Life from non-life. Fact or Fiction?

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Lucaspa: 2. Some proteins also replicate themselves and replicate other proteins.
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DNAunion: Judging from your inability and/or unwillingness to do so in the past, I doubt asking you for supporting material and references will result in your actually providing support for your position. So, how about it?

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Lucaspa: 3. RNA can make itself.
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DNAunion: Misleading for more than one reason. I’ll explain as soon as I finish quoting you.

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Lucaspa: RJ Davenport, Making copies in the RNA world. Science 292: 1278, May 18, 2001. Used in vitro evolution to make ribozyme that can faithfully copy other RNA molecules up to 14 nucleotides long. Uses any RNA as sequence as template. Ribozyme itself is 189 nucleotides long. 98.5% accurate (99.9% for RNA polymerase). Screened 10^15 ribozymes. Primary paper is WK Johnston, PJ Unrau, MS Lawrence, ME Glasner, DP Bartel, RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science 292: 1319-1326, May 18, 2001.
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DNAunion: So why is the statement “RNA can make itself” misleading as far as the paper published in Science goes?

1) The RNA molecule was completely incapable of making itself, or any other RNA molecule like itself. The ribozyme (catalytic RNA molecule) was over 180 nucleotides in length yet copied a maximum of only 14 nucleotides in the experiments performed. That RNA can’t make a copy of itself, it can copy only a small fraction of itself.

2) The RNA molecule doesn’t make RNA as much as it stitches together ribonucleotides. Saying that it can make RNA suggests (but does not require) that the ribozyme can take “raw materials” – such as ribose, phosphate, and nitrogenous bases - and hook them up together properly to form beta-D-ribonucleotides, then string those together to form a strand of RNA. The ribozyme mentioned in the Science article could not make the RNA nucleotides themselves (nor, if I remember correctly, sort out the proper enantiomeric forms during polymerization). It basically stitched together into a chain (in a template-directed manner) preexisting monomers that were “fed” to it.

3) The ribozyme was the end result of in vitro evolution. As far as origin of life purposes goes, this invalidates the experiment (since it is not prebiotically plausible). All the experiment could hope to do in that arena is show how complex or simple a self-replicating RNA molecule can be or has to be, from which better probabilities for the spontaneous formation of a self-replicating RNA molecule could be calculated.

Based on the Science article you reference, less misleading than “RNA can make itself” would have been “Scientists have been able to use prebiotic-invalidating directed evolution to produce as an end product an RNA molecule that can copy about 8% of itself”. Hardly has the same impact, though, does it.

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DNAunion: Random chemical reactions on the primitive Earth had molecules combining, breaking apart, reforming new combinations, and so on for multiple millions of years. By chance, many somewhat complex biologically relevant molecules - such as sugars - were formed.
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Lucaspa: Not random nor chance.
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DNAunion: Sure they were random.

Random : … lacking a definite plan, purpose, or pattern. (www.m-w.com)

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DNAunion: Are you, Lucaspa, claiming that the prebiotic chemical reactions that occurred did so according to a definite plan or purpose? If not, then they were random, as I used the word.

As far as the phrase “by chance”, as it was used…to say that an event happened by chance means, basically, that it did not occur because of intent, foresight, or (conscious) direction. The phrase is commonly used in this manner (even by people like Richard Dawkins).

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DocBrown: How about just raising the dead? All the major componets are in place (DNA, cells and everything) wouldn't that be an easy way to demonstate how life can come from non-life?
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DNAunion: If you mean something like, why not take a living cell, kill it - leaving all of its major components close together - and then see if it can be brought back to life by natural processes, the answer is almost assuredly, no. Here is something from my personal notes on this. It ends with a question (a clumsily worded one too).



DNAunion: For our second thought experiment involving bacteria, let’s start with the individual building blocks and see if life appears spontaneously (the bottom up approach). Take a single bacterium (which by a reductionist view is just a collection of atoms and molecules arranged in particular ways) and rupture its outer protective barriers (the cell wall and plasma membrane). What would happen? The bacterium’s "guts" (cytosol, ribosomes, circular DNA, etc.) would leak out: the vital concentration gradient would be gone, the cellular reactions would cease, and the cell (and all its components) would be dead (this is in fact one method employed by bacteria to kill others: they produce an oligopeptide that forms a leaky pore in the other bacterium’s membrane/wall). To aid in the re-assembly process, consider the contents to remain confined to an area immediately surrounding the ruptured bacterial cell. Furthermore, all nutrients the bacterium required for survival (glucose, for example) are maintained in the same concentrations throughout the thought experiment.

Now the question is, will those intact and preexisting, enzymes, DNA, ribosomes, RNAs, etc. – all the same ingredients that a moment ago constituted a living, functioning cell - reform a functioning cell? No, of course not. This process is irreversible (following "times arrow"): the chemical reactions will not self-organize back into a sustained metabolism capable of supporting life and the bacterium will not re-assemble from its now-disordered "parts". This is true even if one introduced various forms of undirected energy – say by heating the petri dish, or exposing it to intense UV, or by subjecting it to physical agitation (jarring it around), or exposing it to radioactivity: the individual constituents (building blocks) would still not be able to self-organize back into a functioning cell.

The interesting thing is that the starting point just mentioned (concentrated, intact enzymes, DNA, etc.) is far, far above the level of organization that OOL researchers have achieved: no prebiotically-plausible mechanisms for the generation of complex enzymes, DNA, ribosomes, RNA, etc. exist. So even if OOL researchers were handed all of these, for free, they still could not leave them to the undirected forces of nature and expect a functioning cell to be generated. So the next question is, if one can start with every single physical and operational entity of a functional cell – all 20 amino acids; all five mononucleotides; all vital polysaccharides and lipids; all tRNAs, mRNAs, & rRNAs; a full genome and its associated enzymes, such as DNA polymerase, DNA ligase, DNA helicase, single-stranded binding protein, and RNA primase; plenty of ribosomes as well as the genetic code; all the individual parts needed for transcription, translation, replication, anabolic and catabolic pathways, etc. - and allow them to become disordered spontaneously simply by making the enclosing wall/membrane leaky, and even these still won't self-organize back into a functioning cell, then why is it not valid to question the much bigger leap of faith involved in believing that pools of far fewer, and/or far less concentrated, and/or far simpler, randomly arranged organic molecules could have become organized – against the principle that disorder tends to increase spontaneously - in the complex ways associated with a bacterium, by the same kind of undirected natural processes that fail here?

Originally posted by Hank
Non-atheists can interrupt at any given time.  

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As a Christian, an Engineer, and a Science buff I find the whole topic interesting, informative, and a legitimate debate.

The Pope himself found Fox's work fascinating as well.

Originally posted by lucaspa

1. Protocells, because they reproduce and "inherit" the material of the parent, can be be selective units for natural selection.

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Let's back up to this statement.  Is it known yet how protocells actually reproduce? and what 'kind' of material is passed on to the daughter protocell?

Originally posted by DNAunion
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Lucaspa: 2. Some proteins also replicate themselves and replicate other proteins.
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DNAunion: Judging from your inability and/or unwillingness to do so in the past, I doubt asking you for supporting material and references will result in your actually providing support for your position. So, how about it?

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When I gave you the evidence, you abandoned the thread, DNAUnion.

I thought I posted the references.  One of them is:
A chiroselective peptide replicatorAlan Saghatelian, Yohei Yokobayashi, Kathy Soltani & M. Reza GhadiriDepartments of Chemistry and Molecular Biology and the Skaggs Institute for

Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA..............The origin of homochirality in living systems is often attributed to the generation of enantiomeric differences in a pool of chiral prebiotic molecules1,2, but none of the possible physiochemicalprocesses considered1±7can produce the significant imbalance required if homochiral biopolymers are to result from simple coupling of suitable precursor molecules. This implies a central role either for additional processes that can selectively amplify an initially minute enantiomeric difference in the starting material 1,8±12, or for a nonenzymatic process by which biopoly-mers undergo chiroselective molecular replication13±16. Given thatmolecular self-replication and the capacity for selection are necessary conditions for the emergence of life, chiroselective replication of biopolymers seems a particularly attractive process for explaining homochirality in nature 13±16. Here we report that a 32-residue peptide replicator, is capable of ef®ciently amplifying homochiral products from a racemic mixture of peptide fragments through a chiroselective autocatalytic cycle. The chiroselective ampli®ca-tion process discriminates between structures possessing even single stereochemical mutations within otherwise homochiral sequences. Moreover, the system exhibits a dynamic stereochemical `editing' function; in contrast to the previously observed error correction20, it makes use of heterochiral sequences that arise through uncatalysed background reactions to catalyse the pro-duction of the homochiral product. These results support the idea that self-replicating polypeptides could have played a key role in the origin of homochirality on Earth.

Originally posted by Smilin
Let's back up to this statement.  Is it known yet how protocells actually reproduce? and what 'kind' of material is passed on to the daughter protocell?

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Protocells reproduce by chemical means.  When a protocell reaches a certain size, the interactions between it and the surrounding water cause it to split in two.  Each daughter protocell gets part of the membrane and "cytoplasm".  So each daughter cell gets part of the material of the original protocell.

Originally posted by DNAunion ****************************
DNAunion: Random chemical reactions on the primitive Earth had molecules combining, breaking apart, reforming new combinations, and so on for multiple millions of years. By chance, many somewhat complex biologically relevant molecules - such as sugars - were formed.
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Lucaspa: Not random nor chance.
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DNAunion: Sure they were random.

The collision of molecules were random, but the chemical reactions were not.

As far as the phrase “by chance”, as it was used…to say that an event happened by chance means, basically, that it did not occur because of intent, foresight, or (conscious) direction. The phrase is commonly used in this manner (even by people like Richard Dawkins).

Then you should say "conscious intent" and not "chance".  That Dawkins may use it this way in no way makes it more correct.  Chemical reactions are not chance in that any old chemical reaction can happen. And that is the other common meaning of chance.  If you wish precision, then you distinguish between these two meanings. Say instead what you mean: that the reactions were not at the result of conscious intent.

Originally posted by DNAunion
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Lucaspa: 2. Some proteins also replicate themselves and replicate other proteins.
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DNAunion: I doubt asking you for supporting material and references will result in your actually providing support for your position. So, how about it?

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Nature 1996 Aug 8;382(6591):525-8 Related Articles, Links  

A self-replicating peptide.

Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR.

Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA.

The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.

Originally posted by DNAunion
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Lucaspa: 3. RNA can make itself.
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DNAunion: Misleading for more than one reason. I’ll explain as soon as I finish quoting you. 

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You are correct. That paper did not self-replicate, but it did make RNA.  So the statement in the narrow sense is correct. Now, if you want an RNA that makes itself (I'm surprised you didn't find it yourself on your own PubMed search):


Proc Natl Acad Sci U S A 2002 Oct 1;99(20):12733-40<SPAN><IMG alt="Click here to read" src="http://www.ncbi.nlm.nih.gov/entrez/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-notfree-pnas-entrez.gif" border=0>&nbsp;</SPAN>
<B>Inaugural Article: a self-replicating ligase ribozyme.</B>

<B>Paul N, Joyce GF.</B>

Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

A self-replicating molecule directs the covalent assembly of component molecules to form a product that is of identical composition to the parent. When the newly formed product also is able to direct the assembly of product molecules, the self-replicating system can be termed autocatalytic. A self-replicating system was developed based on a ribozyme that catalyzes the assembly of additional copies of itself through an RNA-catalyzed RNA ligation reaction. The R3C ligase ribozyme was redesigned so that it would ligate two substrates to generate an exact copy of itself, which then would behave in a similar manner. This self-replicating system depends on the catalytic nature of the RNA for the generation of copies. A linear dependence was observed between the initial rate of formation of new copies and the starting concentration of ribozyme, consistent with exponential growth. The autocatalytic rate constant was 0.011 min(-1), whereas the initial rate of reaction in the absence of pre-existing ribozyme was only 3.3 x 10(-11) M.min(-1). Exponential growth was limited, however, because newly formed ribozyme molecules had greater difficulty forming a productive complex with the two substrates. Further optimization of the system may lead to the sustained exponential growth of ribozymes that undergo self-replication.

Originally posted by DNAunion
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(3) The ribozyme was the end result of in vitro evolution. As far as origin of life purposes goes, this invalidates the experiment (since it is not prebiotically plausible).&nbsp;

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In vitro selection doesn't invalidate OOL. The situation inside the test tubes are prebiotically possible, since they do not involve anything except saline solutions and nucleotides.&nbsp; Shoot, the tst tubes are even in an oxygen environment.&nbsp; Also, since replication is being selected for -- the production of offspring -- then that is perfectly Darwinian.&nbsp; As you point out, all the experiment has to show is that the RNA is possible.

DNAunion: never mind: double post (see post below)

DNAunion: No time tonight, but I have a lot of rebuttals to Lucaspa's ill-informed statements in this thread. The most important point is that the peptides he claims can self-replicate can't - he's been mislead by the exaggerated terms used in the articles. I have read both of them before and they don't say what he things. More later when I have time.

Originally posted by DNAunion
DNAunion: No time tonight, but I have a lot of rebuttals to Lucaspa's ill-informed statements in this thread. The most important point is that the peptides he claims can self-replicate can't - he's been mislead by the exaggerated terms used in the articles. More later when I have time.

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I look forward to your presenting data from the articles. Since at least one of them is online, this should be interesting.

DNAunion: Here are some attempts to explain why the "self-replicating" peptide mentioned in both articles (what others have referred to as the "Ghadiri Ligase", which I will follows) is not a True Self-Replicator

First, I will use an analogy that employs the letters of the English alphabet and a short sentence in order to demonstrate why the Ghadiri ligase is not a true self-replicator.

For this analogy, I will equate the 23-character “sentence” METHINKSITISLIKEAWEASEL with the 32-amino-acid Ghadiri ligase. Each of the letters represents an amino acid residue along the length of the GL (my abbreviation for the Ghadiri ligase) where each of the individual “letters” is covalently bonded to its nearest neighbor(s) on the same strand (analogous to the same physical sentence, when there are two). The covalent bonds between the units will be represented with dashes (-) between the “letters” (M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L).

A true self-replicator can extract its individual building blocks (monomers/letters) one at a time from its surroundings (a pool of monomers/letters) and construct a functional copy of itself using itself as a template for the sequencing of the units, followed by release of the copy. In order to allow them to separate from each but to not decompose, they should not be covalently bonded together but both the template and the copy should be covalently bonded internally. Note that the letters can’t simply line up according to the template’s sequence and be done with it; they also have to be covalently linked to their nearest neighbors in the growing copy after being non-covalently attached to the template. Forming this bond between units within the same strand requires either a catalyst or the pre-activation of each of the building blocks. And since we are looking for a true self-replicator, the sequence itself should be performing the function, whether it is catalyzing the bond directly or pre-activating incoming monomers. The process we will look at (the less involved of the two) involves two basic steps for each monomer added: first, the correct monomer is “chosen” from the stocked pool of monomers and lines up along the template, then the template sequence covalently bonds the new monomer to the elongating string.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M (correct monomer lines up non-covalently with template)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M E (correct monomer lines up non-covalently with template)
M-E (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E T (correct monomer lines up non-covalently with template)
M-E-T (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T H (correct monomer lines up non-covalently with template)
M-E-T-H (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H I (correct monomer lines up non-covalently with template)
M-E-T-H-I (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I N (correct monomer lines up non-covalently with template)
M-E-T-H-I-N (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N K (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K S (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S I (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S-I (template sequence covalently bonds new monomer to growing string)

[next 26 steps omitted to save space]

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E L (monomer lines up with template)
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L (final monomer covalently bonded to others)

So how does the actual Ghadiri ligase measure up? Not very well. Using the same analogy, here is how the GL functions.


The first PREEXISTING half of the sequence -- M-E-T-H-I-N-K-S-I-T, which for some unknown reason just happens to be floating around nearby, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T


The second PREEXISTING half of the sequence -- I-S-L-I-K-E-A-W-E-A-S-E-L, which is also just floating around nearby for some unknown reason, already covalently linked together -- lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T I-S-L-I-K-E-A-W-E-A-S-E-L


The two halves are covalently bonded together – BUT NOT BY ANY EXTRA ACTION PERFORMED BY THE TEMPLATE SEQUENCE ITSELF, BUT BY THE SEPARATE TWO HALVES THEMSELVES, BECAUSE ONE OF THEM WAS PRE-ACTIVATED.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L

How is it that the needed halves just happen to be floating around? Because the researchers intentionally synthesize those exact two sequences, preactivate the copies of one of the sequences, and then supply both for reaction.

This analogy points out some conceptual reasons why the Ghadiri ligase is not a true self-replicator: it absolutely requires (1) the correct 15- and 17-aa sequences already be available in the surroundings, (2) both halves to already be held together by covalent bonds, and (3) one of the two halves to already be activated. The Ghadiri ligages is powerless to recreate itself from the individual building blocks that make it up.



Let’s try looking at it with a second analogy.

What do we know that truly self-replicates? The most obvious answer is, life. To make sure that we are not throwing in excess complexity, what is the simplest form of life known? A bacterium (or to be more precise, the bacterium Mycoplasma genitalium). Let’s double check…does a bacterium self-replicate? Yes. Okay, how?

In very simple terms, a bacterium takes in simple, raw materials from its surroundings and then the bacterium uses those simpler precursors to build extra copies of its own constituents – such as DNA, proteins, mRNA, etc. – and then divides to form two bacteria, each like the original.

Now, is this similar to the way the GL “self-replicates”? No, not at all. If the GL were a bacterium, it would require two preexisting halves of another bacterium that would then simply line up with it and join together to form a whole bacterium. In the real world, a bacterium is given only simple raw materials such as inorganic substances and sugars, that it uses to build a complete copy of itself from scratch; whereas in the “GL world” the bacterium has to be handed EVERYTHING already setup, for free, and just joins the two preexisting halve together.


Okay, let’s try looking at this from an informational point of view.

A true self-replicating protein would not need any help by being supplied large amounts of very specific, external information; the needed information for self-replication would be contained in the self-replicator itself. But for the GL ligase, it requires being handed approximately 130 bits of information*. How much is that? Suppose a random process were used to select a single number between 1 and 429,000,000,000,000,000,000,000,000,000,000,000,000,000, and that you know nothing other than the range and that the integer was chosen randomly, with each integer in that range being just a likely to have been selected as any other. Now, handed 130 bits of information, you'd be able to correctly pick that one integer in one try. And even if the rough calculation is too high by 10 orders of magnitude, or even 20 orders of magnitude, the fact still remains that the GL requires a huge amount of preexisting information to be handed to it for free in order for it to “self-replicate”.

However you slice it, the GL is not a true self-replicator.

So is the GL a catalyst? Yes – it accelerates the rate of the two halves joining without itself being altered in the process. It has been shown that even in the absence of the GL, the preexisting, pre-activated 15-aa and 17-aa fragments will bond together to form the full 32-aa GL. In the presence of the full GL, this rate of combination of the halves to form the full template is increased, and after doing so, the original template is ready to align another set of two halves so that they too will bond together. What the GL does is to orient two preexisting, pre-activated, specific sequences in the correct manner so that they can interact more readily (of course the probability of two halves finding each other and being properly oriented in order to link up is much greater when they are aligned linearly in tandem on a template than when colliding randomly in a solution). So yes, the GL is a true catalyst.

So does the term autocatalytic fit the GL? Yes – it is a catalyst whose product is itself.

Is the GL a true self-replicator? No.


* The information calculation was done very quickly in “back-of-the-napkin” fashion. The complete peptide is 32 amino acids long, and the rule is that living cells use 20 amino acids in the production of peptides. Since we are not looking at preexisting life in order to evolve the correct sequence, and since intelligent direction is not involved either, the sequence of monomers would be generated by undirected, basically random forces. So, using that assumption that each amino acid is just as likely as any other to be incorporated at position X, we have 20 equally likely possibilities for each of 32 positions. That gives a total of 20^32, or about 4.29 x 10^41, possible unique sequences. On a piece of paper, in just four lines of “code”, I calculated that 4.29 x 10^41 is about 2^130 (the first number is actually almost 1,000 times greater than the second, but I was trying to avoid doing a complicated calculation and also didn’t want to overestimate). With 2^130 equally likely possibilities, you need, on average, 130 bits of information to find the one correct outcome. Also, note that I mention above in the actual discussion that the infomation calculation's being too high by even 20 orders of magnitude would not alleviate the problem with the GL ligase. That is, if a more detailed calculation came out to 10^21, it would still require about 70 bits of information, which is still probably enough to win a state lottery twice in a row.


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PS: Edited the day after it was posted to correct the analogy explanation of how much 130 bits of information is (I realized the error just as soon as I left school last night, so couldn't fix it until now).
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DNAunion: 3) The ribozyme was the end result of in vitro evolution. As far as origin of life purposes goes, this invalidates the experiment (since it is not prebiotically plausible).

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Lucaspa: In vitro selection doesn't invalidate OOL.

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DNAunion: Yes it does. In vitro evolution requires protein polymerases (or other complex “enzymes”) to replicate the DNA or RNA. By way of introduction of those polymerases, you have replication of DNA or RNA, which you don’t have prior to the origin of life (if you have replication of DNA or RNA, you already have life: so the experiment models POST origin of life). You also have user-specified, function-specific selection. That also does not model prebiotic chemistry. What you have in in vitro evolution is EVOLUTION. You have mutation, selection, and replication of nucleic acids, used to EVOLVE as a final product a ribozyme. Since evolution was used to produce the ribozyme, and there would not be evolution prior to the origin of life, then using evolution invalidates the experiment as far as origin of life purposes goes (although it could give us a better handle on how complex an RNA molecule needs to be to be self-replicating).

Lucaspa: The situation inside the test tubes are prebiotically possible, since they do not involve anything except saline solutions and nucleotides.

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DNAunion: Uhm, and replicating enzymes that are NOT formed spontaneously in the test tube, but are taken from living organisms and added with the intent and goal of replicating the selected molecules, which are incapable of replicating themselves.

Lucaspa: Shoot, the tst tubes are even in an oxygen environment.

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DNAunion: Which has no bearing on what I said.

Lucaspa: Also, since replication is being selected for -- the production of offspring -- then that is perfectly Darwinian.

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DNAunion: Darwinian evolution was used to PRODUCE the ribozyme. You don’t have Darwinian evolution before the origin of life, so using it invalidates the experiment in regards to the origin of life.

DNAunion: Have two things to add. Here's the most relevant part of my previous post for the first point.

DNAunion: A true self-replicating protein would not need any help by being supplied large amounts of very specific, external information; the needed information for self-replication would be contained in the self-replicator itself. But for the GL ligase, it requires being handed approximately 130 bits of information*. How much is that? Suppose a random process were used to select a single number between 1 and 429,000,000,000,000,000,000,000,000,000,000,000,000,000, and that you know nothing other than the range and that the integer was chosen randomly, with each integer in that range being just a likely to have been selected as any other. Now, handed 130 bits of information, you'd be able to correctly pick that one integer in one try. And even if the rough calculation is too high by 10 orders of magnitude, or even 20 orders of magnitude, the fact still remains that the GL requires a huge amount of preexisting information to be handed to it for free in order for it to “self-replicate”.

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DNAunion: I failed to point out something significant in that paragraph.

What do we get for supplying that huge amount of information to the GL? A SINGLE copy! If we want a second copy, we have to hand the GL another 130* bits of information. And if we want a third copy, you guessed it, we have to hand the GL yet ANOTHER 130* bits of information. Each copy we want requires an additional input of 130* bits of information.

Second point, I came across this just today.

"David Lee and his colleagues at the Scripps Research Institute in La Jolla, California, have now shown that autocatalytic capabilities are not confined to RNA or DNA or even PNA. They isolated a small peptide, part of a protein made by yeast, and shows that it could catalyze the joining together of two fragments of itself to make more copies of the complete peptide.

Here again, of course, the result is far from a completely self-replicating molecule. Such a molecule would have to start not with two pieces of itself but with a set of building blocks -- in this case a collection of amino acids -- and make a copy of itself from scratch." (bold italics added, Chirstopher Wills & Jeffrey Bada, The Spark of Life: Darwin and the Primeval Soup, Perseus Publishing, 2000, p136)

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DNAunion: Just like I said.

Abiogenesis is also called(and really is)*Organic Evolution*.

Show me proof by conduction an experiment under Evolutions standerds to make it fact.

Untill that is done,it is equal to Fiction(if not worse).

God Bless,

Hector