Mutate or die

When life began on Earth it didn’t resemble modern cells, with their modern fancy DNA and cell nuclei and ribosomes. The fundamental property shared by all living systems is replication with heredity, and the first things that naturally arose on Earth capable of doing that weren’t complex modern microbes… most likely they were tiny constellations of tangled nucleic acids. Our biosphere seems to have begun as an “RNA World”, where nucleic acids bubbled and stewed inside the plumbing of seafloor hot springs, replicating and complexifying over time. Millions of different types of RNA tangles occupied such places, constantly reforming and copying themselves, constantly making copy-errors. Errors leading to better replication were naturally preserved… while molecular swarms that didn’t hold themselves together very well got cannibalized by competing assembly reactions. Eventually some forms of RNA tangles grew to dominate their little plumbing-worlds. Those are the ones that led to true cells.

That’s the vision offered by modern origins-of-life research. A recent study carried out by botanists working on planet pathogens has made that vision a little clearer. Selma Gago and colleagues at the University of Valencia in Spain have measured the rate at which mutations occur in a plant-disease viroid called Chrysanthemum chlorotic mottle. Viroids are simple life forms composed of just a few RNA strands bound together in a tiny bundle. Inside plant cells viroids insert themselves into the cellular machinery and co-opt it into making more of themselves, but early in Earth’s history the simplest forms of life to first arise were probably something akin to viroids. In Earth’s primordial seas, RNA bundles capable of building themselves from the sea-soup of amino acids were the first replicators… the first RNA replicons, which preceded true cells probably by several million years at least. Gago and colleagues’ new study measured the mutation rate of their viroid subject, and found that it’s a veritable mutation machine, with a stunningly high rate of approximately one mutation per copy. At that rate, a human embryo would quickly melt apart into a sickening goo of stuttering, dying cellular machinery.

Mutations add diversity to our genetic code, but too many mutations at once can be deadly. In simpler life forms mutations occur more frequently, partly because simpler life forms reproduce faster, but also because simpler life is beholden to less complicated and finicky bodily infrastructures in which mistakes can be costly. Bacteria mutate much more than animals do, but bacteria can double exponentially in hours… offering plenty of cannon fodder to the battle for genetic survival. Animal reproduction is more costly and yields fewer offspring, making mutations more dangerous and instilling stronger selective pressures favoring error-correction. But bacteria just don’t need to worry as much (metaphorically speaking) about such things.

Viroids worry even less. As genome size decreases, mutation rates increase… and according to Gago and company’s new study the rate at which viroids can mutate hedges very close to the highest mutation rate possible prior to absolute molecular disintegration. Enough mistakes and you shatter, but mutation rates lower than that critical threshold allow very simple replicators to persist with maximum adaptability. RNA replicons in Earth’s primordial oceans would have likely behaved similarly… pushing the limit of mutability, beyond which lay total fragmentation, but within which a tiny tinkertoy complex of folded RNA could wobble and transfigure itself into any composition that yielded working copies. Given those circumstances, it’s not all that surprising that at least one successful lineage was born that could survive down the eons in open water.

As Dawkins says, there are vastly more ways of being dead than of being alive. The trick with mutable replication is throwing out enough modified copies of yourself to explore as much potentially-being-alive territory as possible. The simpler the replicon, the more it can afford to vary… and those lucky few that stumble upon good engineering solutions to life’s challenges are the ones who can push further into possibility-space.

mutationrates_2

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~ by Planetologist on March 17, 2009.

20 Responses to “Mutate or die”

  1. Planetologist, some of the links were unreachable, and some that I could reach didn’t allow access. A search turned up some better links for the early papers:

    (1995) Haas J. R., Shock E. L. and Sassani D. C.
    (1998) Haas J. R., Bailey E. H. and Purvis O. W.
    (1999) Haas J. R. and Shock E. L.
    (2001) Haas J. R., DiChristina T.J. and Wade R. Jr.
    (2002) Haas J. R. and DiChristina T.J.

    (2004) Haas J. R.

    I’m not sure what the blogging software will do to my formatting, but the HTML I’m sending should be able to be cut/pasted (line for line) into your pubs section if you want.

  2. Planetologist: Thank you for your answer. I was wondering what happened to my comment.

    Your call for a search for mechanisms that might arise in a mix of ALL random molecules is itself a red herring, because no such natural chemical environments exist. In any geologic setting the conditions of pressure, temperature and bulk composition will dictate that some compounds will be more stable than others. Unstable compounds are destroyed, or never form.

    That’s not consistent with any sort of chemistry I’ve heard of. Stability itself is a function of concentration, and less stable compounds will be present in smaller concentrations than more stable, but still present.

    To pick an extreme example, phosphate is far more stable than pyrophosphate. In most cells, there is a good concentration of inorganic pyrophosphatase such that when pyrophosphate is released from a triphosphate (such as ATP, GTP, UTP, and TTP in RNA polymerization), it is quickly hydrolyzed to two phosphates. However, there is still a certain amount of pyrophosphate in the cytoplasm, (very) roughly one millionth the concentration of phosphate. Again very roughly, for every 1/10th electron volt yielded in a transformation at equal concentrations, the equilibrium concentrations will vary by another factor of 10. Thus, since at equal concentrations pyrophosphate (or any diphosphate) will yield about 0.6 electron volts on hydrolysis, therefore the equilibrium concentrations will vary by a very rough factor of a million (10**6).

    The same is true of precursor compounds in a primeval environment, but more so because the difference in stability is much less. For instance, there’s almost no difference in stability among various types of sugars (e.g. ribose vs. ribulose), so they will be present in roughly equal quantities. Assuming sufficient catalysis of all transformations, a vast number of 3-, 4-, 5-, 6-, and 7- carbon sugars will be present, each with roughly equal probability of being incorporated into pseudoneucluotides.

    Kauffman has a discussion of the primeval world that is fairly good (although he doesn’t discuss all the entropic implications I mentioned above) in The origins of order.

  3. planet pathogens</i”? (You might delete this line after fixing.)

    [… T]he first things that naturally arose on Earth capable of doing that weren’t complex modern microbes… most likely they were tiny constellations of tangled nucleic acids. Our biosphere seems to have begun as an “RNA World”, where nucleic acids bubbled and stewed inside the plumbing of seafloor hot springs, replicating and complexifying over time. Millions of different types of RNA tangles occupied such places, constantly reforming and copying themselves, constantly making copy-errors. Errors leading to better replication were naturally preserved… while molecular swarms that didn’t hold themselves together very well got cannibalized by competing assembly reactions. Eventually some forms of RNA tangles grew to dominate their little plumbing-worlds.

    This is a very common picture, but I find it totally implausible. Successful RNA polymerization requires not only the substrate monomers, but a total absence of thousands of other, similar monomers that would poison and randomize the reaction. But there is no indication that the early environment lacked these other monomers. (AFAIK experiments in random creation of small molecules creates the whole batch, not just the specific ones needed.) Thus, the “RNA world” would require a sophisticated surround to isolate it from them. (AFAIK controlled RNA polymerization also requires monomer triphosphates, which also require a source.)

    IMO the RNA world is a red herring, and those speculating about the origins of life need to return to square one and look for mechanisms that could arise in a surround of all random molecules rather than just the ones we find in the cytoplasm today.

    • AK, thanks for the comments. While true that the modern, highly sophisticated and therefore finicky process of RNA replication that occurs in modern cells could not stand up to unregulated mixing with other exogenous monomers, this level of exclusivity is not required for much simpler nucleic acid complexes. Basically, it’s unfair to look at the (so far) end result of billions of years of evolution and conclude that the processes that originated that evolutionary lineage had to cobble the entire thing together in one go. The RNA World hypothesis is based on a lot of work, not only theoretical but solidly experimental, showing that RNA can catalyze its own polymerization. ATP isn’t necessarily needed… polyphosphate can do the job too, and there is some evidence that other molecules containing phosphate can provide sufficient energy to motivate the process.

      I’m short on time at the moment, so for now I’ll direct you to a previous post on my blog, wherein I discuss a recent experimental study on RNA self-organization and selective enrichment in vitro. The upshot is that even under conditions where lots of different subunits are present, stochastic interactions naturally tend to conserve those polymerized configurations that have more efficient assembly kinetics. In the study I blogged about, some highly successful self-replicating RNA assemblies arose from particular linkages of particular subunits… to the detriment of other configurations. The first stages of competitive selection, basically.

      Your call for a search for mechanisms that might arise in a mix of ALL random molecules is itself a red herring, because no such natural chemical environments exist. In any geologic setting the conditions of pressure, temperature and bulk composition will dictate that some compounds will be more stable than others. Unstable compounds are destroyed, or never form. If you’re uncomfortable with the idea of abiogenesis on planets, just look at meteorites… where lots of organic chemistry occurred in the total absence of life. There, particular amino acids formed in response to the prevailing chemical conditions inside those rocks as they orbited the ancient Sun…. they don’t contain ALL random molecules, they don’t contain random molecules at all… they contain molecules produced according to the laws of thermodynamics and chemical kinetics.

      The RNA world idea is exactly what you get by actually going back to square one and looking objectively at the problem.

      • I haven’t seen my most recent comment yet, but it occurs to me that I failed there to address one of your points:

        If you’re uncomfortable with the idea of abiogenesis on planets, just look at meteorites… where lots of organic chemistry occurred in the total absence of life. There, particular amino acids formed in response to the prevailing chemical conditions inside those rocks as they orbited the ancient Sun…. they don’t contain ALL random molecules, they don’t contain random molecules at all… they contain molecules produced according to the laws of thermodynamics and chemical kinetics.

        I certainly am not “uncomfortable with the idea of abiogenesis“, on planets or anywhere else. Rather, I’m uncomfortable with the insistence on stripping things down to the simplest system possible when that is totally inconsistent with chemical thermodynamics. IMO researchers do this for their own convenience, because it’s easier to model and experiment with such stripped down systems, not because it actually represents the kind of environment that existed on the early Earth’s surface.

        As for the chemicals forming “inside those rocks as they orbited the ancient Sun“, I’ve seen at least one model where they actually formed within planetesimals, which were then shattered in collisions creating meteoroids. If you want links I’ll try to track them down later, but I’m hoping you’re already aware of the articles I’m thinking of. But even if they actually formed as you suggest, these conditions are not anything like those on the surface of the early Earth.

      • AK: It seemed from the tone of your previous comment that you were moving in the general direction of an argument from personal incredulity. My mistake, if you weren’t.

        When I mentioned rocks orbiting the Sun, I was talking about planetesimals, actually. Chemical differentiation inside larger planetesimals would have gone on more or less during accretion – or soon thereafter – allowing organics and volatiles to react and spawn interesting chemistry. This process is thought to be responsible for some of the more complex organics we find in meteorites, as well as the predominantly left-handed chirality of amino acids life now uses.

        Of course researchers break down systems into the smallest possible parts in order to study them. There’s no other way. But that doesn’t mean the work stops there. A common complaint from people with no science training (based on your comments I think that doesn’t include you) is that scientists are too reductionist, but that’s a red herring. Scientists who do quality work are only reductionist to the extent that it helps understand something. As soon as the smaller parts are understood, the research goes upscale… literally, moving up the magnitude scale to larger and more complex systems. Then the tests might involve verifying whether or not expectations based on more simple models hold up when more complex systems are involved. Non-scientists act like this kind of thing has never occurred to scientists, but we do stuff like that all the time. In my own field of geochemistry, people interested in, say, the environmental threat of lead (Pb) study the locations of individual Pb atoms on mineral surfaces at the atomic scale, and other people study how Pb atoms in water behave in water with mineral grains, and other people scale that up to more complex experiments with Pb and minerals and bacteria and organic matter, and other people work on Pb in lakes and rivers, and other people study Pb cycling on a global scale. In each case the people working at one scale are constantly looking at others’ work, trying to get everything right and not leave out anything. Seriously, that’s how we do it. Don’t worry… we’ve got it covered, man. 🙂

        Okay, on to chemical thermodynamics… because I’m nothing if I’m not a total thermodynamics geek.

        You have it partly right, when you say that lots of different things will be present at different concentrations in a given system, according to the laws of chemistry. But don’t forget that chemical reactions are governed not only by the concentrations of reactants and products, but by the laws of mass action controlling which direction a reaction will spontaneously proceed. Some reactions will simply be unfavored, and will not proceed at all. Others will proceed strongly. Some compounds will form in huge concentrations while others will be consumed in reactions until very little is there… like you say, sometimes a compound might be a millionth as abundant as another. But a millionth is nothing…. in most cases there will be droves of compounds present at concentrations like ten to the -50th, or -100th moles/L, or something equally small. At that point they’re effectively unimportant to the system… they’re below the detection limits of the best instruments, and they don’t participate in a controlling way in other reactions happening in the same system.

        The upshot of this is that in any geologic environment where organics are cooking, there will be a set of abundant chemical species that determine most of the chemistry, and there will be lots of trace constituents… and then there will be the ultra-trace species that just don’t matter very much.

        One last thing… you made an argument about sugars as an example of how lots of things can be equally stable…. but actually they can’t be. Those sugars may seem equally stable, qualitatively, but when you count the calories (or Joules) a different picture emerges. Let’s take your example of ribose and ribulose. Here are the thermodynamic properties of the two:

        DELTA G DELTA H S V Cp
        NAME (cal/mol) (cal/mol) (cal/mol/K) (cc/mol) (cal/mol/K)
        ——————– ————- ————- ————- ————- ————-
        ribose -177660.0 -250294.0 41.990 94.420 44.70
        ribulose -175894.0 -244508.0 55.282 95.08 77.35

        Hopefully that formatting works. Note that in terms of their standard partial-molal Gibbs free energy of formation (DELTA G), the two are fairly similar… only 234 cal/mole (979 J/mole) separate their stabilities. Those data are from the SUPCRT92 thermodynamic database for minerals, gases and aqueous species. Note also that their enthalpies (DELTA H) differ too, by a larger amount. Their molar volumes (V) are similar, but their Third Law entropies (S) are pretty different and so are their molar volumes (V). The two compounds are not equally stable. Now, before you think I’m splitting hairs, bear with me.

        Let’s take those two compounds a write a reaction converting one to another:

        ribose <> ribulose

        For which we can write an equilibrium expression and calculate the mass action parameters. The log of the equilibrium constant of that reaction at 25 C and 1 bar is -1.29, meaning that the forward reaction is disfavored, and at equilibrium not only will ribose not convert to ribulose (at standard conditions where each is present at 1 mole/L at 25 C and 1 bar), but ribulose will spontaneously react back to form ribose. The equilibrium constant is the ratio products/reactants, and the log is negative, meaning that the concentration ratio will be something like 1 ribulose to 30 ribose, roughly. The reaction under those conditions is driven by about 1766 cal/mole… 1.766 food calories per mole (1 mole = 150 grams). That’s quite a bit of energy, all things being equal.

        It gets better. If you turn up the heat to 350 C, which corresponds to a hydrothermal vent or cooking interior of a planetesimal, the log K switches to 4.36, meaning that ribulose is more stable and will be present at equilibrium at a concentration roughly 10,000 times greater than ribose. In such a system, any chemistry where ribose or ribulose can participate will be skewed by a factor of 10,000 in the direction of using ribulose, because for every 10,000 molecules of one there will only be 1 molecule of the other. Those numbers aren’t exact, but hopefully you get the idea.

        Now, at some intermediate temperature (it’s around 115 C) both will be equally stable and at equilibrium the concentrations of both will be equal… but only at that temperature and pressure, where both are initially present at 1 mole/L each in liquid water. Nowhere else. At all other conditions in water, one will react to change into the other to some degree. If they’re solids, like minerals or condensates, they convert completely… it’s either one or the other.

        So, that’s how I can say that chemistry dictates some things will be more abundant than others, and still others will be present in such low abundances that it doesn’t matter for all practical purposes. When you do the math it becomes clear.

        And again, sorry to have taken so long to reply… some weeks you get the bear, and some weeks the bear gets you. 🙂

      • Thanks for your reply, Planetologist.

        I won’t dispute your numbers (but won’t take the time to confirm them), but I can’t agree with your interpretation. For my purposes (and, IMO, for purposes of modelling early Earth) a 30:1 ratio is next best thing to equal amounts. It certainly is within the modern cell.

        I’m hoping this is a typo or something:

        […] meaning that the forward reaction is disfavored, and at equilibrium not only will ribose not convert to ribulose (at standard conditions where each is present at 1 mole/L at 25 C and 1 bar), but ribulose will spontaneously react back to form ribose.</blockquote) In the very next sentence you reference an “equilibrium constant” such that “concentration ratio will be something like 1 ribulose to 30 ribose, roughly.” In my understanding of chemistry, this means that at equilibrium they are at your 30:1 ratio (not equal amounts), and neither is being changed into the other.

        So what would happen if you start with a solution of pure ribose in water, and add some catalyst for interchange with ribulose. Some of the ribose will be changed to ribulose, until the 30:1 ratio is achieved; just as if you start with equal amounts some (most) of the ribulose will be changed to ribose until the 30:1 ratio is achieved. Thus this and almost all reactions are completely reversible, although sometimes for simplicity it’s assumed otherwise.

        AFAIK the same is true of the more extreme case I mentioned. If you start with a solution of 10**-2 Molar of -phosphate (with appropriate cations) and add the right amount of -pyrophosphatase, you’ll soon have around 10**-8 Molar of pyrophosphate (very roughly). There must be a limit where the energy of transformation is just too great relative to the average thermal collision energy (at 25C which I’m assuming), but AFAIK it’s considerably larger than 0.6 ev. In fact, I’d guess that it’s larger than the 1-1.2 ev involved in splitting off a pyrophosphate such as in DNA/RNA polymerization or charging tRNA with its appropriate amino acid. (Of course, you need the catalyst, since AFAIK the half-life for degradation of the diphosphate bond is measured in weeks.)

        Which brings me to my primary objection to unprotected RNA molecules replicating, involving the energy costs of accurate information. I’m going to lean on your thermodynamic expertise here, as I’ve seen developments of what I’m talking about, but don’t understand them well enough to debate them.

        It takes around 1-1.2 ev to add one RNA/DNA monomer with a correct match to the template during cellular replication/transcription (powered by splitting off the pyrophosphate as mentioned above). I’ve seen this described as the entropic cost of accurate information (my paraphrase). Even so, the error rate is unacceptable, so a further “proofreading” step is required (powered by hydrolytic splitting off of the erroneous base). If accurate replication/transcription were possible without this major energy expenditure, it’s hard to imagine it wouldn’t be happening. So where, in this world of unprotected RNA and RNA monomers, is this energy to come from.

        If we assume a reasonable level of random/universal catalysis, you can’t have ATP/GTP/UTP/CTP (or even ADP/GDP/UDP/CDP) floating around, because even tiny levels of catalysis would quickly degrade those very high-energy diphosphate bonds. Only by protecting the replicating nucleic acids (and their monomers) from the random environment, and sharply limiting what catalysis takes place, can the ordered polymerization of either nucleic acid (or any based on phosphodiester bonds) take place.

        This is very different from random polymerization; that is polymerization with random sequences. Here, I can believe that simple dessication might provide the necessary impetus.

        Since I last commented here, I’ve had a chance to read several chapters of Ruse and Travis’s (eds.) “Evolution the first four Billion Years“, especially chapter 2: “The Origin of Life” by Jeffrey L. Bada and Antonio Lazcano. I found that it makes much the same arguments I did, but better phrased and with references. (However, it didn’t go into the thermodynamics.)

        One particularly cogent quote regarding early planetary atmosphere: “It is generally agreed that free oxygen was absent from the primitive earth, but there is no general agreement on the composition of the primitive atmosphere; opinions vary from strongly reducing (CH4 + N2, NH3 + H2O or CO2 + H2 + N2) to neutral (CO2 + N2 + H2O). In general, those working on prebiotic chemistry lean toward more reducing conditions, under which the abiotic syntheses of amino acids, purines, pyrimidines, and other compounds are very efficient, while nonreducing atmospheric models are favored by planetologists. A weakly reducing or neutral atmosphere appears to be more in agreement with the current model for the early earth.

        Personally, I find myself favoring the “strongly reducing” model, especially as I’m not convinced by planetological arguments for more neutral models. However, I have to point out that if there is elemental hydrogen and nitrogen, there’s going to be ammonia, at equilibrium, unless some process removes it. If there is ammonia and carbon dioxide, some of it will precipitate into ammonium carbamate (not carbonate) (in cloud droplets if nowhere else), which can in turn polymerize into all sorts of larger molecules (e.g. urea), some of which (AFAIK) can act as dyes, absorbing high energy photons (high in the atmosphere) and yielding high energy electrons in solution with at least semi-random results. Correct me if I’m wrong, but such processes have the potential to create all sorts of molecules that would never show up at thermodynamic equilibrium.

        I’m not a chemist (although I’ve had some scientific training as you noticed). One big clue is that I prefer to think of reactions in terms of single molecules and energy in electron volts/molecule rather than more experimentally inclined measures. It’s intuitively more obvious (and easier to relate to photons). So I’ll rely on you to point out my errors, although I think I’m entitled to my bias towards a highly reducing atmosphere.

        I’d be interested in your opinion of the Bada/Lazcano chapter.

      • AK,

        Thanks very much for the great and well thought-out reply. You’re pretty much right on the money about everything you said, although I might be able to help correct a couple of details. One is a quibble with your definition of equilibrium: I’m not sure if you meant to really say that once a system is at equilibrium everything is settled and stops… the formal definition of an equilibrium chemical process is the sum of the rates of forward and backward reactions, because at the level of molecules, things are always moving around and interacting stochastically, bumping around and reacting, at a mean velocity determined by their medium (solid, liquid, gas) and temperature. If you start with a bunch of reactant and a favored forward reaction, barring kinetic limits the system will slide toward equilibrium because the intrinsic rate of the forward reaction is faster than the reverse… the product is more stable, less vulnerable to destroying reaction events, than the reactants are in that setting.

        Anyway, you’re right that 30:1 isn’t much… it’s only a log unit difference in activity (thereabouts). But under conditions where that activity difference is wider, as in the ribose/ribulose example at 350 C, a difference of four log units is pretty significant…. and pretty decisive about which types of chemical species are around to reaction with other abundant species. Under any set of conditions, no matter what, there will be a list of very stable species that will be abundant and a much longer list of species that will be rare. To replicate, a molecular complex has to use up raw material, and the larger the supply the better. That’s all I mean, when I say that the geologic environment where replicators arise has total control over what those replicators can be made out of. This makes the origins of life testable. As we close in on the proper conditions, we eliminate possible origins of life models where that key chemistry is maximally disfavored. That allows us to close in tighter on what kinds of places and processes to look for. The more we learn about life’s chemistry and our planet and solar system’s chemistry, the clearer a picture we get of how life most likely got started.

        Okay, so far I think we’re in agreement, basically. But where I think you went off-target slightly was in assuming that abiogenesis took place in the open water column. That’s very unlikely for the very reasons you mention… components drift away from each other and local chemical gradients smooth out by diffusion into the bulk medium. Life had to begin in a restricted physical space, compartmentalized in some way that the working parts of replication stay together. The conventional model for this is micelle formation, where fatty acids that are also components of the replicator spontaneously assemble into wet bubbles, suds, that trap the suite of key replicator components inside the micelles. This has been demonstrated in the lab, and it’s almost impossible to stop from happening if the relative concentrations of fatty acids fall within a wide window of values in a reaction vessel. Double-walled micelles, even, can form on their own spontaneously in aqueous solution.

        But that’s only part of the issue with enclosure… the suds need to stay together. Fortunately that’s easy, for example in vugs, voids, channels, cracks, fissures and plumbing works underlying geothermal and hydrothermal vent systems. The physical environment inside a hot spring at depth is porous, permeable, with void spaces at different scales inside a vast network of fluid-filled reactor-volumes, where mineral-laden – and in the late Hadean organic-laden – water constantly pumps, gushes, back-flushes, and rushes. Inside those void spaces you can cook up all sorts of organic chemistry, in congealed layers of hydrocarbons, amino reductions, redox-active metal ions and reactive phosphate. Inside foam and sludge buildups in the geothermal plumbing nooks, complex reactions would start up, including self-sustaining reaction loops that spread with the suds. It’s a smooth slope from there to slightly higher in the geothermal system, then the edge, then nearby, then loose to wander the ocean and look for fuel…. as long as a chain of useful mutations in the replicator code allows for modifications that confer persistence of the engine as local conditions change. At that point you’d have something resembling “life” on our familiar terms.

        This is a common mistake people make when thinking about life’s origins; that it only happened once, that it happened suddenly when one cell fell together. Far more likely is an early Earth where lots of complex soupy chemistry was going on inside geothermal systems all over the planet, and in most of them the basic chemistry of life was brewing up. Conditions passed through a geochemical optimum window, like the oil formation “window” of composition, time, pressure and temperature, and stayed there long enough for some population of replicators to start. There were likely many competing flavors, mostly similar in broad chemical terms but with key incompatible differences depending on which vent system they started in. Among those, only a few persisted over the long ages, spreading widely and competing directly, until one lineage remained. At that point there were probably already lots of variations on that one lineage. Farther still down the road we get to the last common ancestor (LUCA)… millions of years past the necessary milestones of acquiring a working ability to make your own cell membrane fatty acids, abstract electrons from oxidized ambient chemicals and reduce CO2 to organic matter, establish a codon system, etc. But yes, micellar enclosure has to come along very early.

        There’s a lot of argument about exactly how reducing the early Earth was before abiogenesis… whether it was mainly an atmosphere of CO2, N2 and H2O vapor, with trace ammonia and methane, or a rich and foggy reducing atmosphere of methane and ammonia. That’s unclear, but we received a lot of cometary organics in the Hadean, and with those comets and their organics would have come CH4, CO, CHO and NH3. However much we got, apparently it was enough.

      • Thanks, Planetologist. You’re right that it’s only the net amounts that stop changing at equilibrium.

        My first reaction to your discussion of the conditions was to perceive a contradiction with the discussion in your original article, but looking at what you wrote, I realize that I had interpolated views I’d read elsewhere regarding “original life”. This was the idea that the first “life” consisted of nothing but RNA molecules capable of self-replication. Your mention of “tangles” suggested something like an open water column, or at least a space measured in hundreds of microns (at least), where the potential for reaction poisoning by unwanted molecules and catalysis would be very high. I suppose allowing cracks and voids to scale down to microns or smaller avoids this problem, although I would express “personal incredulity” at these tangles emigrating to the surrounding environment as viable life without first gaining a protective membrane and a suite of metabolic reactions (and catalytic ribozymes) to support it.

        There’s a lot of argument about exactly how reducing the early Earth was before abiogenesis… whether it was mainly an atmosphere of CO2, N2 and H2O vapor, with trace ammonia and methane, or a rich and foggy reducing atmosphere of methane and ammonia. That’s unclear, but we received a lot of cometary organics in the Hadean, and with those comets and their organics would have come CH4, CO, CHO and NH3. However much we got, apparently it was enough.

        IMO there is no really good evidence for a less than strongly reducing atmosphere, and this certainly improves the chances for abiogenesis.

        The key question is the relative rates of cooling of the earth, reducing infall, and hydrogen loss via Solar Wind. You mentioned infall of “CH4, CO, CHO and NH3“, but not elemental iron and carbon, both of which have reducing potentials greater than hydrogen and thus would have reacted with water (as liquid or gas) to produce it. If the Earth became cool enough for water to condense while large amounts of hydrogen remained in the atmosphere, methane and ammonia would have been far more common than elemental nitrogen.

        IMO there is some evidence that the earliest incarnation of chlorophyll-based photosynthesis was actually involved in oxidizing methane (or other hydrocarbons) by transporting electrons to a negative enough voltage that they could produce free hydrogen. Depending on whose textbook you believe, the voltage achieved by Photosystem I in the z-scheme is sufficient to produce hydrogen (note that the highest voltage electron acceptors are buried in the protein, where they can’t come into contact with floating protons), and if not certainly some slight differences in the protein sequences would be sufficient for the necessary voltage. (Of course, the voltage, and that necessary to remove electrons from methane, would depend on the partial pressure, AFAIK.)

        Since this photosynthesis is highly dependent on sophisticated proteins, it would imply that the invention of proteins took place at a time when hydrogen and/or ammonia were abundant enough in the atmosphere that carbon dioxide was effectively absent. I’ll point out that hydrogen and carbon dioxide cannot both be present in significant amounts in a modern-style biosphere because biosynthesis is a forward process when electrons can be taken directly from hydrogen into NADH or NADPH.

        (IIRC there’s some evidence of early “snowball earth” events that might represent the switchover from methane to carbon dioxide as the primary greenhouse gas.)

        Let me start (over) with the “RNA World”: Personally, I’m skeptical about the whole idea, much less that this was the the first sort of life to arise on Earth. There is simply no justification whatever for this assumption. Even if the “RNA World” existed, it may well have been intermediate somewhere between some earlier form of life, and what we know today.

        IMO there is very strong evidence that the immediate predecessor to “life as we know it” was not an “RNA World” but a “DNA=>RNA World”, with ribozymes performing many (or most) of the functions performed by proteins today but also with DNA performing much the same function as it does today. (I’d place the development of sophisticated gene expression control to after the invention of proteins, but not the use of introns. IMO the inventor of proteins was structurally much more similar to Eukaryotes (without mitochondria, of course), than prokayryotes. The similar stripped down form of eubacteria and archaea can be well explained as homoplasy. As with many times simpler forms evolve (especially in parasites), if the same structural complexities are unneeded, they will be tossed overboard leaving superficially similar forms.)

        My earlier comment about “stripping things down to the simplest system possible” was referring to the insistence on RNA being used for all purposes: holding the information as well as applying it. This might make sense if you insist that it evolved in a completely abiotic world, but there’s no good reason for assuming that. If we assume that the entire system of nucleic acids arose as part of a pre-existing system of life, then it makes more sense that DNA and RNA arose together, performing different functions. Then, they took over most of their modern functions, and the earlier life-forms were driven into extinction.

        At this point I’ve justified (in my own view) a scenario where life arose on a strongly reducing earth surface. As for the “open water column“, I’ve done some calculations based on most of the oxygen in the present atmosphere being balanced by buried reduced carbon, and it provides for amounts of hydrocarbons over the entire surface measured in meters. I haven’t been able to work out all the implications from first principles, but given appropriate catalysis I would assume an equilibrium among methane, hydrogen, and various hydrocarbons. I would also assume some sort of equilibrium between hydrocarbons and partly oxidized hydrocarbons (or among them and hydrogen and water). Some of the molecules formed would be amphiphilic, providing for membranes, or at least very small droplets of hydrophobic material. Adding in ammonia gives the potential for amino and nucleic acids. If we assume an amount of ammonia equivalent to current atmospheric nitrogen, there’s enough for quite large amounts of these materials.

        Where I’m still at a loss is the balance involving formaldehyde and its polymers. Carbon will steal an oxygen from water to produce CO, but not the second one. The balance between CO, H2, and formaldehyde is critical (IMO) because if it forms some sort of equilibrium with roughly equal amounts (no more than two orders of magnitude difference, say), subsequent polymerization of formaldehyde into simple sugars will take place (especially in an omni-catalytic environment) with reasonable ratios. These sugars, in turn, will polymerize among themselves and with amino and nucleic acids, oxidized hydrocarbons, and perhaps phosphates.

        I have roughly estimated the ratio monomers to polymers as 1:10 based on the energy involved in hydrolysis. Have I missed something here? If not, while the amount of each polymer would be around 1/10th of its constituents, the number of possible polymers grows much faster than the concentration ratio, which means the ultimate result would be most of the mass taken up as very large polymers, but with miniscule amounts of each.

        Although I can’t even put a rough order of magnitude on the amounts involved, I can’t rule out a whole water column involved in this process. More importantly, many of these polymers would be light enough to float, providing high enough concentrations for all sorts all sorts of life to arise.

        My gut reaction is that life would have arisen in this environment long before the solar wind would have removed enough hydrogen from the earth to limit abiogenesis to hot spring vents.

        Obviously I’ve said a lot of things that require supporting arguments, but time constraints (yours as well as mine) suggest that I wait, especially as I don’t know which things I’ve said you’d already agree with.

        One last thing I’ll mention is that in a strongly reducing atmosphere, even trace amounts of CO2 could result in complex dye-like polymers in water/ammonia droplets at the top of the cloud layer(s), providing another mechanism for isolating small subsets of the total reaction set.

      • AK, thanks for the reply. I appreciate your interest in this stuff, so what I’ll try to do is put together a reference list for you, of recent papers that deal with some of the issues you raise. The RNA World idea is based on a lot of solid work, and rests on both the ability of RNA to catalyze its own formation and the ribosomal function of making proteins directly. DNA isn’t necessary as a mechanical contributor to that process, and is a fairly complex add-on that proved a headache to explain for years, until RNA auto-catalysis was observed and explored. It’s a case of Occam’s Razor, where far more difficulties arise in trying to insist that DNA was there from the beginning, rather than the simpler model of RNA.

        Also, when it comes to assessing a scientific question, never trust your gut… it’s only good for processing biomass, not information. 😉

        Regarding life in the water column: remember that by the time cells leave the vents and enter the open water, they’d already have a membrane…. a micelle membrane, which as I said has been demonstrated in practice to easily self-assemble under the conditions of interest. The science behind micelle formation is pretty uncontroversial.

        Your approach to atmospheric compositions misses one big issue: kinetics. Chemical reactions can be favored thermodynamically and yet still may not proceed due to kinetic inhibitions. N2 is a perfect example: you have to break that triple bond, either with lots of heat or with enzymes. CO2 and CH4 can coexist in an atmosphere without reacting, if there isn’t sufficient activation energy for wholesale conversion reactions. The atmosphere of Titan has CH4, N2, NH3, CO and CO2, for example. Redox disequilibrium is very common under abiotic conditions, and in fact is a necessary precondition for biocatalytic systems to arise… biocatalysis exploits kinetically-inhibited reactions. That’s more or less the whole point of life, chemically. Remember that paper, wood and you don’t spontaneous combust, because of activation energy barriers. You can’t run an equilibrium calculation for the bulk atmosphere and get meaningful results… you’ve got to factor in kinetics or else your results will be way off.

        You’ve touched on a lot of things, so like I said above, I’m going to try and attach some references here for you. It might be easier that way, instead of having me describe what’s in the literature, for you to take a gander directly. I’ve got a few good review papers in PDF form, I’m pretty sure, that deal with the issues in question and provide a lengthy list of back-references that one can have many hours of fun digging into. 🙂

        One thing that stops me cold, though, I have to admit:

        If we assume that the entire system of nucleic acids arose as part of a pre-existing system of life, then it makes more sense that DNA and RNA arose together, performing different functions. Then, they took over most of their modern functions, and the earlier life-forms were driven into extinction.

        Before I jump to any conclusions based on misunderstanding, I need to ask: Are you implying some variety of panspermia here?

      • Okay, here are a couple of references for now… more later. The first one deals with the chemistry of prebiotic synthesis, the second reviews the state of current understanding of the origins of metabolism, including discussion of the RNA world hypothesis, and the third is a really great review of how the Earth’s atmosphere evolved from the Hadean to the Proterozoic. The fourth one I blogged about here a few months ago; it discusses the role of methane and CO2 in heat retention in the early Earth’s atmosphere. In each case I’ve chosen review articles or articles of particular significance to the stuff we’ve been discussing, which are recent and therefore include reference lists that are comprehensive to the state of current knowledge in that particular topic. Enjoy! 😀

        Douglas E. LaRowe & Pierre Regnier (2008) Thermodynamic Potential for the Abiotic Synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in Hydrothermal Systems. Origins of Life and Evolution of Biospheres 38, 383–397. [PDF]

        Gustavo Caetano-Anollésa, Liudmila S. Yafremavaa, Hannah Geea, Derek Caetano-Anollésb, Hee Shin Kima, Jay E. Mittenthalb (2009) The origin and evolution of modern metabolism. The International Journal of Biochemistry & Cell Biology 41, 285–297. [PDF]

        George H. Shaw (2008) Earth’s atmosphere – Hadean to early Proterozoic. Chemie der Erde 68, 235–264. [PDF]

        Jacob D. Haqq-Misra, Shawn D. Domagal-Goldman, Patrick J. Kasting, and James F. Kasting (2008) A Revised, Hazy Methane Greenhouse for the Archean Earth. Astrobiology 8(6), 1-13. [PDF]

      • Thanks again, Planetologist, for the papers. My preliminary comments:

        Thermodynamic Potential for the Abiotic Synthesis of Adenine, Cytosine, Guanine, Thymine, Uracil, Ribose, and Deoxyribose in Hydrothermal Systems by Douglas E. LaRowe & Pierre Regnier

        My first reaction is that while this article investigates the likelihood of the necessary bases, it ignores the large number of alternative bases that could have poisoned any system of “simple” RNA. Without the appropriate calculations showing that the necessary bases are the only ones to form in significant concentrations, IMO the viability of an “RNA World” developing in this environment remains to be demonstrated.

        The assumption that the concentrations of the species in ancient and modern hydrothermal fluids are similar is reasonable because the composition of hydrothermal fluids are primarily determined by their interactions with mantle-derived rocks, whose composition (i.e., oxidation state) has not changed significantly in the last four billion years (Delano 2001).

        (The referenced paper is Redox History of the Earth’s Interior since ∼3900 Ma: Implications for Prebiotic Molecules by John W. Delano.) I’ve seen estimates of 4400 MYA for the initial condensation of liquid water, so this leaves 400 MYears for a strongly reducing atmosphere to support the development of life which could, in turn, have produced its own changes. In addition, reading the abstract I see: “Results indicate that the Earth’s mantle hasbeen at-or-near its current oxidation state (±0.5 log-unitfO2) since at least 3600 Ma, and probably since at least 3960 Ma.”, which means that that actual figure is 3.4 GYear, not 4.

        The origin and evolution of modern metabolism by Gustavo Caetano-Anollésa, Liudmila S. Yafremavaa, Hannah Geea, Derek Caetano-Anollésb, Hee Shin Kima, Jay E. Mittenthal

        An impressive paper. It’s going to take detailed study for me to determine whether these results actually support the notion that proteins appeared before the establishment of a complete metabolism, especially if we assume a hydrogen-rich atmosphere for the previous, ribozyme-based metabolism. (See my comments on the next two papers.)

        Earth’s atmosphere – Hadean to early Proterozoic by George H. Shaw

        I note the emphasis on the speculative nature of all conclusions. I started to compile a list of key quotes supporting my position for a highly reducing atmosphere, then decided the whole paper does that.

        One point regarding the assumptions is the absence of pre-oxygenic energy cycles. We know today of the sulfur cycles (e.g. Black Sea, many eutrophying mud columns) interconverting between H2S and elemental or oxidized sulfer, but another potential cycle involves nitrogen and ammonia, used to oxidize the CH bond in organics. Although this reaction is perhaps 1/5 as energetic as O2/H2O, I would think it to be in the same range as the sulfur cycles.

        Another, earlier, possibility, first proposed in or before the ’50’s, is the use of hydrogen to “oxidize” the carbon-carbon bond, retrieving energy from hydrocarbons and yielding methane or short-chain hydrocarbons. In a quick search I couldn’t find any evidence of this reaction in use today, perhaps because the ubiquity of CO2 has supported competition by hydrogenophiles that use CO2 for biogenesis.

        Both of these reactions, if widely used very early in the Earth’s life, would have important implications for atmospheric composition. If life arose while the partial pressure of hydrogen was in the 10’s of bars or more, the entire process from abiogenesis to development of proteins could have occurred during this stage, before the solar wind reduced hydrogen to trace levels.

        A Revised, Hazy Methane Greenhouse for the Archean Earth by Jacob D. Haqq-Misra, Shawn D. Domagal-Goldman, Patrick J. Kasting, and James F. Kasting

        This is an interesting paper, but I doubt the conclusions can be applied to the earliest stage of the Earth’s existence (4.4-3.6 GYA). I would assume that if the atmosphere began as very strongly reducing, with a high partial pressure of hydrogen, the development of life and especially the nitrogen cycle (analogous to the modern oxygen cycle) would have produced a CO2/N2/H2O atmosphere by, say, 4GYA. The changeover from CH4 to CO2 as primary greenhouse gas would have been roughly synchronous to the disappearance of ammonia in favor of N2. This probably would have occurred along with the disappearance of significant H2.

      • Review papers are a really good way of catching up on the current state of a discipline, for those whose expertise is in a different area but whom are interested in the topics. An advantage of review articles is they tend to be less technical, and more accessible to a wider range of readers who are otherwise scientifically literate.

        I’m glad you read the LaRowe & Regnier paper; that’s only one example of the current state of experimental knowledge about life’s origins. There’s a lot more out there. To your reaction, though… I think you may be “stuck” on this idea of “the large number of alternative bases that could have poisoned any system” of RNA… I’m not sure where this idea came from, to you, but it really is not the problem you assess it to be. In any geologic system the number of pertinent, abundant chemical species will be limited in number based on their stability. That’s a pretty basic, demonstrable fact of chemistry. Take a practical example: carbonaceous chondrites. Under the conditions that carbonaceous chondrites formed in the solar nebula, particular chemical species were more stable than others, and the results are shown clearly and unambiguously in the compositional profiles of the meteorites in question. They contain a list of compounds at high concentrations (amino acids, saccharides, PAHs, etc.), some at low to trace concentrations, and not others. Another example is the Miller-Urey experiment. Despite it’s shortcomings, and there are a few, that experiment started with a few simple gases and volatiles and then cooked up a discrete suite of amino acids, peptides, hydrocarbons and other organics… the ones that were stable under the experimental conditions. You could run that experiment a thousand times, and if you repeated the setup the same way every time you’d get similar results every time, with a similar profile of products. Thermodynamics and kinetics rule, basically. There will never, under any conditions in the universe, be a system where all organic compounds are stable and equally – or even near-equally – abundant. It simply does not work that way.

        Thanks for the discussion. I write this blog to try and communicate science to people outside a classroom situation, and I’m really glad when people like yourself are interested enough in the topics to go read the scientific literature. I wish more people would do that. Whenever I get into it with some nutcase who’s got a pet theory about an expanding Earth, or that life was started by “intelligent design”, or some other woo, it’s very frustrating to be able to point to mountains of unbiased, critical studies that soundly disprove their cherished notions, only to have all that dismissed out of hand without even a cursory glance on their part. Students in my classes are ignorant of science, but only because they’re students and haven’t seen any of it before. That’s not a problem… the problems come from the global climate change deniers, the Holocaust deniers, the evolution deniers… people who are willfully ignorant, or stubbornly fixed in the concrete of own pet delusions. Okay, enough jabbering… I’ve got to get to class. 🙂

      • Thanks again, Planetologist, for your continued response. Concerning:

        I think you may be “stuck” on this idea of “the large number of alternative bases that could have poisoned any system” of RNA… I’m not sure where this idea came from, to you, but it really is not the problem you assess it to be. In any geologic system the number of pertinent, abundant chemical species will be limited in number based on their stability.

        It actually came originally from Stuart Kauffman’s “Origins of Order“. I carried the idea forward myself, including teaching myself the basics of thermodynamic biochemistry (I’d read a textbook, but skipped the thermodynamic aspects until I discovered I needed them). My first question is why you assume that the bases used in RNA would be the “abundant chemical species“, if nobody has done similar calculations on the many alternatives? My second question involves the difference between a ribozyme that catalyzes RNA polymerization when only the appropriate monomers are present, vs. one that can recognize the appropriate bases while excluding the literally thousands of alternatives that are possible. Wouldn’t the latter, because of its much greater specificity, would be far less likely to occur through random activity?

        Take a practical example: carbonaceous chondrites. Under the conditions that carbonaceous chondrites formed in the solar nebula, particular chemical species were more stable than others, and the results are shown clearly and unambiguously in the compositional profiles of the meteorites in question. They contain a list of compounds at high concentrations (amino acids, saccharides, PAHs, etc.), some at low to trace concentrations, and not others.

        Perhaps, but consider Carbonaceous chondrites: tracers of the prebiotic chemical evolution of the Solar System by Anja C. Andersen and Henning Haack (which was the first paper to come up on my Google search):

        Around 70 amino acids have been identified in meteorites among the 159 possible C2 to C7 isomers (Cronin and Chang, 1993; Botta and Bada, 2002; Ehrenfreund et al., 2002). Only eight of the 20 amino acids that life is using have so far been identified in meteorites.

        Cooper et al. (2001) have found a variety of polyhydroxylated compounds such as sugars, sugar alcohols and sugar acids in amounts comparable to the amino acids which were found.

        Although I wouldn’t suggest that the formation process is identical to that in the atmosphere of early Earth (or hot springs), this seems much closer to what I’ve been describing than something where only the specific monomers required are present. (70 out of 159!)

        Another example is the Miller-Urey experiment. Despite it’s shortcomings, and there are a few, that experiment started with a few simple gases and volatiles and then cooked up a discrete suite of amino acids, peptides, hydrocarbons and other organics… the ones that were stable under the experimental conditions. You could run that experiment a thousand times, and if you repeated the setup the same way every time you’d get similar results every time, with a similar profile of products. Thermodynamics and kinetics rule, basically. There will never, under any conditions in the universe, be a system where all organic compounds are stable and equally – or even near-equally – abundant. It simply does not work that way.

        IIRC there was also a brown sludge of polymerized something. In any event, I wasn’t trying to say either that all the possible compounds would show up, or that the ones that did would show up in equal amounts (30:1 is roughly equal), only that a very large number would be present, and any catalysis that took place had to be specific enough to exclude all that were present as well as including the required molecules.

        Anyway, my thesis isn’t so much that it’s impossible for life to arise under these circumstances, but that the type of life that would arise would be very different than the “RNA World” with only a single type of molecule doing everything. Long before an “RNA World” would have gotten started (probably, IMO) something more tolerant of the very wide variety of available monomers would already have established itself.

        If we must look for vestiges of the original type of life within the modern cell, rather than RNA I would look to the process of assembling sugars, sugar-carboxylic acids, and ammoniated sugars and sugar-carboxylic acids present in the endoplasmic lumen and Golgi bodies. Even that may be somewhat chauvinistic, as this system also might be a relative late-comer compared to what arose first. (And certainly the system of SNAREs etc. is; IMO these protein-based systems replaced an RNA-based system shortly after the invention of proteins, pending further study of the Caetano-Anollésa et al paper and similar.)

      • My first question is why you assume that the bases used in RNA would be the “abundant chemical species“, if nobody has done similar calculations on the many alternatives?

        I’m not assuming the answer, I’m talking about taking the answer we have (i.e. the bases that are used) and trying to back out from that what conditions would have promoted those particular chemical species. Most experiments are based around trying to figure out what conditions favor organosynthesis, and what subset of those conditions favor our kind of organosynthesis. I’d never assume ours is the only kind of life possible, but instead I form a null hypothesis that our kind of life is self-evidently possible, try to work how it happened, and look for other chemical optima that could produce self-replication. There are probably many possibilities that occur on many worlds out there, we just don’t have them worked out yet.

        My second question involves the difference between a ribozyme that catalyzes RNA polymerization when only the appropriate monomers are present, vs. one that can recognize the appropriate bases while excluding the literally thousands of alternatives that are possible. Wouldn’t the latter, because of its much greater specificity, would be far less likely to occur through random activity?

        Nope. Again, you’re looking at the wrong end of the telescope. 🙂 You’re making the lottery fallacy, as in what are the chances of anyone winning tomorrow’s lottery, versus you winning it (if you bought a ticket)? Answer: exactly the same odds. Only in retrospect does it appear miraculous that you won over all those other people.

        The simplest explanation is that non-specific RNA subunits acted as ad hoc ribozymes in the primordial sludgeworks…. where some interactions produced more efficient self-replication results than others. By definition, those that worked better at copying themselves became more abundant and scavenged aminos etc. from the milieu more quickly or completely than competing systems. Among those thousands of options (collectively, in every geographic location where abiogenesis was happening) the most competitive alternatives would naturally tend to become more successful… and the complexes capable of constructing ad-hoc ribozymes of slightly better efficiency and specificity, as the system pared itself down to a smaller, more efficient set of building blocks, would take over. The specificity you see today is very far down a long, winding and branching road…. and you’re only seeing the winner.

        My original blog post that started this discussion shows how this works. The most primitive life forms that only use RNA (viroids) mutate the most, today…. as life built complexity beyond that level of simplicity it could tolerate fewer and fewer parameter changes – mutants past a certain degree of deviation simply died, narrowing the field further. Evolution plays variations on themes, and not all variations work, or even work particularly well.

        …catalysis that took place had to be specific enough to exclude all that were present as well as including the required molecules.

        Again, turn that ‘scope around. Catalysis only had to be specific enough to get started… after that, variations included better, neutral and worse combinations. The better combinations worked better, and used available parts (aminos, etc.) to cobble together copy after copy after copy… constantly tossing away modifications from that starting version that didn’t work well, and retaining those that did. The whole thing is pretty automatic.

        Anyway, my thesis isn’t so much that it’s impossible for life to arise under these circumstances, but that the type of life that would arise would be very different than the “RNA World” with only a single type of molecule doing everything. Long before an “RNA World” would have gotten started (probably, IMO) something more tolerant of the very wide variety of available monomers would already have established itself.

        Well, clearly it’s not impossible. 😉

        Why would you assume life would have to be different from an RNA world, though? I’m not claiming – nor does any other origins of life expert, to my knowledge – that RNA is the only possible molecular construct that could form the working basis of life. In fact some of my own research is based around the premise that other options are probably likely, and we need to figure out what those options might be, as much as we possibly can lacking working examples.

        I think it’s very likely that not only RNA but many other molecular systems of coded, repeated sequences in a molecular framework template could do the job, potentially. On Earth, conditions favored RNA and maybe some other things, but RNA won the race in the end. I think it’s completely fascinating to consider what other options might work, but one must always temper that fascination with a critical appraisal of which options are more feasible to actually occur under constrained physical conditions, and which can’t occur. Was RNA the only setup on the early Earth that could have gotten itself up and running as a replicator? I don’t know, man. Maybe, maybe not. If so, we need evidence of that, or else we’re just speculating without constraint. Experiments and calculations could provide the necessary constraints. If RNA wasn’t the only option, RNA still won (and led eventually to the invention of DNA) here on Earth, and I think it’s interesting to explore how that happened.

      • Thanks again, Planetologist, for your continued response. I hope your continued questions mean that you’re willing to continue the conversation. I’m learning a lot as well as enjoying myself with it.

        I’m not assuming the answer, I’m talking about taking the answer we have (i.e. the bases that are used) and trying to back out from that what conditions would have promoted those particular chemical species.

        […]

        You’re making the lottery fallacy, as in what are the chances of anyone winning tomorrow’s lottery, versus you winning it (if you bought a ticket)? Answer: exactly the same odds. Only in retrospect does it appear miraculous that you won over all those other people.

        […]

        Why would you assume life would have to be different from an RNA world, though? I’m not claiming – nor does any other origins of life expert, to my knowledge – that RNA is the only possible molecular construct that could form the working basis of life.

        […]

        On Earth, conditions favored RNA and maybe some other things, but RNA won the race in the end.

        […]

        If RNA wasn’t the only option, RNA still won (and led eventually to the invention of DNA) here on Earth, and I think it’s interesting to explore how that happened.

        I’m going to answer all of these at once, because they address the same failure to communicate my actual thesis.

        You’re making the assumption that because we have a world based (partly) on RNA today, and evidence that proteins were invented somewhat late in the game, that RNA was involved in the original form of life that led to ours. I’ll agree that in this it’s “simpler” (but in only one respect) to leave DNA out of the original scenario, however your suggestion to “turn that ’scope around” depends on that assumption. When you compare it to the scenario I’m proposing (modified somewhat from Kauffman) it looks like circular argument to me.

        Here’s my scenario in a nutshell (well, a big one):

        1. At the time the Earth’s surface cooled to the point that liquid water could stand on the surface, there was a strongly reducing atmosphere composed mostly of hydrogen (with smaller amounts of water, ammonia, and methane, and traces of CO, CO2, CH2O, and perhaps HCN, C2H2, CnHn+2 saturated hydrocarbons as well as a host of others at even smaller concentrations).

        2. Even by this point a great deal of synthesis would have taken place in cloud droplets at temperatures down to -40C, where, extrapolating from fig. 1 of LaRowe &Regnier (2008) the activity of CH2O would have been perhaps three orders of magnitude greater than that at 150-200C assumed for peripheral hot springs. That for HCN five or six orders of magnitude. And that doesn’t allow for the much higher partial pressure of hydrogen. This would have begun under the influence of repeated desiccation and sunlight, but as random polymerization took place some of the polymer molecules would have had dye-like characteristics, and started filling their associated droplets with with high-energy electrons which would have increased the process.

        3. Many of these polymer molecules would have had some sort of catalytic ability, random like the polymers themselves (that is the selection in any droplet would have been random). Much of that catalysis would have involved further polymerization, but much would also have supported interconversion among sugars, amino acids, nucleic acids, etc.

        4. Thus, even by the time the surface cooled to the point that water could be liquid, enough catalysis would have been present in the atmosphere (as droplets) to maintain an equilibrium. And we mustn’t forget the carbonizing effect of volcanic activity on polymer particles, producing more heat-resistant random particles with random catalytic ability.

        5. In this environment, the cooling ocean became covered with a floating layer of foamy slime containing hydrocarbons, oxidized hydrocarbons, sugars (sometimes carboxylated and/or ammoniated), amino and nucleic acids, and all sorts of other monomers. It also would have had polymers of these, in reducing concentrations for each polymer, but the fraction of any molecular weight would have been larger with larger weight because of the exponentially increasing number of possible polymers.

        6. Sunlight would have mostly been stopped at the cloud tops, where dye-like molecules would have absorbed the light and converted a large fraction of it to high-energy electrons in solution, which in turn would have stimulated the synthesis of high energy molecules. Many of these molecules would have been reasonably slow to degrade into lower-energy molecules without catalysis, “due to kinetic inhibitions.” A good fraction of these would have diffused, or been washed by rain, to the surface where they would have driven a sea-based energy cascade.

        7. Life, in my scenario, arose in this environment. Unlike the simplified environments favored by most, this environment has “complexity for free”, especially membrane topology and distribution of catalysts. IMO “lifelike” configurations arose frequently, mostly capable of growing but not dividing, but even those capable of dividing weren’t viable. Kauffman has a fairly good description of the process of interacting catalysts, although IIRC there are some problems with his thermodynamics.

        8. In this scenario, the earliest viable life consisted of complete (if somewhat simple) metabolisms capable of capturing high-energy molecules from the surrounding medium and using the energy to create an environment in which the array of catalysts could replicate themselves as well as enable the metabolism.

        9. As competition increased, one of the more successful varieties of life developed a system using nucleic acids. This system may have had only a minor function at first, but using DNA for info storage, and RNA (usually modified after transcription) for other functions, perhaps something like what the system of SNAREs etc. does today, controlling the movement, merging, and splitting of vesicles with their associated synthesis. Note that since this earlier life already had a system of catalysis, which would have driven DNA replication and transcription as well as the metabolism and its own system of replication, there is no need to look for a complete replicating life based on RNA, or DNA=>RNA, until the new system “took over” this function in the same way that proteins later “took over” the function of catalysis. This also allows that RNA never needed to perform catalysis without modification, something that AFAIK it doesn’t do today (except for some limited functions regarding transcript modification, e.g. self-excising introns). It also means that there was never the problem of separating “informational” RNA from catalytic RNA. Until the invention of proteins, RNA had no function but catalysis.

        Now, if we assume this scenario to be plausible, we have to compare the probability that it would take place with that for the “Original RNA World” (if I may coin a term for the thesis you describe). Among the differences is that my scenario allows a full ocean surface, with at least several meters depth, to be given over to the random “tries” at viable life. Since we aren’t limited by the specific molecules used today, there is no issue with the probability of necessary molecules: whatever thermodynamics favored was what was incorporated into it. Compare this with the need for isolating the specific ingredients often enough for random “trials” to create viable life.

        Note that the statement “[i]f RNA wasn’t the only option, RNA still won (and led eventually to the invention of DNA) here on Earth” now becomes unsupported, since it’s based on circular logic. (OK, technically if RNA arose in and replaced an earlier life form it still “won“, but you know what I mean.)

        Obviously, time constraints have limited how much I could discuss of this scenario, as well as my not knowing whether you’re familiar with Kauffman’s proposals (and thus how much I need to discuss). Kauffman’s scenario(s) involve what I call a “plaster of Paris” model of catalyst creation (I don’t recall whether he uses the term). The important thing about this model is that it doesn’t depend on any specific monomers: whatever is present (within constraints) can be used to create catalysts.

      • Thanks, and it does look like you’ve been giving this some solid thought, which is good. I’d argue with some of your specifics, but this is an active area of research and all the questions aren’t answered yet.

        The main problem I see with your scenario is one of setting. I know others have proposed the idea that life may have started in tide pools, or the ocean surface water, or even in clouds. I personally don’t put much value on those hypotheses, for the principal reason of reaction kinetics. In a homogeneous medium like a solvent or a gas, a lot of chemical reactions are difficult to activate, no matter the driving potential. Heterogeneous reactions are far easier to activate, as a general rule, and definitely in the specific case of aqueous-phase reactions involving dissolved chemical species and mineral surfaces. There’s a gigantic literature on this, actually…. like, seriously gigantic. I’ve done some work in adsorption of aqueous complexes onto minerals and bacteria, and this was actually one of my major research foci during the last several years. That list of “Pubs by Me” lists some of those papers.

        Anyway, heterogeneous reactions are much easier to activate on mineral surfaces, usually, and easier by many orders of magnitude. Nearly all modern research on origins of life processes tends to focus on heterogeneous catalysis as a starting point for true biosynthesis. This isn’t bias, nor is it dogma. Experimental data are very clear on this point: homogeneous reactions involving organic molecules in the gas or aqueous phases occur, but their feeble kinetics lead to absurdly low yields for complex molecules like peptides and nucleic acids… unless those reactions take place at the mineral-water interface. When you involve mineral surfaces, especially redox-active mineral surfaces like iron oxides and iron sulfides, rates and yields increase dramatically. That’s why most origins of life models are linked with clays, or hydrothermal vents and metal-sulfide mineralogy. I personally don’t like the clay-life models, because although clays can promote adsorption of organics they don’t impart any energy to the adsorbates, or drive redox chemistry in any significant way. Transition-metal sulfide minerals (e.g. pyrite, pyrrhotite, arsenopyrite, chalcopyrite, etc…) are wonderful at this task, and in a pre-biotic world such minerals are mostly found in association with hydrothermal vents. Clouds processes just can’t do the heavy lifting, in this regard…. or at least not under conditions that are remotely realistic to the early Earth.

        As I mentioned in a previous post, according to everything I’ve learned about this issue, hydrothermal vent systems in the oceans best satisfy the constraints imposed by the chemistry of abiogenesis. Seafloor vent systems could have occurred in shallow water or deep water, and that is an active research issue…. specifically the question of whether sunlight played in proximal role in the chemistry of life’s origins on this planet. Obviously sunlight cooked up organics in meteors prior to accretion, but those reactions don’t appear to have advanced to the level of replicons (but if they did, that would be mineral-water interface chemistry, too).

        One last thing…. it isn’t accurate to say my statements on RNA are circular. There’s no circularity to it…. RNA is the only viable model for the earliest stages of life that led directly to Earth’s known biota, because RNA is the common functional thread running through all life on Earth. It’s not circularity, it’s simply observation. Any origin of life would have to invoke RNA at some early stage, because RNA is common to all life. That statement is not true concerning DNA, which is not common to all life. Observationally, RNA is a necessary if not sufficient requirement for known life…. but DNA isn’t a necessary condition. This isn’t controversial. There are a lot more reasons why DNA can’t work at the beginning, such as it’s physical complexity and instability under a wide range of conditions, whereas RNA is much more resilient. Also RNA is single-stranded, which gives it much greater functional versatility and makes it much easier to assemble. DNA is an add-on, apparently, that solves issues of permanent data storage.

        Now, this obviously leaves open the idea that life on Earth started without RNA, but at some later point RNA had to come into the process. There’s nothing more circular to that than there’d be in observing that life requires carbon. Life on Earth appears to require carbon, and it appears to break down functionally to an RNA engine. The question addressable by research in the lab (or in other star systems) is: can an alternate starting system that involves a pre-RNA replicon be assembled and tested, then compared with models that try to go straight from primordial organics to an RNA-based working model of life. So far, the experimental evidence points to it being a feasible model to consider RNA as an original, primordial replicon as the LUCA. The jury is still out, the science is still being done, but that’s the model that so far makes the most sense, compared with all the other options so far examined.

        Side note: The need for mineral surface interactions is also why I tend to reject ideas about life in the clouds of Venus. Yes, there are bacteria in Earth’s clouds, but only because they’re swept up there from starter populations on the ground or in the ocean, which get entrained in sea spray and find their way into the clouds along with sea-salt crystals. But just like sea-salt, those bugs rain out pretty quickly in precipitation. There might be self-sustaining populations of microbes in Earth’s troposphere that never reach the surface, but I’m not betting any money on it. 🙂

        Okay, I’m off to rake even more leaves.

      • And… I must say, this is by far the longest rational discussion I have ever seen or experienced on the internet. I salute you, sir.

      • Thanks, Planetologist. I’m going to take your responses as indicating you’re willing to continue.

        I personally don’t put much value on those hypotheses, for the principal reason of reaction kinetics. In a homogeneous medium like a solvent or a gas, a lot of chemical reactions are difficult to activate, no matter the driving potential. Heterogeneous reactions are far easier to activate, as a general rule, and definitely in the specific case of aqueous-phase reactions involving dissolved chemical species and mineral surfaces.

        […]

        Anyway, heterogeneous reactions are much easier to activate on mineral surfaces, usually, and easier by many orders of magnitude.

        […]

        Experimental data are very clear on this point: homogeneous reactions involving organic molecules in the gas or aqueous phases occur, but their feeble kinetics lead to absurdly low yields for complex molecules like peptides and nucleic acids… unless those reactions take place at the mineral-water interface. When you involve mineral surfaces, especially redox-active mineral surfaces like iron oxides and iron sulfides, rates and yields increase dramatically.

        OK, I didn’t know this (I think). That is, I knew that such reactions aren’t going to take place (very fast) without catalysis. My assumption is that once you get enough polymers into existence some of them will be catalytic. However, getting that jump start remains a problem.

        Of course, in today’s environment, virtually all water droplets in clouds condense around particles of rock or salt (or smog, pollen, bacteria, etc.). I don’t know whether that would remain true without an ozone layer, perhaps the ionization trail from UV would provide enough nuclei that clay particles wouldn’t get into it.

        I’m certainly going to look at the papers you mentioned and try to estimate how viable a theory it is that clay nuclei of cloud droplets could be responsible for solving the catalytic problem (I’m assuming my use of “catalysis” refers to the same phenomenon that you do with “kinetics”.) Of course, if you have a back-of-the-envelope guess, I’d like to know it.

        My reference to circular logic had to do with the “Original RNA World” being the actual beginning of life. Once you admit of plausible alternatives for the first life, and a plausible model for progress from that to one involving RNA, then we can no longer know that it was first. Therefore the relative probabilities have to be evaluated. If, for instance, several Purines, such as Hypoxanthine or Xanthine, turned out to be more stable than Guanine (I know Adenine is the most stable, as has been shown in many experiments), then estimates of the probability of the “Original RNA World” relative to other scenarios would have to be revised. Thus, once plausible alternatives are admitted, the expanded stability calculations become relevant.

        And… I must say, this is by far the longest rational discussion I have ever seen or experienced on the internet. I salute you, sir.

        Thank you sir. Good as it makes me feel personally to hear that, it’s disappointing in a general sense. Given the internet’s potential for allowing interested amateurs to participate in scientific speculation, it’s too bad more people don’t take advantage of it. Perhaps it’s because understanding these things does require a good deal of work.

      • Thanks, Planetologist.

        I haven’t actually missed the kinetics aspect, I’m making some assumptions regarding omni-catalysis that I probably should have gone into more deeply. However, even without catalysis, we have radiation. Although I suppose there’s a limiting partial pressure of hydrogen necessary before UV would stimulate the creation of ammonia (or hydrazine, etc.) from N2 and H2.

        I tried to discriminate in my arguments between prebiotic times and those where life already existed (“[…] hydrogen and carbon dioxide cannot both be present in significant amounts in a modern-style biosphere“). Still, in the absence of oxygen I would expect the presence of many general catalysts (e.g. nickel powder) that would influence the abiotic environment.

        Before I jump to any conclusions based on misunderstanding, I need to ask: Are you implying some variety of panspermia here?

        Not really, just something based on lower energy bonds (than phosphoester) and greater complexity of membrane topology.

        And thanks for the references. I’ll read them before posting back.

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