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Thread: Designer enzymes

  1. #121
    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by lee_merrill View Post
    No, I asked some questions which have not yet been answered.
    You deflected and ran from the question you were asked so fast you left skid marks.

    Here is the question again. Try to answer it honestly for a change:

    Where are the effects of feedback from natural selection accounted for in your "calculations"?

    HINT: the answer is you didn't include the effects at all because your "calculations" are based on the usual Creationist science-free stupidity. That's why they are completely worthless.

    I just want to see how far you'll go to deny the obvious. Exposing Creationist dishonesty is always a win for the pro-science side.

  2. Amen shunyadragon amen'd this post.
  3. #122
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    The bottomline is taking into the natural determining factors that constrain the influence of the randomness of the occurence of each mutation event greatly increases the probability of the processes of evolution.
    Quote Originally Posted by HMS_Beagle
    Where are the effects of feedback from natural selection accounted for in your "calculations"?
    I selected a biomolecule that is not self-replicating, so it has to form randomly. You need replication and competition for natural selection, for evolution to work.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  4. #123
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    I selected a biomolecule that is not self-replicating, so it has to form randomly. You need replication and competition for natural selection, for evolution to work.
    Huh?!?!!?

    Source: https://www.google.com/search?q=biomolecule+definition&oq=biomolecule&aqs=chrome.2.0j69i57j0l4.10039j1j8&sourceid=chrome&ie=UTF-8


    biomolecule -A biomolecule or biological molecule is a loosely used term for molecules and ions present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development.

    © Copyright Original Source



    Biomolecules do not act alone in the biological processes of replecation. No, the formation of biomolecules are determined by chemistry of physiology not randomness. They do not form randomly.

    Still the question has not been answered. Where are the effects of feedback from natural selection accounted for in your "calculations"?

    Apparently you are changing the subject, not clear, 'arguing from ignorance' concerning what you perceive as unknown in abiogenesis concerning biomolecules(?) and not the science of evolution. In the physiology of life there is nothing random about biomolecules and role in the physiology and replication of cells.

    Even in the chemical processes in the biomolecules the cause and effect evts are all that is random. The resulting reactions and products are determined by the Laws of Nature via the laws of chemistry. I mentioned before the limited reactions to achieve the desired geometry of organic chemistry is not random, would also be true in abiogenesis.
    Last edited by shunyadragon; 07-18-2019 at 03:50 PM.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  5. #124
    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by lee_merrill View Post
    I selected a biomolecule that is not self-replicating, so it has to form randomly.
    No you didn't. You posted a 2001 paper you didn't read and don't understand describing the origin of self-replication

    The RNA world hypothesis regarding the early evolution of life relies on the
    premise that some RNA sequences can catalyze RNA replication. In support of
    this conjecture, we describe here an RNA molecule that catalyzes the type of
    polymerization needed for RNA replication.
    The paper said nothing about the molecule having to form randomly by falling together all at once like your IDiot "calculations" require. That was your lie.

    Keep up the lying for Jesus Lee. You'll guarantee your spot in Heaven.

  6. #125
    tWebber HMS_Beagle's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Huh?!?!!?

    Source: https://www.google.com/search?q=biomolecule+definition&oq=biomolecule&aqs=chrome.2.0j69i57j0l4.10039j1j8&sourceid=chrome&ie=UTF-8


    biomolecule -A biomolecule or biological molecule is a loosely used term for molecules and ions present in organisms that are essential to one or more typically biological processes, such as cell division, morphogenesis, or development.

    © Copyright Original Source



    Biomolecules do not act alone in the biological processes. No, the formation of biomolecules are determined by chemistry of physiology. They do not form randomly.

    Still the question has not been answered. Where are the effects of feedback from natural selection accounted for in your "calculations"?
    Lee has on his "Pants on Fire" hat today. He's busted and he knows it.

  7. Amen shunyadragon amen'd this post.
  8. #126
    tWebber shunyadragon's Avatar
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    If you are shifting the subject to the issue of abiogenesis and biomolecules. Well, yes there are many unknowns, which is a given concerning abiogenesis. . . . but yes, there are many advances in the science of abiogenesis that explain the role of the biomolecules in the primitive forms that lead to the first life forms as follows in this reference.

    Source: https://www.sciencemag.org/news/2015/03/researchers-may-have-solved-origin-life-conundrum



    Researchers may have solved origin-of-life conundrum

    By Robert F. ServiceMar. 16, 2015 , 12:15 PM

    The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule—something like DNA or RNA—capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can’t copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids.

    Now, researchers say they may have solved these paradoxes. Chemists report today that a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.

    “This is a very important paper,” says Jack Szostak, a molecular biologist and origin-of-life researcher at Massachusetts General Hospital in Boston, who was not affiliated with the current research. “It proposes for the first time a scenario by which almost all of the essential building blocks for life could be assembled in one geological setting.”

    Scientists have long touted their own favorite scenarios for which set of biomolecules formed first. “RNA World” proponents, for example suggest RNA may have been the pioneer; not only is it able to carry genetic information, but it can also serve as a proteinlike chemical catalyst, speeding up certain reactions. Metabolism-first proponents, meanwhile, have argued that simple metal catalysts, as opposed to advanced protein-based enzymes, may have created a soup of organic building blocks that could have given rise to the other biomolecules.

    The RNA World hypothesis got a big boost in 2009. Chemists led by John Sutherland at the University of Cambridge in the United Kingdom reported that they had discovered that relatively simple precursor compounds called acetylene and formaldehyde could undergo a sequence of reactions to produce two of RNA’s four nucleotide building blocks, showing a plausible route to how RNA could have formed on its own—without the need for enzymes—in the primordial soup. Critics, though, pointed out that acetylene and formaldehyde are still somewhat complex molecules themselves. That begged the question of where they came from.

    For their current study, Sutherland and his colleagues set out to work backward from those chemicals to see if they could find a route to RNA from even simpler starting materials. They succeeded. In the current issue of Nature Chemistry, Sutherland’s team reports that it created nucleic acid precursors starting with just hydrogen cyanide (HCN), hydrogen sulfide (H2S), and ultraviolet (UV) light. What is more, Sutherland says, the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of reactions could have given rise to most of life’s building blocks simultaneously.

    Sutherland’s team argues that early Earth was a favorable setting for those reactions. HCN is abundant in comets, which rained down steadily for nearly the first several hundred million years of Earth’s history. The impacts would also have produced enough energy to synthesize HCN from hydrogen, carbon, and nitrogen. Likewise, Sutherland says, H2S was thought to have been common on early Earth, as was the UV radiation that could drive the reactions and metal-containing minerals that could have catalyzed them.

    That said, Sutherland cautions that the reactions that would have made each of the sets of building blocks are different enough from one another—requiring different metal catalysts, for example—that they likely would not have all occurred in the same location. Rather, he says, slight variations in chemistry and energy could have favored the creation of one set of building blocks over another, such as amino acids or lipids, in different places. “Rainwater would then wash these compounds into a common pool,” says Dave Deamer, an origin-of-life researcher at the University of California, Santa Cruz, who wasn’t affiliated with the research.

    Could life have kindled in that common pool? That detail is almost certainly forever lost to history. But the idea and the “plausible chemistry” behind it is worth careful thought, Deamer says. Szostak agrees. “This general scenario raises many questions,” he says, “and I am sure that it will be debated for some time to come.”

    © Copyright Original Source

    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  9. #127
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by HMS_Beagle View Post
    No you didn't. You posted a 2001 paper you didn't read and don't understand describing the origin of self-replication

    Source: Johnston et. al.

    The RNA world hypothesis regarding the early evolution of life relies on the
    premise that some RNA sequences can catalyze RNA replication. In support of
    this conjecture, we describe here an RNA molecule that catalyzes the type of
    polymerization needed for RNA replication.

    © Copyright Original Source

    Right, it's a catalyst for replicating RNA, so the ribozyme doesn't replicate.

    The paper said nothing about the molecule having to form randomly by falling together all at once like your IDiot "calculations" require. That was your lie.
    Well, how else would the ribozyme form? It's not replicating, so natural selection is not involved.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  10. #128
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    Biomolecules do not act alone in the biological processes of replecation.
    Certainly not.

    No, the formation of biomolecules are determined by chemistry of physiology not randomness. They do not form randomly.
    Yes, they do form randomly, if they do not replicate.

    Still the question has not been answered. Where are the effects of feedback from natural selection accounted for in your "calculations"?
    But repeating the question will not change my reply: I selected a biomolecule that is not self-replicating, so it has to form randomly. You need replication and competition for natural selection, for evolution to work.

    Even in the chemical processes in the biomolecules the cause and effect evts are all that is random. The resulting reactions and products are determined by the Laws of Nature via the laws of chemistry. I mentioned before the limited reactions to achieve the desired geometry of organic chemistry is not random, would also be true in abiogenesis.
    Well, what distribution would explain the interactions of molecules in solution, if not a uniform random one?

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

  11. #129
    tWebber shunyadragon's Avatar
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    Quote Originally Posted by lee_merrill View Post
    Right, it's a catalyst for replicating RNA, so the ribozyme doesn't replicate.


    Well, how else would the ribozyme form? It's not replicating, so natural selection is not involved.

    Blessings,
    Lee
    Your moving around the goal posts and basing your argument on the very jello-like 'argument of ignorance' concerning the the question of the origin of the ribosomes, and actually not reading the references, and NOT responding to the references, nor The Lurch,.

    Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/



    Origin and Evolution of the Ribosome
    George E. Fox

    Abstract
    The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. Central to its development were RNAs that spawned the modern tRNAs and a symmetrical region deep within the large ribosomal RNA, (rRNA), where the peptidyl transferase reaction occurs. To understand pre-LUCA developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. Using such timing events, the relative age of various proteins and individual regions within the large rRNA are inferred. An examination of the properties of modern ribosomes strongly suggests that the initial peptides made by the primitive ribosomes were likely enriched for l-amino acids, but did not completely exclude d-amino acids. This has implications for the nature of peptides made by the first ribosomes. From the perspective of ribosome origins, the immediate question regarding coding is when did it arise rather than how did the assignments evolve. The modern ribosome is very dynamic with tRNAs moving in and out and the mRNA moving relative to the ribosome. These movements may have become possible as a result of the addition of a template to hold the tRNAs. That template would subsequently become the mRNA, thereby allowing the evolution of the code and making an RNA genome useful. Finally, a highly speculative timeline of major events in ribosome history is presented and possible future directions discussed.

    A major commonality of all cellular life is the coupling between translation and transcription mediated by the genetic code. Comparative genomics has further refined this by revealing the presence of an “RNA metabolism” (Anantharaman et al. 2002) or “Persistent proteome” (Danchin et al. 2007) that is basically a compendium of essentially universal genes involved in translation, transcription, RNA processing and degradation, intermediary and RNA metabolism, and compartmentalization. DNA replication likely arose later because the core enzymes involved in the process are not related (Bailey et al. 2006 and others). Together these universal genes comprise what is frequently referred to as LUCA, the last universal common ancestor (Benner et al. 1993; Lazcano 1994; Mushegian and Koonin 1996; Kyrpides et al. 1999). It is noteworthy that no matter how they are defined, by far the largest numbers of genes in LUCA are associated with translation. Indeed, the translation machinery as represented in LUCA is essentially complete indicating that major events in its origins occurred before LUCA. Thus, it might appear that the origins of the translation machinery would be hopelessly obscured by time. Nevertheless, as will be discussed herein, substantial although necessarily incomplete, evidence relating to the origins and early development of the translation machinery and its relation to other core cellular processes continues to exist in the primary sequences, three-dimensional folding, and functional interactions of the various macromolecules involved in the modern versions of the translation machinery.

    The modern ribosome consists of small and large subunits (30S and 50S in Bacteria and Archaea) that come together during the initiation of protein synthesis remain together as individual amino acids are added to a growing peptide according to information encoded on the mRNA, and finally separate again in conjunction with the release of the finished protein. Each subunit is an RNA/protein complex. In Bacteria and Archaea, the 50S subunit typically contains a 23S rRNA and a 5S rRNA whereas the 30S subunit contains the 16S rRNA. Peptide bond synthesis occurs in the 50S subunit at the peptidyl transferase center, (PTC), and codon recognition occurs at the decoding site, which is in the small subunit. Transfer RNAs, (tRNA), bridge the two subunits occupying, at various times in the synthesis cycle, the A, P, or E (exit) sites of the 50S subunit and the decoding site in the 30S subunit. A universal CCA sequence at the 3′ end of the tRNA is the point of attachment of the amino acid and later the growing peptide chain to the tRNA. The A, P, and E sites are partly in the small subunit and partly in the large subunit such that a tRNA can be in a hybrid site (e.g., the A site in the 30S and P site in the 50S. The mRNA is exclusively found in the small subunit where it interacts with the anticodon loops of the tRNAs. As the nascent protein is synthesized it passes through an exit tunnel that begins at the PTC center and ultimately exits from the back of the 50S subunit. Synthesis is a dynamic cyclic process in which tRNAs enter the ribosome bringing amino acids as specified by the mRNA and move through the machinery, which undergoes a series of coordinated motions that drive the process (Steitz 2008). These include the movements of the tRNAs between sites, opening and closing of the L1 stalk on the 50S subunit and the ratcheting of the small subunit relative to the large subunit (Frank and Agrawal, 2000), which has recently been elucidated in structural detail (Zhang et al. 2009).

    Diverse species (Escherichia coli, Haloarcula marismortui, Thermus thermophiles, and Deinococcus radiodurans) are represented among the various atomic resolution ribosome structures now available (Ban et al. 2000; Yusupov et al. 2000; Wimberly et al. 2000; Schuwirth et al. 2005; Selmer et al. 2006; and others). These structures encompass 30S and 50S subunits as well as the whole 70S ribosome. In addition, cryoelectron microscopy studies have revealed dynamic motions associated with the ribosome (Frank and Agrawal 2000; Connell et al. 2007; and others). These ongoing high resolution structural studies provide the opportunity to examine the relative age of features within the ribosome such as the A, P, and E sites, the exit tunnel, the L7/L12 region, and the L1 region that facilitate the entry and exit of tRNAs.


    It is believed that the peptidyl transferase center, (PTC), which encompasses the large subunit portions of the A and P sites of the ribosome, is structurally the same in both the 50S and 70S subunits (Steitz 2008). When comparing 50S subunit structures between Archaea and Bacteria one again finds that the structures are essentially the same. However, the E site structure is different. In Archaea L44e interacts with the E-site tRNA but this protein is missing in Bacteria with the result that the tRNA CCA end is positioned differently. Hence, the A and P sites likely predate the E site, which may have been added post-LUCA (Steitz 2008).

    The portion of 23S rRNA comprising the PTC contains a region of approximately 165 bases that shows high twofold pseudo symmetry (Agmon et al. 2005; Zimmerman & Yonath 2009). The two 82 nucleotide halves of the symmetrical region correspond to the 50S portion of the A and P sites of the ribosome. In fact, the essence of this region is contained in a single contiguous self-folding RNA (Smith et al. 2008). The PTC is located in Domain 5 of the 23S rRNA structure.

    Recently, Hsiao et al. (2009) superimposed the structure of the large subunit RNAs from two ribosome crystal structures and sectioned the resulting structure into concentric shells with the PTC at the center. They, like others (Ban et al. 2000; Wimberly et al. 2000), found that ribosomal proteins (r-proteins) are effectively absent from the PTC region, which is why the ribosome is regarded as fundamentally an RNA machine. To the extent that protein elements are in proximity to the PTC, they are short, largely unstructured peptides rather than globular elements. The globular regions are mainly on the surface of the ribosome (Ban et al. 2000; Wimberly et al. 2000). A major stabilizing element in the PTC region is instead Mg2+ interactions. In many cases, the phosphate oxygen atoms act as inner sphere Mg2+ ligands (Hsiao et al. 2009; Hsiao and Williams 2009). Thus, consistent with the notion of a preceding RNA world, the structure of the PTC seems to have evolved before the availability of proteins.

    Although the modern translation machinery is very complex, two small RNAs, the PTC RNA fragment and tRNAs are at its core. Both of these are less than 100 nucleotides in length, and their importance supports the notion that the translation machinery was originally a discovery of the RNA world. In fact, the ability to synthesize coded peptides of increasing complexity would eventually terminate the RNA world and create the RNA/protein world. The seldom discussed issue is whether such a termination would have occurred before (e.g., brief RNA world) or after the discovery of an RNA replicase (extended RNA world). If peptide synthesis arises quickly, then their will neither be time nor need for extensive catalysis of biochemical reactions by RNA. If reasonable, the rapid appearance of a translation system may even eliminate the need to validate the RNA world by demonstrating the self-replicating RNA system that has proven experimentally difficult to achieve.

    Go to:
    tRNA ORIGINS AND INCREASING RNA COMPLEXITY
    Because of its obvious importance, considerable attention has been focused on the origins of the tRNA and numerous models have been proposed and recently reviewed (Di Giulio 2009). The most popular model (Noller 1993; Maizels and Weiner 1993 and 1994; Schimmel et al. 1993; Schimmel and Henderson 1994), envisions the tRNA as having two domains, each encompassing half the molecule. One domain contains the terminal CCA sequence to which the incoming amino acid or growing peptide is attached. The second domain contains the anticodon and associated loop that interact with the mRNA. The two domains are frequently envisioned as being of different age with the CCA domain being older. Support for this idea stems from the fact that the CCA domain alone forms a “minihelix” to which modern tRNA synthetases can readily attach specific amino acids. Such aminoacylation has also been shown with evolved ribozymes (Lee et al. 2000), which can be surprisingly small (Chumachenko et al. 2009). In fact, aminoacylation has been reported without any enzyme or ribozyme at all (Tamura and Schimmel 2004). Furthermore, it has also been reported that a minihelix when incorporated into the 50S subunit can participate in peptide bond formation (Sardesai et al. 1999). Indeed, even the addition of a single cytosine (equivalent to C75 of modern tRNAs) to puromycin is apparently sufficient to allow peptide bond formation (Brunelle et al. 2006). Thus, it may initially only be necessary to have the CCA segment alone (Nissen et al. 2000). The 5′ domain of the tRNA is not consequential to peptide bond formation and could have been added later. If the tRNAs evolved from the one domain structure or an even simpler structure, then protein synthesis would likely have begun as a noncoded process (Schimmel and Henderson 1994). Single domain or even smaller aminoacylated RNAs are especially attractive in an RNA world where synthesis of larger RNAs is likely to be difficult. Synthesis of random oligomers in the 20–40 size range has been shown (Joshi et al. 2009; Powner et al. 2009; Szostak, 2009; Ferris et al. 1996) but the path to prebiotic synthesis of large RNAs is not without difficulties (Orgel, 2004).

    How does one obtain RNAs of increasing complexity, such as those of modern tRNAs or the PTC RNA, without a true RNA replicase? There are two core possibilities, ligation and hybridization. RNA ligation has been shown to be feasible in an RNA World (Hager et al. 1996; Hager and Szostak 1997; McGinness and Joyce 2002). Thus, it is of interest that the tRNA “cloverleaf” secondary structure can be formed by a direct duplication, e.g., ligation, of an appropriate stem loop structure (Di Guilio 2002). The possible relevance of this idea was enhanced further by the demonstration that it was possible to actually replicate all the major tertiary interactions seen in modern tRNAs when two appropriate stem loop structures were ligated together (Nagaswamy and Fox 2003).

    An alternative method of readily obtaining more complex structures is to simply hybridize small fragments to one another such that a larger RNA with many “nicks” is assembled. These nicks might or might not be sealed at a later stage. In Nanoarchaeum equitans, several tRNAs are encoded as partially complementary half molecules, which are then ligated together to form a tRNA (Randau et al. 2005a and b). In Euglena gracillis the large subunit rRNA is comprised of 14 discrete RNA fragments held together by hybridization events that form various helical elements. Not only are the fragments not coded in the order they appear in the final RNA but they are actually intermingled in the genome with similar fragments of the small subunit RNA (Smallman et al. 1996).

    © Copyright Original Source



    It may help if you read the whole article, and respond to the other posts and references you have avoided.
    Glendower: I can call spirits from the vasty deep.
    Hotspur: Why, so can I, or so can any man;
    But will they come when you do call for them? Shakespeare’s Henry IV, Part 1, Act III:

    go with the flow the river knows . . .

    Frank

    I do not know, therefore everything is in pencil.

  12. #130
    tWebber lee_merrill's Avatar
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    Quote Originally Posted by shunyadragon View Post
    If you are shifting the subject to the issue of abiogenesis and biomolecules. Well, yes there are many unknowns, which is a given concerning abiogenesis. . . . but yes, there are many advances in the science of abiogenesis that explain the role of the biomolecules in the primitive forms that lead to the first life forms as follows in this reference.
    Here they describe precursors to nucleotides and lipids and amino acids. In my example, I assume the presence of nucleotides in abundance. You still need a ribozyme to assemble, for instance.

    Blessings,
    Lee
    "What I pray of you is, to keep your eye upon Him, for that is everything. Do you say, 'How am I to keep my eye on Him?' I reply, keep your eye off everything else, and you will soon see Him. All depends on the eye of faith being kept on Him. How simple it is!" (J.B. Stoney)

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