Darwinism Evolution Intelligent Design

Latest origin of life theory – “RNA reactor” preceded life – prompts question

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At Physorg , Lisa Zyga reports on a new origin of life theory, “RNA reactor could have served as a precursor of life” (July 11, 2011):

The biggest piece of support for RNA molecules as pre-life forms is that RNA can act as both genes (to store information) and enzymes (to catalyze chemical reactions). Like DNA, RNA is made up of a long chain of nucleotides. However, scientists do not know how a self-replicating RNA system could have arisen from a pool of random polynucleotides.

Some researchers have turned to natural selection among precursors to RNA replicators.

As described in previous research, RNA replicators can transmit information from one molecule to another so that the information survives even when the original carrier molecules have become degraded. Here, the researchers have investigated how RNA replicators may have arisen from simpler RNA reactors billions of years ago.

[ … ]

Most importantly, the computer simulations showed that the RNA reactor can perform weak replication based on information transmission by hybridization of the RNA strands. As the researchers explained, evidence of information transmission appears as an unexpected increase in the lifetime of certain sequences.

Now they hope to try it in the lab.

Question: If any of these origin of life these scenarios work, why isn’t life spontaneously generating all around us? The only answer so far encountered is that Darwinian natural selection would immensely favour the more complex, developed life forms, so no new ones could start.

But that’s not very convincing. Darwinian natural selection does not necessarily favour the more complex over the less complex – humans and horses over bacteria and viruses, for example. It’s not that we seldom see it. We don’t see it at all.

Another response is that the conditions on Earth are no longer right. Okay, so they are favourable to the preservation of life but not to its origin. In that case, we should see many failed attempts at origin. Do we?

Zyga informs us that “Nobody knows quite how life originated on Earth, but most scientists agree that living cells did not abruptly appear from nonliving cells in a single step.”

Here’s a thought: If after all this time, “most scientists” (scratch that, all scientists) have produced only a mass of conflicting theories, maybe we shouldformulate a new principle:

When what “most scientists agree” on produces no progress, most scientists are probably wrong at a basic level.

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13 Replies to “Latest origin of life theory – “RNA reactor” preceded life – prompts question

  1. 1
    kairosfocus says:

    Soo, what’s happening in your friendly local soup-can?

  2. 2
    bornagain77 says:

    Quite apart from these highly speculative ‘just so’ stories about how life may have spontaneously arisen from purely materialistic processes, the ACTUAL evidence is anything but encouraging for the atheistic materialist who refuses to even consider God’s providence:

    ==================

    notes: for example,,,

    Materialists have not even created all 4 ‘letters’ of RNA by natural means:

    Scientists Say Intelligent Designer Needed for Origin of Life Chemistry
    Excerpt: Organic chemist Dr. Charles Garner recently noted in private correspondence that “while this work helps one imagine how RNA might form, it does nothing to address the information content of RNA. So, yes, there was a lot of guidance by an intelligent chemist.” Sutherland’s research produced only 2 of the 4 RNA nucleobases, and Dr. Garner also explained why, as is often the case, “the basic chemistry itself also required the hand of an intelligent chemist.” http://www.evolutionnews.org/2......html#more

    Stirring the Soup – May 2009
    “essentially, the scientists have succeeded in creating a couple of letters of the biological alphabet (in a “thermodynamically uphill” environment). What they need to do now is create the remaining letters, and then show (actually demonstrate) how these letters were able to attach themselves together to form long chains of RNA, and arrange themselves in a specific order to encode information for creating specific proteins, and instructions to assemble the proteins into cells, tissues, organs, systems, and finally, complete phenotypes.”
    Uncommon Descent – C Bass:
    http://www.uncommondescent.com.....-the-soup/

    Abiogenic Origin of Life: A Theory in Crisis – Arthur V. Chadwick, Ph.D.
    Excerpt: The synthesis of proteins and nucleic acids from small molecule precursors represents one of the most difficult challenges to the model of prebiological evolution. There are many different problems confronted by any proposal. Polymerization is a reaction in which water is a product. Thus it will only be favored in the absence of water. The presence of precursors in an ocean of water favors depolymerization of any molecules that might be formed. Careful experiments done in an aqueous solution with very high concentrations of amino acids demonstrate the impossibility of significant polymerization in this environment. A thermodynamic analysis of a mixture of protein and amino acids in an ocean containing a 1 molar solution of each amino acid (100,000,000 times higher concentration than we inferred to be present in the prebiological ocean) indicates the concentration of a protein containing just 100 peptide bonds (101 amino acids) at equilibrium would be 10^-338 molar. Just to make this number meaningful, our universe may have a volume somewhere in the neighborhood of 10^85 liters. At 10^-338 molar, we would need an ocean with a volume equal to 10^229 universes (100, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000, 000) just to find a single molecule of any protein with 100 peptide bonds. So we must look elsewhere for a mechanism to produce polymers. It will not happen in the ocean.
    http://origins.swau.edu/papers.....fault.html

    Refutation Of Hyperthermophile Origin Of Life scenario
    Excerpt: While life, if appropriately designed, can survive under extreme physical and chemical conditions, it cannot originate under those conditions. High temperatures are especially catastrophic for evolutionary models. The higher the temperature climbs, the shorter the half-life for all the crucial building block molecules,
    http://www.reasons.org/LateHea.....iginofLife

    The origin of life–did it occur at high temperatures?
    Excerpt: Prebiotic chemistry points to a low-temperature origin because most biochemicals decompose rather rapidly at temperatures of 100 degrees C (e.g., half-lives are 73 min for ribose, 21 days for cytosine, and 204 days for adenine).
    http://www.ncbi.nlm.nih.gov/pubmed/11539558

    Chemist explores the membranous origins of the first living cell:
    Excerpt: Conditions in geothermal springs and similar extreme environments just do not favor membrane formation, which is inhibited or disrupted by acidity, dissolved salts, high temperatures, and calcium, iron, and magnesium ions. Furthermore, mineral surfaces in these clay-lined pools tend to remove phosphates and organic chemicals from the solution. “We have to face up to the biophysical facts of life,” Deamer said. “Hot, acidic hydrothermal systems are not conducive to self-assembly processes.”
    http://currents.ucsc.edu/05-06/04-03/deamer.asp

    Self Replication and Perpetual Motion – The Second Law’s Take On The RNA World
    http://theory-of-evolution.net.....tion-4.php

    Problems of the RNA World – Did DNA Evolve Twice? – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4564682

    Moreover, because of Shannon channel capacity, the first DNA code of life on earth had to be at least as complex as the current DNA code found in life:

    Shannon Information – Channel Capacity – Perry Marshall – video
    http://www.metacafe.com/watch/5457552/

    “Because of Shannon channel capacity that previous (first) codon alphabet had to be at least as complex as the current codon alphabet (DNA code), otherwise transferring the information from the simpler alphabet into the current alphabet would have been mathematically impossible”
    Donald E. Johnson – Bioinformatics: The Information in Life

    Biophysicist Hubert Yockey determined that natural selection would have to explore 1.40 x 10^70 different genetic codes to discover the optimal universal genetic code that is found in nature. The maximum amount of time available for it to originate is 6.3 x 10^15 seconds. Natural selection would have to evaluate roughly 10^55 codes per second to find the one that is optimal. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. (Fazale Rana, -The Cell’s Design – 2008 – page 177)

  3. 3
    Mung says:

    The only answer so far encountered is that Darwinian natural selection would immensely favour the more complex, developed life forms, so no new ones could start.

    That seems a bit ad hoc to me.

    Another response is that the conditions on Earth are no longer right.

    Also seems ad hoc.

    but most scientists agree that living cells did not abruptly appear from nonliving cells in a single step.”

    From nonliving cells?

    But why not? At what point does a cell become alive?

  4. 4
    Elizabeth Liddle says:

    Mung:

    But why not? At what point does a cell become alive?

    Well, that’s the point – if the process of transition isn’t abrupt, there won’t be a “point”.

    Just as, in fact, there isn’t a “point of death” either. Or is there?

  5. 5
    Mung says:

    I’m at the point of death every moment. Aren’t we all?

    We just don’t like to think about it.

  6. 6
    bornagain77 says:

    ,,as to this question: ‘Just as, in fact, there isn’t a “point of death” either. Or is there?’

    Actually there is;

    The Unbearable Wholeness of Beings – Steve Talbott
    Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary.
    http://www.thenewatlantis.com/.....-of-beings

    ,,, Moreover there is strong warrant for believing the extremely high level of ‘missing regulatory information’, which is suddenly missing at the ‘point of death’ is in fact quantum information. Quantum information which is not reducible to matter-energy time-space constraints i.e. it is ‘transcendent’ information.

    Quantum Entanglement – The Failure Of Local Realism – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    ,,,Moreover it is shown that this quantum information is ‘conserved’, i.e. that this quantum information cannot be created or destroyed;

    Quantum no-hiding theorem experimentally confirmed for first time – March 2011
    Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed.
    http://www.physorg.com/news/20.....tally.html

    How Teleportation Will Work –
    Excerpt: In 1993, the idea of teleportation moved out of the realm of science fiction and into the world of theoretical possibility. It was then that physicist Charles Bennett and a team of researchers at IBM confirmed that quantum teleportation was possible, but only if the original object being teleported was destroyed. — As predicted, the original photon no longer existed once the replica was made.
    http://science.howstuffworks.c.....ation1.htm

    Quantum Entanglement and Teleportation – Anton Zeilinger – video
    http://www.metacafe.com/watch/5705317/

    ===================

    ,,,moreover this suddenly missing, ‘cannot be created of destroyed’, quantum information, at the ‘point of death’, goes along very well with the extremely ‘consistent evidence’ we now have from Judeo-Christian cultures pointing to a ‘eternal’ life after death;

    The Scientific Evidence for Near Death Experiences – Dr Jeffery Long – Melvin Morse M.D. – video
    http://www.metacafe.com/watch/4454627

    The Day I Died – Part 4 of 6 – The Extremely ‘Monitored’ Near Death Experience of Pam Reynolds – video
    http://www.metacafe.com/watch/4045560

    Blind Woman Can See During Near Death Experience (NDE) – Pim von Lommel – video
    http://www.metacafe.com/watch/3994599/

    Kenneth Ring and Sharon Cooper (1997) conducted a study of 31 blind people, many of who reported vision during their Near Death Experiences (NDEs). 21 of these people had had an NDE while the remaining 10 had had an out-of-body experience (OBE), but no NDE. It was found that in the NDE sample, about half had been blind from birth. (of note: This ‘anomaly’ is also found for deaf people who can hear sound during their Near Death Experiences(NDEs).)

  7. 7
    Elizabeth Liddle says:

    Interestingly, that model is essentially my “Duplo Chemistry” model.

  8. 8
    NickMatzke_UD says:

    Question: If any of these origin of life these scenarios work, why isn’t life spontaneously generating all around us? The only answer so far encountered is that Darwinian natural selection would immensely favour the more complex, developed life forms, so no new ones could start.

    It’s not the only answer so far encountered. You yourself list another one below. Exaggerate much?

    But that’s not very convincing. Darwinian natural selection does not necessarily favour the more complex over the less complex – humans and horses over bacteria and viruses, for example. It’s not that we seldom see it. We don’t see it at all.

    Hmm. So many dubious unquestioned assumptions here.

    For example: It’s not like if it was happening, it would hold up a big fat sign so you could see it while you were walking down the street to the pub. Even on a prebiotic earth, it would be a microscopic event (really, a long series of microscopic events, perhaps taking decades or millenia) in some corner of the planet. If it was going on today, it would have to be in some nook even more obscure.

    More importantly, in today’s world, what happens to organic molecules like amino acids and nucleotides when they are released into the environment today? Do they sit there long enough so that they can perhaps gradually form more complex reactions that would eventually lead to a very crude, very slow, very error-ridden proto-replicator?

    Um, no. All those molecules get scooped up and eaten by currently-existing life, which is pretty much everywhere.

    Another response is that the conditions on Earth are no longer right. Okay, so they are favourable to the preservation of life but not to its origin. In that case, we should see many failed attempts at origin. Do we?

    These sorts of vague plausibility arguments you are making are just bizarre. There are well-known differences between the modern environment and the prebiotic one. One, of course, is we have life everywhere at the moment, eating everything that is eatable.

    Another is that the current biosphere is highly oxidized — again, due to life. Oxygen chews up organic molecules and converts them to inert CO2. This would stop the process of building up large organic molecules most places most of the time at present. The statement “we should see many failed attempts” isn’t even meaningful in this context.

    There are debates about details, but it is clear that there was a *lot* less free oxygen around before 2.5 billion years ago. This is a huge and obviously OOL-relevant difference between then and now.

  9. 9
    bornagain77 says:

    As to Nick’s comment;

    ‘Even on a prebiotic earth,’

    And yet if we look beyond Nick’s imagination to actual evidence for a ‘prebiotic’ earth we find:

    The Sudden Appearance Of Photosynthetic Life On Earth – video
    http://www.metacafe.com/watch/4262918

    U-rich Archaean sea-floor sediments from Greenland – indications of +3700 Ma oxygenic photosynthesis (2003)
    http://adsabs.harvard.edu/abs/2004E&PSL.217..237R

    Moreover, evidence for ‘sulfate reducing’ bacteria has been discovered alongside the evidence for photosynthetic bacteria in the oldest sedimentary rocks ever found on earth:

    When Did Life First Appear on Earth? – Fazale Rana – December 2010
    Excerpt: The primary evidence for 3.8 billion-year-old life consists of carbonaceous deposits, such as graphite, found in rock formations in western Greenland. These deposits display an enrichment of the carbon-12 isotope. Other chemical signatures from these formations that have been interpreted as biological remnants include uranium/thorium fractionation and banded iron formations. Recently, a team from Australia argued that the dolomite in these formations also reflects biological activity, specifically that of sulfate-reducing bacteria.
    http://www.reasons.org/when-di.....pear-earth

    Dr. Hugh Ross – Origin Of Life Paradox – video
    http://www.metacafe.com/watch/4012696

    it is also commonly, and erroneously, presumed in many grade school textbooks that life slowly arose in a primordial ocean of pre-biotic soup. Yet there are no chemical signatures in the geologic record indicating that a ocean of this pre-biotic soup ever existed. In fact, as stated earlier, the evidence indicates that complex photosynthetic life appeared on earth as soon as water appeared on earth with no chemical signature whatsoever of prebiotic activity.

    The Primordial Soup Myth:
    Excerpt: “Accordingly, Abelson(1966), Hull(1960), Sillen(1965), and many others have criticized the hypothesis that the primitive ocean, unlike the contemporary ocean, was a “thick soup” containing all of the micromolecules required for the next stage of molecular evolution. The concept of a primitive “thick soup” or “primordial broth” is one of the most persistent ideas at the same time that is most strongly contraindicated by thermodynamic reasoning and by lack of experimental support.” – Sidney Fox, Klaus Dose on page 37 in Molecular Evolution and the Origin of Life. http://theory-of-evolution.net.....p-myth.php

    New Research Rejects 80-Year Theory of ‘Primordial Soup’ as the Origin of Life – Feb. 2010
    “Despite bioenergetic and thermodynamic failings the 80-year-old concept of primordial soup remains central to mainstream thinking on the origin of life, But soup has no capacity for producing the energy vital for life.”
    William Martin – an evolutionary biologist
    http://www.sciencedaily.com/re.....101245.htm

    Life – Its Sudden Origin and Extreme Complexity – Dr. Fazale Rana – video
    http://www.metacafe.com/watch/4287513

    ===============

    Nick I’ll give you a solid clue where all life comes from:

    Evanescence – Wake me Up Inside – Lyrics
    Excerpt: Only you are the life among the dead.
    http://www.lyrics007.com/Evane.....yrics.html

    Evanescence – “Bring Me To Life” – Video
    http://www.youtube.com/watch?v=3YxaaGgTQYM

    Wake Me O Lord

    Wake me O Lord from this sleep of mine
    To the living wonders of creation that are so fine
    With a “Oh, that’s nice” I shall not content
    NO, only when You speak shall my heart be spent
    Others may suffice their cravings of Awe
    With an “Oh Well” shrug of the wonders they saw
    But I know You are in each piece of reality
    Yes, in the wind, the stars, and even the sea
    So this vow to You I make
    No rest in me my heart will take
    Till Your face and hands again I see
    In the many waters of reality
    For the truth be known to You indeed
    That if I see You not with my heart and head
    I’m not really born again, but instead am dead

    Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University
    Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007

  10. 10
    Chris Doyle says:

    Lizzie,

    Apologies for continuing a discussion from another thread, onto this one. The former appears to have closed but there is overlap on this thread so here we go:

    Thank-you for your most recent response on the subject of self-replication. In it, you affirm that what you consider self-replication is, as I worded it, merely the “ability to split down the middle, and for both halves to then attract to each now-unmated unit”. However, you did not deal with the fatal error that this line of reasoning leads to: the most likely outcome would be for the two halves of the peptide chain to merely come back together again. Until you do, then what you have is not self-replication at all: merely the endless separation and integration of the two halves of just one single molecule.

    You go on to say that it is “not necessarily” the case that “the ability of the first self-replicating molecule to self-replicate (a small part of which may involve splitting down the middle) comes from its molecular shape and content so, that will include its sequence.” So, presumably you reject the RNA world hypothesis? If things like the shape and content of the first self-replicating molecule are not necessary, then what do you think is necessary? If the answer to that question is the “ability to split down the middle” then where does that ability come from, if not the shape and content?

    Do you accept the serious possibility that the reason we have failed in all of our attempts to recreate the first self-replicating molecule is because such a thing cannot arise in naturalistic conditions? If not, why do you still believe it happened?

    At the very least, it must have been a very difficult, complex and improbable synthesis. On what grounds can you assume that there is more than one winning formula?

    To assert that:

    AC
    CA
    CA
    DB

    and

    AC
    CA
    CA
    DB
    BD

    are both molecules equally capable of splitting down the middle (let alone genuinely self-replicating) is paper chemistry gone mad! Just sticking random bits onto molecules and hoping for the best isn’t realistic: anything could, and most likely would, go wrong. Furthermore, in your quest for variation, you have neglected something which is much more important about life: heredity.
    So, either we have perfect cloning or wild variation: neither outcome moves us beyond the first self-replicating molecule.

  11. 11
    Chris Doyle says:

    Lizzie, just to add to the above, I wish to highlight another excellent point made by VJ Torley (post 15 of the “To Dream The Impossible Dream” thread):

    My second substantive criticism of Nowak and Ohtsuki’s paper is that it fails to address Meyer’s “error catastrophe problem” head-on. In his book, Meyer wrote:

    [Oparin] proposed that natural selection initially would act on unspecified strings of polypeptides of nucleotides and amino acids. But this created another problem for his scenario. Researchers pointed out that any system of molecules for copying information would be subject to a phenomenon known as “error catastrophe” unless these molecules are specified enough to ensure an error-free transmission of information. An error catastrophe occurs when small errors – deviations from functionally necessary sequences – are amplified in successive replications.[14] Since the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately, Oparin’s proposed system of initially unspecified polymers would have been highly vulnerable to such an error catastrophe.

    Notice that in his book, Meyer cites research involving real chemicals: polypeptides. He points out that “the evidence of molecular biology shows that unspecified polypeptides will not replicate genetic information accurately.”

    This is what I’ve been trying to get at when I’ve been expressing concerns about “wild variation”, how damaging copying errors would be to the first self-replicating molecule and lack of heredity.

  12. 12

    Ah, yes, a variation on the fading “RNA world” hypothesis. I love these OOL theories.

    Don’t get me wrong, there is value in researching some of these things, so that we have an understanding of just what is required for life. It’s just the wild speculation and ludicrous blind faith in the power of chance and necessity that grow a bit tiring . . .

    This is the most telling line in the summary: “However, scientists do not know how a self-replicating RNA system could have arisen from a pool of random polynucleotides.”

    Indeed.

  13. 13

    Nick wrote:

    “TThere are well-known differences between the modern environment and the prebiotic one. One, of course, is we have life everywhere at the moment, eating everything that is eatable.”

    Yes, that is the fallback position (not at all different or more substantive from what Darwin proposed a century and a half ago) as to why we don’t see abiogenesis today. It may or may not be accurate, but let’s assume for a moment that existing life would prevent new life from taking hold, as you suggest.

    On this basis that you’ve proposed, let’s be clear about your position. Are you taking the position that simple life is in fact still being formed today, but that it is being “eaten” up before anyone notices it? Or are you saying that simple life no longer forms for some reason? Or are you saying you don’t know whether abiogenesis is still taking place? In any case, it should be pretty simple to bring the experiment into the laboratory, right?

    I’ll spot you all the nucleotides or amino acids you want, in just the right ratio, in the perfectly hospitable environment, with no interfering cross reactions, with stability and no rapid breakdown of nascent formations. Now exactly what is your theory about how these nucleotides or amino acids come together to form simple life?

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