What is the origin of life on Earth?

Discussion in 'Biology & Genetics' started by valich, Oct 10, 2005.

  1. Crunchy Cat F-in' *meow* baby!!! Valued Senior Member

    The question is asking what was / were the first chemical automation(s) that could reproduce and led to today's life forms. We might get lucky someday and find some record of whatever they were; however, I don't see an accurate answer being derivable with our present knowledge and technology.
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  3. .... em, actually Nexus the "antithesis" I was talking about would have been the difference between the conditions space formed hydrocarbons would have formed in (if your going with the Pan Spermia hypothesis) and those they would have been finding themselves being deposited into if been deposited on the Earth back around 4.5 billion years back.

    Possibly a poorly considered sentence I've no doubt, but I was only being very, very general in my positing.

    Basically all I was saying to Ophiolite was that, on the one hand, Pan Spermia offers a means by which rich, lovely, useful spaced formed hydrocarbons (or else the materials for the making there off) can be collected up and and introduced into Earths chemistry set - but on the other hand, as soon as introduced, those conditions of higher temperature and pressure rip the those self same elements apart in the process meaning that processes here on Earth have to find a way of reconstituting them back into things vital for the subsequent basis of organic chemistry to begin.

    However, if your saying water formed as early as 4.3 billion years ago - that's a different kettle of proto-fish altogether...

    And actually, I freely confess I've no idea how we got onto this subject in the first place....

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    I you're burying the plane ticket old boy, count me in. Might get in spot of Marlin fishing whilst I'm about it... Nothing in the world better than being tanked to the gills in a boat. Except, obviously, being tanked to the gills in a boat with the Vulcan woman off Enterprise, a bottle of baby oil and her sisters...

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    Personally Valich, I don't. It's that simple. It's just me and Ophiolite were batting it back and forth regarding the subject of Pan Spermia and I was simply outlining a few of the problems I have with the notion in general is all, really.

    Whole things seems to have gone off at a tangent from there. No idea why...

    As to the use of the word "forged", its just to convey the idea of something taking place at temperature and pressure considerably over and above the extreme colds of space. Again, associated wholly with my conversation with Ophiolite. Probably very little to do with anything else.

    One thing though, question I'd like to run round all of you since your here - bear with me.

    Valich - y'seem to be going on ahead now looking for ways in which either amino acids or proto-amino-acids could possibly have first formed. I understand why, but is this actually the thing y'should be looking at?

    I'll give you my reasoning here, and if it comes over as an almost philosophical question, forgive it its trespasses but give it a mull over anyway.

    You're looking to understand how, ultimately, the building blocks to life got started and your going for, ultimately, DNA - but is DNA actually Life?

    In a system where life exists DNA (or anything that performs a similar function) is indeed both the blue prints and pre-cursor of how life is reproduced. That's a given, you can put that in the bank a gain interest on it.

    But is DNA actually the what causes life to exist, or is DNA actually a consequence itself of Life process - ie, the formation of amino acids being a process that takes place at the behest of something living so that it possessed a chemical blueprint which will effectively reproduce it?

    There's a biological imperative in differentiating between the two things, because both paint a very, very different picture of how life first kicks off.

    Get them the wrong way round and you end up putting the cart before the horse, hence my wanting you to be very clear about what it is you think your looking for - you may very well just be chasing an assumption based on what we know of the workings of a Life rich world.

    The origins of that aren't necessary guaranteed to be the same merely as a consequence. In fact, the very origins of life are practically guaranteed to be quite, quite different to what learns to develop subsequently.
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  5. Ophiolite Valued Senior Member

    We may consider that life requires a suite of four things:
    1) Metabolism
    2) Replication
    3) Raw materials
    4) Energy

    The last two are inputs, the first two are outputs.
    There is no problem with energy: we can look to radiative energy or chemical energy as the more probable, though not the only, sources.
    There is abundant evidence for the abundance of a large variety of organic molecules in interstellar space and a perfect delivery system in comets. No doubt these were supplemented by in situ generation of pre-biotic molecules.
    It is the output side of the equation that is problematic.
    It may be misleading to assume that we have to have metabolism and replication developing simultaneously within the same chemical system. For example, we can envisage a complex of autocatalytic reactions occuring with the mix of organic moelcules entrapped within water droplets suspended in the atmosphere, yet incapable of reproduction and hence Darwinian evolution.

    So, to identify the first life we have first to identify possible candidates for a) a self sustaining metabolic system b) a self-replicating system, ideally associated with the former. Now that shouldn't take to long should it? (On a geological time scale.)
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  7. valich Registered Senior Member

    As was stated in ane early post by CharonZ, backed up by a citation, RNA came before DNA. There's no definitive consensus that life formed or was "forged" in hot extreme environment under pressure. Thermophiles thrive in it but other, just as ancient, primitive types of bacteria don't: Methagons only need CO2, Hallophiles only live in salty environments, both are not heat seeking organisms.

    A very very relative article was justed posted on CNN about a new type of flagellite now in the process of being created, emphasizing the role of endosymbiosis in life. Put the right ingredients enclosed in a membrane and endosymbiosis can take over to form life:

  8. valich Registered Senior Member

    Your repeating exactly what I've been saying over-and-over again: a self-replicating metabolic system, and it wouldn't have to be necessarily encapsulated. That could come later to make it more self-sustaining as a unique type of species.

  9. Y'see, you really are taking to this business we were discussing earlier terribly well! Keep up the good work -

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  10. Ophiolite Valued Senior Member

    You may have misunderstood me. I meant it shouldn't take too long to find candidates, not that the process wouldn't take too long.
    Tomorrow, if the wind is up, I'll post some thoughts on the metabolic side of things.
  11. valich Registered Senior Member

    I think I've got it. My recent dwellings on thermodynamics made me aware that the 2nd law provides the "Driving Force" to produce order out of disorder. Then I remembered what I was taught about Sol Spiegelman's and his successor's experiments. He was able to produce self-replicating polymerase ribozymes (self-replicating bits of RNA polynucleotides, nucleic acids consisting of 220 bases) under experimental conditions somewhat akin to the Miller/Urey experiments (test tube, salts, nutrient solution, mix the ingredients - wham!). And the same is true of crystals in Nature. Though not metabolic, crystallization is a self-replicating system. Therefore, what came first was a self-replicating system: not a metabolic system. This then could have easily been encapsulated by a lipid membrane (the origin-of-life "bubble theory") and through endosymbiosis the remaining ingredients could have been easily obtained to create a metabolic self-contained self-replicating system: self-replication of an inorganic polypetide (a pre-RNA world) led to self-replication of RNA (an RNA world) that was then the origin of our RNA-DNA world.

    Starting with the Miller/Urey experiments that produced amino acids out of nitrogen, ammonia, methane, and hydrogen, there have been other experiments that produced nucleic base pairs, and there's that experiment that produced glyceraldehide out of a formaldehyde mixture experiment. Glyceraldehide is used in the glycolysis cycle to produce the basic energy molecule used in organisms (ATP) is one of the oldest energy producing mechanisms known. Its main input is simply sugar (glucose), but they couldn't get it to self-replicate. Therefore, if a self-replicating system was already encapsulated in a membrane, there's no reason why endosymbiosis couldn't have engulfed it into the system, combined it with the existing bases to create a replicating coding system; thus the origin of life. Any missing loop hole ingredients in the pre-biotic world four billion years ago could've been picked up from an extraterrestrial source at anytime in the history of earth no matter what those pre-biotic conditions were, since we're not yet sure what they were.
  12. Idle Mind What the hell, man? Valued Senior Member

    I don't get the relevance of drawing a connection between crystal formation and a self-replicating organic molecule.
    I'm interested to see how you think this is possible. Jumping from an encapsulated self-replicating nucleotide to a nucleotide sequence that codes for a particular molecule. [Keeping in mind, of course, that in order for a portion of glycolysis to be formed, you would need to have a code for either the enzyme triosephosphate isomerase or aldolase which generate phosphoglyceraldehyde in the glycolytic cycle from either dihydroxyacetone or fructose-1,6-bisphosphate respectively. Or, at the very least an ancestral enzyme to the aforementioned.]

    And, even if you were able to have a portion of the pathway and are able to generate phosphoglyceraldehyde, what good will that do without the other steps?
  13. valich Registered Senior Member

    Glyceraldehyde and most of the other basic sugars have already been experimentally formed by condensation of formaldehyde and we already know the abiotic route to almost all RNA. We've experimentally formed almost all the necessary amino acids, nucleotide bases, components of all nucleic acids: the major bases of RNA. I don't see it as a big "quantum leap" to put them all together to start a coding?
  14. Idle Mind What the hell, man? Valued Senior Member

    Unfortunately, that's not how it works. You don't go backwards from a product of an enzymatic reaction in a pathway to a gene that codes for the enzyme that catalyzes the reaction. Do you understand how gene transcription and translation work?

    I realize that glyceraldehyde was present, as well as nucleotides, amino acids, and other precursor and monomer components, but to say that a self-replicating (and I use bold and italicized text for a reason, maybe you should focus there for a second or two) nucleotide sequence which becomes encapsulated beside a glyceraldehyde molecule and rearranges itself to begin formation of that molecule is mystifying to say the least.
  15. valich Registered Senior Member

    I think it would just be a jump in Nature: not a quantum leap. More like a fusion within the cell, like genome fusion occurs:

    "Cairns-Smith shows that in addition to the carbon-based self-replicating crystals of DNA and RNA, there are also much simpler (he calls them “low-tech”) silicon-based self-replicating crystals, and these silicates, as they are called, could themselves be the product of an evolutionary process. They form the ultra-fine particles of clay, of the sort that builds up just outside the strong currents and turbulent eddies in streams, and the individual crystals differ subtly at the level of molecular structure in ways that they pass on when they “seed” the processes of crystallization that achieve their self-replication. Cairns-Smith develops intricate arguments to show how fragments of protein and RNA, which would be naturally attracted to the surfaces of these crystals like so many fleas, could eventually come to be used by the silicate crystals as “tools” in furthering their own replication processes."

    see also "A Self-Replicating Hexadeoxynucleotide," byDr. Günter von Kiedrowski, Chemical Evolution Laboratory, The Salk Institute

    see also "Kinematic Self-Replicating Machines," by Robert A. Freitas Jr. and Ralph C. Merkle, Landes Bioscience, 2004.


    "phosphate is an unlikely component of the first replicating system. This is due to the low solubility of phosphate in the present ocean (3 x 10(-6) M), as well as the difficulty of prebiotic activation of phosphates.
  16. valich Registered Senior Member

    "The crystallization event that led to the selection of RNA as the principal prebiotic biopolymer can be more thoroughly explored. If nucleotide analogs preceded nucleotides as monomeric building blocks, then it should be possible to selectively polymerize activated ribonucleosides on "unnatural" templates. Very little is known about the production of hybrid helices involving both RNA and "other" strands, yet such structures must be postulated as transitory intermediates on the way to contemporary genetic material. In addition, the self-selection of particular RNA oligonucleotides can be attempted from random sequence mixtures or from mixtures in which some of the oligonucleotides have been "poisoned" by inclusion of enantiomerically impure monomers (e.g., mixed ribose-arabinose backbones). Ligation may avoid the problems of enantiomeric cross-inhibition described for polymerization."
    "Experimental Testing of Theories of an Early RNA World," by Andrew D. Ellington.

    We've already been able to experimentally create oligonucleotides.

    "Examples of self-assembly: (A) Crystal structure of a ribosome. (B) Self-assembled peptide-amphiphile nanofibers. (C) An array of millimeter-sized polymeric plates assembled at a water/perfluorodecalin interface by capillary interactions (D) Thin film of a nematic liquid crystal on an isotropic substrate."
    "SELF-ASSEMBLY AT ALL SCALES," by: Whitesides, George M., Grzybowski, Bartosz, Science, 00368075, 3/29/2002, Vol. 295, Issue 5564
  17. Idle Mind What the hell, man? Valued Senior Member

    Those links are all nice and irrelevant and such, and I am aware that oligonucleotides and other pre-biotic molecules have been experimentally created. I am not contesting that. What I am contesting is your proposed mechanism for the origin of a part of the glycolytic pathway. And, I have never used the term quantum leap in this thread, or anywhere else, so where you got that from is a mystery.

    Answer me this: do you understand how gene transcription and translation works?
  18. valich Registered Senior Member

    I guess I shouldn't be using the term "quantum leap" on a science forum but in the layman use of the word, as I am using it (this thread is not about quantum mechanics, right?), I'm simply meaning a dramatic big transition or jump.

    If you consider that the RNA-world came before the DNA-RNA world did, then translation had to come before transcription, right? So transcription wouldn't even be relative yet. Ribosomes have already been experimentally created so the amino acid sequence is already there. It is commonly being hypothesized that tRNA came first; therefore I guess you would have the codon and three-base sequence already there. Don't know. But that seems to be the most scientific consensus amongst evolutionist. I'm still researching and reading a lot about it, but I find it fascinating.
  19. Idle Mind What the hell, man? Valued Senior Member

    Ribosomes have been experimentally created? Fully functioning with all subunits and RNA sequences up to 4700 nucleotides in length? This done with a Miller-Urey type experiment? I find that very difficult to believe. So difficult in fact, that I will have to see the original published research before I will take your word for it.

    What codon is already there?
  20. valich Registered Senior Member

    The RNA world was between 4.2-3.8 bya, DNA/proetin world 3.8-3.75 bya. origin of life 3.8-3.7 bya. from "Biological Evolution," by Kardong 2005.
    But we have fossil evidence from Western Australia of ancestorial cyanobacteria dating back to 3.86 bya.

    The first form of life probably would have replicated by direct RNA copying, like in viroids (viroids are single-stranded RNA molecules with only about 250 nucleotides with base pairings and codons in the RNA). The linear sequence of nucleotides present would direct the linear sequence of amino acids just like in mRNA translation. Wouldn't it make sense that tRNA came first since it is the smallest RNA molecule, yet still very similar to mRNA? We've already produced many of the organic compounds of RNA and DNA through simulated Earth early atmosphere experiments, but not replication.

    What I'm doing is proposing a very plausible hypothetical construct. What can you contribute to it?

    "Viroids and satellite RNAs are of great interest because they are the smallest and simplest replicating molecules known and they may represent living fossils of pre-cellular evolution."
    from "Viroids and other sub-viralpathogens of plants:the smallest living fossils?," by Nicola Spence & Dez Barbara, MicroBiology Today, vol.27 2000.

    "The discovery that RNA molecules can act as catalysts provides a possible solution to a long-standing dilemma: DNA encodes the genetic information of proteins but DNA replication and transcription requires proteins. So which came first in the evolution of life? But if RNA can serve both as a repository of information (in its sequence of nucleotides) and as a catalyst, then it has both properties needed for life. This provides the basis for the notion that life began as RNA - the so-called "RNA World". However, all the reactions described above involve RNA acting on RNA (not protein) and (except for Ribonuclease P) are self-limited. There is evidence that RNA can catalyze the synthesis of proteins?

    The Ribosome is a Ribozyme: Ribosomes are huge aggregates containing 3 (4 in eukaryotes) rRNA molecules and scores of protein molecules. The three-dimensional structure of the large (50S) subunit of a bacterial ribosome was published in August 2000. It clearly shows that formation of the peptide bond that links each amino acid to the growing polypeptide chain is catalyzed by the 23S RNA molecule in the large subunit. The 31 proteins in the subunit probably provide the scaffolding needed to maintain the tertiary structure of the RNA world."
  21. Idle Mind What the hell, man? Valued Senior Member

    Viroids can't replicate themselves. They require the translation 'machinery' that is present in the nucleus of eukaryotic cells (their hosts are mostly plants). Viroids and viruses likely came about later, once transposons and other such sequences started becoming more common.
    No, you aren't. You are reading what a bunch of experts who have dedicated their entire careers to research in this area have written, and adding your own uneducated spin on what they are saying. Your hypothetical is completely implausible. What can I add to it? I can show you where you are in error, and have you rethink sections so that they are plausible. But you refuse to take what I say and rework your thinking, just like in the evolution thread. You post a bunch of studies and try to defend your flawed position. That's not science.
  22. valich Registered Senior Member

    What I proposed was that a self-replicating system could have first been encapsulated by a lipid membrane and then this system could have fused with many other organic compounds were engulfed by endosymbiosis to eventenually lead to a encapsulated self-replicating metabolic system. there is a lot of literature on individual aspects of this hypothetical construct, but they are all speculating too. Just like I am.

    One similar theory to my hypothetical construct is Lerman's Bubble Theory arising on turbuent coastal shores but he does not address the issue of self-replication. His hypothetical construct is that an oily bubble enclose a prebiotic reactor. I think my construct is more plausible as it acounts for replication: a precursor to reproduction.

    It is not known for sure yet whether viroids require the plant's translation machinery. Some biologists refer to viroids as the simplest automatic replicator without the need for the host's RNA polymerase or other machinery. We just do not know yet.

    In any case, just as in some - but definitely not all! - of the other forums, many participants are quick and long on criticism, but short on any productive thought. This is very very sad and serves to stifle creative thought. I guess this is how they get their immature jollies: by cutting other people down, rather than contributing any progress, knowledge or information.

    While I speculate myself, I am comparing everything that I can find in the literature, while treading along in my own educational research career.
  23. Idle Mind What the hell, man? Valued Senior Member

    This is not endosymbiosis. Endosymbiosis is the engulfing and incorporation of another living organism which can live symbiotically inside the engulfing organism. Endosymbiosis does not include endocytosis of organic molecules.
    I disagree entirely, for we are not trying to prevent you from thinking, but rather we are trying to get you to think in a way that is a little less uneducated. We are guiding through our criticisms, and showing you where your thinking is false, or where you have misinterpreted something, so that you can revise your thoughts and create more realistic and fulfulling explanations.

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