biosph., 28 (1998), pp. 47–60AVS
April 7, 2014
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The environment of hydrothermal vents has already been shown to be conducive to the formation of nucleotides. Inactivated nucleotides can cross the membrane, and upon activation lose their ability to cross back out of the cell. This effectively increases their concentration within the cell. No matter what you learn, your just going to scream that it's a just-so-story, so why bother.AVS
April 7, 2014
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AVS: "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." Give the references, and let's see how likely is that such a thing happens in a natural prebiotic environment. And, is it happens, the sequence would be random. So, are you thinking that such a "natural", undirect synthesis happened billions and billions of times, so that a functional sequence was generated? And then that functional sequence started to self-replicate, was included in a membrane, and so on? In your scenario, it seems that the primordial ocean was busy only with generating the RNA world! It was repleted with free nucleotides, and with volcanoes providing tornados (ehm, I apologize, energy), and very careful not to miss the first ribozyme generated against all probabilities, so that it could be preserved and efficiently incapsulated in membranes, of which obviously the same ocean was fully repleted. And so on, and so on...gpuccio
April 7, 2014
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Oh, I saw the word just fine. It's just a reminder that you committed to the full suite of the metabolization pathways of a self-replicating living organism with no protein.Upright BiPed
April 7, 2014
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