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Probabilities and the Genesis of Life

The important thing to keep in mind concerning probabilities and the origin of life is that proteins, and everything else in a living cell, are manufactured by machinery which is controlled by an abstract-representation digital coding system. Proteins not only don’t self-assemble, they cannot self-assemble, because basic chemistry drives the process in the opposite direction.

Once this is taken into consideration all arguments that assert, “But it could have happened by chance,” are rendered ludicrous on their face.

By way of analogy, the basic Darwinian argument for the origin of life goes something like this:

1) Clay occurs naturally.
2) Bricks are made of clay.
3) Therefore, there is some (given enough time) probability that houses made of clay bricks came about by stochastic processes and the chemistry of clay.

This is the way I see it, and so do most people with common sense. Apparently, one needs a Ph.D. in Darwinian Speculation (or sufficient indoctrination in this academic, “scientific” specialty) not to recognize the obvious.

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144 Responses to Probabilities and the Genesis of Life

  1. Good analogy, even if the brick is waaaay to simple for comparison. But to go with this analogy, hardly any dirt of any type has ever been found, what has been found is the wrong color, and it has never been found to have any tendency to adhere into a clod much less a brick, even if some process to form bricks was known, but none are. A chemist I know backs that 100%.

    Even an atheist expert on origin of life chemistry who believes life-from-chemicals recently said he has “no idea” how life could have gotten started.

    http://pubs.acs.org/cen/covers.....over1.html

    and scroll down to “The origin of life” heading.

    So anyone who thinks they have some idea how life got started from chemicals either (a) knows more than this expert, or (b) is content to let imagination substitute for plausibility.

  2. What a …bizarre post? I’m quite confused.

    Evolution says nothing about the _origin_ of life.

    Abiogenesis is the term which we use to refer to the origin of life.

    Evolution does not equal abiogenesis.

    Abiogenesis does not equal evolution.

    One would imagine that on a blog that champions a “scientific” or even “relevant” alternative to current academic consensus on evolution I wouldn’t have to reiterate this distinction?

  3. James: There are two major connections betwwen OOL and “evolution”.

    (a) I think the main problem ID people have with “evolution” (the term is used in a variety of ways, some of them deceptively) is the undirectedness assumed/demanded for the process. Exactly the same undirectedness is assumed/demanded for OOL, despite chemistry to date not providing anywhere near enough complexity.

    (b) While its true that Darwin’s text dealt with the origin of species (not life), the atheistic worldview his theory so strongly supported requires an abiotic OOL. But even limiting it to the neo-Darwinian claim, in my opinion, the chemistry required for one species to become another is seriously lacking. The whole idea that random mutation/natural selection accounts for all varieties of life is based on a gross extrapolation of microevolution, or in other words, faith.

    It is deceptive to claim that “evolution” does not address OOL when most of the importance of “evolution” is centered around the idea that life, species and everything can “just happen”.

    By the way, can you define evolution for me? Include every way you would use that word.

  4. So what’s the more probable alternative to some sort of chemical abiogenesis?

  5. Evolution says nothing about the _origin_ of life.

    Dear James,

    Evolution says nothing about anything, because evolution is not a person.

    All of modern Darwinian theory is fundamentally based on the presupposition that the first living cell came about by stochastic chemical processes.

    Even given that this impossible event occurred, random errors filtered by natural selection is a preposterous hypothesis concerning the conversion of the first microbial cell into you in such a short probabilistic period of time.

    The origin of the information in the first living cell and the origin of the information that made you represent exactly the same problem.

    You were designed for a purpose. Get used to it.

  6. GilDodgen:

    Even given that this impossible event occurred, random errors filtered by natural selection is a preposterous hypothesis concerning the conversion of the first microbial cell into you in such a short probabilistic period of time.

    You are of course entitled to your beliefs, but I see nothing here but entirely baseless assertions. Do you have a model to demonstrate that 4 billion years is too short a “probabilistic period of time”? Then we would cross our mathematical swords, so to speak. Now there is nothing to talk about.

  7. “Evolution says nothing about anything, because evolution is not a person.”

    So I take you reject sentences like “The theory of gravity says that two objects with mass exert a force on one another”? You have a very odd linguistic community.

    “Even given that this impossible event occurred.”

    I thought it was just extremely unprobable. Making the impossibility claim is a little bit bold. Care to demonstrate that, and care to take an analogy with something that is capable of self-replication, rather than bricks?

  8. Mr. Bond…James Bond,

    The question is what drove the beginning of life AND early life prior to it breaking some supposed threshold where evolutionary processes could kick in.

    After all, that is what TMS does- assumes the beginning of life and the early development stages and then starts at some arbitrary point, where it is speculated that survival and competitive pressures were present enough to allow NS to work.

    An example of an endosymbiosis event, where it is thought that the mitochondria organelle was produced by assimilating a prokaryote into a eukaryote genome. The explanations are a mixed bag of survival pressures where co-option, cooperation, and competition are the drivers.

    Now the first thing that comes to mind is why is this event not explained in terms of physics and chemistry. Why is intelligent design language used to describe a so-called non-teleological, non-directional process?

    But the kicker is how the heck can these evolutionary biologists assert that there was survival pressure 2.7 billion years ago??!!! I mean a 9th grade science student would follow the logic to this simple conclusion.

    Yet, here we are having to peruse loads of so-called scientific papers claiming its all been explained quite nicely thank you through survival pressures creating differentiation that NS can act on.

    Not only is abiogenesis IMOpurposefully disconnected to avoid heavy lifting, but early development (how the first single cell organism split into eubacteria, archbacteria, and eukaryotes) is ignored as well.

  9. IrynaB

    Thank you for your post.

    Do you have a model to demonstrate that 4 billion years is too short a period of time for a house made of clay bricks to arise by stochastic processes?

    More to the point, wouldn’t you agree that if someone were to assert that such a far-fetched scenario was indeed plausible, the onus probandi would lie entirely on them? Wouldn’t you agree that it would be up to them (and not the skeptic) to put forward a step-by-step model, complete with probabilistic calculations, if they wanted their highly implausible claim to be taken seriously?

  10. “But the kicker is how the heck can these evolutionary biologists assert that there was survival pressure 2.7 billion years ago??!!! I mean a 9th grade science student would follow the logic to this simple conclusion.”

    How wasn’t there survival pressure 2.7 billion years ago? There was still an environment, still reproducing organisms with heritable and varying traits… what’s missing?

  11. kevlar,

    Not wanting to simply assume our conclusions, do you have the chemical basis for a drive to survive?

  12. “Not wanting to simply assume our conclusions, do you have the chemical basis for a drive to survive?”

    What do you mean by drive to survive? Do you mean that members of the population require some sort of willing for NS to function? If so, then you’re absurd, as I’d imagine you believe that influenza has a will, since NS functions on the influenza virus after all.

    Or do you mean some kind of tendency to reproduce? How did early cells lack the tendency to reproduce?

  13. Kelvar,

    One of the most prominent features of living things is their very ubiquitous and observable tendacy to seek survival. You may call it whatever you wish, but you cannot deny that it is there.

    The idea of inanimate material coming to life proposes that at some point inanimate chemicals gained this tendacy. Given the extreme problems associated with abiogenesis under whatever view you wish to take of it, one might even reasonably conclude this rather tenacous feature of living things might have even been a necessity from the very start.

    So I may indeed be obsurd, but I am not assuming my conclusions.

    Now, do you have an answer for the question, or not?

  14. Kevlar

    Thank you for your posts. You ask:

    So what’s the more probable alternative to some sort of chemical abiogenesis?

    That’s easy. The more probable alternative is that life of some sort always existed.

    You also write:

    Making the impossibility claim is a little bit bold. Care to demonstrate that, and care to take an analogy with something that is capable of self-replication, rather than bricks?

    I’ll answer that with a quote from an evolutionary biologist whose academic credentials are impeccable:

    Natural selection is differential reproduction, organism perpetuation. In order to have natural selection, you have to have self-reproduction or self-replication and at least two distinct self-replicating units or entities. Prebiological natural selection is a contradiction in terms. — T. Dobzhansky, “Synthesis of Nucleosidase and Polynucleotide with Metaphosphate Esters,” in The Origins of Prebiological Systems (1965), pp. 299, 310. (Emphasis mine – VJT.)

  15. Mr Dodgen,

    Proteins not only don’t self-assemble, they cannot self-assemble, because basic chemistry drives the process in the opposite direction.

    I think this is the principle reason that OOL theorizing now focuses on far from equilibrium chemical dynamics, and whether these dynamics allow reaction products to accumulate faster than they break down, and whether the scenarios are plausible in terms of the surface of the planet 3.5-4 billion years ago.

    An example of this is the famous Miller-Urey experiment. This experiment did not fail because nothing was produced. It is not true that basic chemistry caused all the products to degrade back into simple chemical feedstocks. The opposite is true. The experiment produced results that reacted and combined together and survived – too well!

    If we didn’t know that templates to assist protein self assembly existed in nature, your point that proteins can’t self assemble would have more force.

  16. Mr Vjtorley,

    That’s easy. The more probable alternative is that life of some sort always existed.

    Since the surface temperature of the Earth rises above several hundred degrees centigrade as we go back past 4 billion years, I think this alternative needs further detail, which may render it less probable. If you appeal to life originating in space, and arriving on Earth via cometary bombardment, please be explicit.

    Prebiological natural selection is a contradiction in terms.

    A quote from 1965 is hardly dispositive, even from Dobzhansky. Today we would focus more on his insistence that selection depends on self reproduction from the previous sentence. Chemical or molecular evolution assumes that molecules are reproducing at different rates and levels of error, and that they crowd each other out of feedstock resources. We have already seen this in lab settings.

  17. vjtorley,

    Your quote from Dobzhansky was not exactly accurate. First of all, he was not the author of the article you cited–that was Gerhard Schramm. Dobzhansky was actually commenting on Schramm’s paper. Here is what he actually wrote, with the emphasis on what was left out (I happen to have that book):

    Natural Selection is sometimes described as a mechanism capable of realizing the highest degree of improbability, as Dr Schramm has quite correctly pointed out. I would like, however, to express the belief that the words “Natural selection” must be used carefully. Dr Schramm has so used them. In reading some other literature on the origin of life, I am afraid that not all authors have used the term carefully. Natural selection is differential reproduction, organism perpetuation. In order to have natural selection, you have to have self-reproduction or self-replication and at least two distinct self-replicating units or entities. Now, I realize that when you speak of origin of life, you wish to discuss the probable embryonic stages, so to speak, of natural selection. What those embryonic stages will be are for you to decide.

    I would like to plead with you, simply, please realize you cannot use the term “natural selection” loosely.Prebiological natural selection is a contradiction in terms.

  18. Mr. Nakashima

    Thank you for your response. In response to my proposed default scientific hypothesis that life of some sort has always existed, you write:

    Since the surface temperature of the Earth rises above several hundred degrees centigrade as we go back past 4 billion years, I think this alternative needs further detail, which may render it less probable. If you appeal to life originating in space, and arriving on Earth via cometary bombardment, please be explicit.

    The notion that life arrived from outer space is scientifically tenable. Some bacteria, lichens, spores, and even one animal (Tardigrades) recently survived a 12-day orbital mission followed by a fiery reentry througfh the Earth’s atmosphere (the Foton M-3 unmanned satellite voyage in September 2007). As yet, we do not know if life can survive longer periods in deep space, but bacteria are thought to be capable of surviving inside rocks.

    The umbrella term panspermia embraces a variety of scientific hypotheses. For instance, Earth may have been seeded by aliens, or life could have arrived via a meteorite impact.

    But I suppose you will object that even if life on Earth originated in outer space, or on some other planet, the universe didn’t always exist, so abiogenesis must have taken place at some time in the past.

    Now, even if I were a scientific and/or philosophical naturalist, I would not argue along those lines. Indeed, I would prefer to argue that life had always existed in an eternal universe, than to argue for the plausibility of abiogenesis.

    Think of it this way. Suppose that our astronomical observations suggest that there’s a 99% chance that the Big Bang theory is true. (99% is a rather generous estimate, in my opinion, given the scientific problems attending the theory.) That means there’s a 1% chance that it’s false, in the light of what we know.

    Suppose also that the likelihood of cellular life forms originating somewhere in the universe over a period of ten billion years (the time from the Big Bang to the first life on Earth) as a result of undirected natural processes appears to be far less than 1% – say 0.000001%.

    Anyone can do the math. 1% is 6 orders of magnitude larger than 0.000001%. And if Dr. Stephen Meyer’s Signature in the Cell is anything to go by, 0.000001% is over 100 orders of magnitude too generous.

    Faced with such evidence, if I were a philosophical or scientific naturalist, I would be inclined to discount the Big Bang theory, and posit an eternal universe. I would then propose that life on Earth migrated here from another planet, and so on back in time, ad infinitum. That would be a more defensible position, in my opinion. This would involve an infinite regress, but it would not be a philosophically vicious one. You can have an infinite regress of conditions (A wouldn’t have occurred unless B did, and B wouldn’t have occurred unless C did, and so on). What you cannot have, as Aquinas recognized, is an infinite regress of explanations – or per se causes, in Scholastic terminology. Sooner or later, explanations have to come to a stop, or they don’t explain anything.

    Intellectually speaking, the hypothesis that the universe is eternal, and that life is eternal as well, requires far less in the way of mental gymnastics than the outlandish, speculative hypothesis that life originated by undirected processes acting on simple organic compounds. All it requires one to acknowledge is that we haven’t yet managed to come up with a good explanation of the large-scale features of the universe, which is compatible with the hypothesis of an eternal universe. That I could live with, if I were a naturalist.

    In response to Dobzhansky’s point about the impossibility of prebiological natural selection, you write:

    Chemical or molecular evolution assumes that molecules are reproducing at different rates and levels of error, and that they crowd each other out of feedstock resources. We have already seen this in lab settings.

    I’m not a chemist, or even a scientist, so you’re probably asking the wrong person here. However, if you’re talking about self-reproducing molecules, I take it that you are proposing an RNA world hypothesis or something like it:

    The RNA World hypothesis is supported by RNA’s ability to store, transmit, and duplicate genetic information, as DNA does. RNA can also act as a ribozyme, a special type of enzyme. Because it can reproduce on its own, performing the tasks of both DNA and proteins (enzymes), RNA is believed to have once been capable of independent life. Further, while nucleotides were not found in Miller-Urey’s origins of life experiments, they were found by others’ simulations; the purine base known as adenine is merely a pentamer of hydrogen cyanide.

    Two brief points in reply.

    (1) Dr. Stephen Meyer’s Signature in the Cell contains a detailed refutation of the RNA world hypothesis. I haven’t read it yet, but if I were you, that’s the first place I’d go. In the meantime, for a brief overview of Dr. Meyer’s key points, you might like to have a look at this essay entitled, DNA and the Origin of Life: Information, Specification and Explanation, which Dr. Meyer wrote in 2007, and which appeared in the peer-reviewed volume Darwinism, Design, and Public Education, published with Michigan State University Press. Here’s the address:

    http://www.discovery.org/scrip.....38;id=1026

    See pages 260-262 for a discussion of the RNA world hypothesis.

    (2) One sentence from the Wikipedia article (cited above) reveals the problem with the RNA world hypothesis:

    The properties of RNA make the idea of the RNA world hypothesis conceptually possible, although its plausibility as an explanation for the origin of life is debated. (Italics mine – VJT.)

    “Conceptually.” That’s a word that a philosopher might use, but not a scientist. Real scientists like hard numbers. If the proponents of an RNA world hypothesis can’t specify either and upper or a lower probability bound for their model of how life is supposed to have originated, then they can hardly expect to be taken seriously in scientific circles.

  19. “If we didn’t know that templates to assist protein self assembly existed in nature, your point that proteins can’t self assemble would have more force.”

    Do you have the reference for protein assembly. We are all familiar with the transcription/translation process but what others are there in nature that have nothing to do with life.

  20. Biped,

    Your question is a non-sequitur. If you follow my points with respect to NS’s function, I was rejecting Oramus’ assertion that the environment did not exert any selective pressures over the early cells. See post 8 in this thread.

    As well, reread post 12, my question was with respect to the early cells.

    That said, if drive to survive means ‘tendency to reproduce under certain conditions’ then proteins, and other self-replicating molecules satisfy those conditions. It’s pretty analogous to the ‘drive to survive’ of a single-plant-celled organism, or that of a virus. What drive to survive does the single plant cell have that the peptide chain lacks?

  21. You can’t say that you have solved a non-linear differential equation until you have specified the initial conditions.

    The statement that evolution does not care about how life originated is absurd.

    Name me a single person in the Darwinian camp who says.

    “Ok, I admit that not only is it improbable that the cell originated by chance, but the fact that DNA contains a robust information code that replicates itself and the machinery to replicate itself indicates it must have had an intelligent designer. After this was in place, then it was all Darwinian evolution.”

    The reason they can’t is a central pillar of Darwinian theory is the theory of unguided natural selection. Anything that set the initial conditions a certain way is frontloading. Therefore Darwinian evolution must insist on life starting by chance. Population genetics arguments are complicated and make too many assumptions. It is in the impossibility of OOL scenarios with no intelligent input that Darwinian theory meets its match. If you continue to believe in the improbable, your reason to believe is not scientific, it is religious.

  22. “Are you seriously this ignorant of cosmology?”

    Hmmm….dont make a fool of yourself Kev. Perhaps you need to reread vjtorley’s post..hopefully this time it wont go completely over your head.

    Let me give you a clue

    “Intellectually speaking, the hypothesis that the universe is eternal, and that life is eternal as well, requires far less in the way of mental gymnastics than the outlandish, speculative hypothesis that life originated by undirected processes acting on simple organic compounds”

    Vivid

  23. Mr Jerry,

    Direct templating of amino acids on RNA would be an example.

  24. Dave Wisker

    Thanks for the correction. If you want to know how I obtained the quote, I did a Google search on the phrase “prebiological natural selection” and looked for a Website with the source of the quote.

    What happened next is most instructive. The first match that came up was on http://creation.com and had I gone there, I would have obtained the entire quote, properly sourced and attributed, set in the context of the paper by Schramm, which Dobzhansky was commenting on, as you correctly pointed out in your post (#17).

    Instead of checking out the link, I passed it over. Why? Because I’d read so many complaints about the inaccuracy of scientific quotes on leading creationist Websites by proponents of Neo-Darwinian Evolution on Websites like TalkOrigins and Panda’s Thumb that I automatically assumed that the quote would be erroneous. How wrong I was!

    Instead I checked out another source, which supplied what looked like proper documentation, but gave the quote with no ellipsis and didn’t mention Schramm at all. My apology.

    As I value accuracy, I’d like to ask: is there any good online source of scientific quotes which you’d care to recommend?

    In the meantime, chalk up one to http://creation.com . Give credit where credit is due, I say.

    By the way, are you an RNA world fan?

  25. Kevlar

    You write:

    So what is your explanation for the COBE data? Where do you pull the 1% possibility that the big bang didn’t occur from? Are you seriously this ignorant of cosmology?

    I’ve been following trends in cosmology on and off since about 1970. How about you?

    Three short points in response.

    1. The fact that the Big Bang theory makes some singular predictions that alternative scientific theories don’t, doesn’t make it true. It doesn’t make it 99% probable, or even 9% probable. It just makes it a lot more probable than the proposed alternatives. For all we know, there may well be alternative theories that we haven’t even thought of, which account for the observed facts just as well or better.

    2. This article, which appeared in New Scientist magazine last year, gave me pause:

    Lithium: The hole in the big bang theory by Matthew Chalmers (7 July 2008). One of the selling points of the Big Bang is that it predicts cosmic abundances of helium-4 and helium-3. However, the observed abundances of lithium-6 and lithium-7 appear to be significantly at odds with the theory. Is this a major problem, or will future observations resolve the difficulty? I don’t know.

    3. The Big Bang theory requires scientists to make some extravagant assumptions – for instance, the existence of dark matter and dark energy. While there is some indirect observational evidence for the existence of dark matter, no dark matter particles have been observed in laboratories, to date. As for dark energy: yes, I’m well aware of observational evidence that the universe appears to be accelerating. However, I’m sure you’re also aware of the spectacular failure (by 100 orders of magnitude!) of scientists’ efforts to predict the value of the cosmological constant, which is how the Lambda-Cold Dark Matter Model (the best current Big Bang model) accounts for dark energy.

    Add up all these uncertainties, and factor in the very real possibility that the true explanation for the evolution of the cosmos may simply not have occurred to us yet. All in all, it’s entirely reasonable to say that there’s at least a 1% chance that the Big Bang theory is wrong.

  26. kevlar,

    The post by Oramus that you referred to began with his comment “The question is what drove the beginning of life AND early life prior to it breaking some supposed threshold where evolutionary processes could kick in.”

    In his post he went on to question the value of NS in relation to this central question (which was the topic of the OP).

    You then skipped over that and suggested that to have narural selection operate, one only needs an environment, replication, and heredity. Which, of course, missed the point by a fairly wide margin. Perhaps it couldn’t have been wider.

    You stated “How wasn’t there survival pressure 2.7 billion years ago? There was still an environment, still reproducing organisms with heritable and varying traits… what’s missing?”

    My question was targeted at what you ignore.

  27. Mr Vjtorley,

    Now, even if I were a scientific and/or philosophical naturalist, I would not argue along those lines. Indeed, I would prefer to argue that life had always existed in an eternal universe, than to argue for the plausibility of abiogenesis.

    I am surprised that you express this preference, given that an eternal past would overcome the lack of probabilistic resources upon which Dr Meyer’s argument against chance is built. Do you hold some other reason for this preference?

    I understand the distinction of cause and explanation, but I have often found the physical world indifferent, at best, to our ability to explain it.

    I am in the mddle of Signature in the Cell, but haven’t reached the RNA World chapter yet. I am pretty much forcing myself to read the book word for word inthe order Dr Meyer laid it out, and so far I have found that to be rewarding.

    For the sake of this discussion, I’ll make these comments about the Meyer paper you cite, on the pages referring to the RNA World hypothesis.

    (p 260) Most important for our present considerations, the RNA-world hypothesis presupposes, but does not explain, the origin of sequence specificity or information in the original functional RNA molecules.

    (p 261) Second, for a single-stranded RNA catalyst to self-replicate (the only function that could be selected in a prebiotic environment)…

    In passages such as these, Dr Meyer completely ignores the direct templating of amino acids on RNA and the stereochemical theory of the origin of the genetic code. As Dr Meyer points out in Signature of the cell (for DNA), the sequence of bases create a bumpy surface when they are stacked up. This same bumpiness that allows complementary strands of DNA and mRNA to form also creates a situation in which some amino acids have a preference for sticking to some triplets of RNA over others.

    This affinity for specific amino acids in preference to others can be the source of the information and function that Dr Meyer denies knowing any possible source for. In contradiction to Dr Meyer, it does explain the origin of sequence specificity. The ligated peptide bonds of the templated amino acids are another property upon which natural selection can operate.

    Dr Meyer here, and I expect in Signature in the Cell also, does not so much refute the RNA world hypothesis as ignore an important part of it. a part developed by many scientists over the years. It is hard to say which implication is worse – that Dr Meyer is ignorant of this literature, or that he simply is refusing to engage directly with the most relevant challenge to his views.

    With respect to the way the Wikipedia entry is worded, I don’t find the use of ‘conceptually’ to be inapt. Reordering slightly, the conceptual possibility of the (idea of the) hypothesis is grounded in the properties of RNA. I think this reflects the historical flow that scientists realized that RNA could self catalyze, and from the discovery of that property came the OOL hypothesis. Similarly, the knowledge that clays can adsorb nucleotide chains make the clay assisted hypothesis conceptually possible. In contrast, there is no salt hypothesis because there is no property of salt that would make such a hypothesis conceptually possible, even before any experiment was performed.

    Of course, scientists are not comfortable stopping at conceptual possibility, and have performed experiments to justify continuing to entertain the RNA World hypothesis. Real scientists do indeed like hard numbers, though upper and lower bounds on a probability model are unlikely to be the numbers that get updated first!

  28. Nakashima,

    Do you look at the tire and wheel on a car and say they do not necessarily indicate design, given that their shape, size, and construction make them suited to the job they do?

    To look at the enrirety of the biological system and say that it is not designed because it works! is a measure of utter blindness.

    Its incredible that we would find that the individual parts within the translation system actually are well-fitted to do the job they do and then turn our heads from the context.

    The entire body is made of up context-specific reactions and interplay between chemical constituents that have nothing whatsoever to do with each other outside of the context of the system they are coordinated within. cAMP has absolutely nothing to do with glucose.

    Do we just go from the front bumber to the tailights, examining each part along the way, and ignore it all?

    You go ahead. Not me.

  29. vjtorley,

    I’m glad the creationist site got the quotation right, though I would have preferred that they had interpreted it correctly. But that would have meant them actually reading the paper by Schramm, in which he talks about the possibility of self-replication of nucleic acids in a prebiological setting, and how selection could ensure the replication of some template sequences over others. If you recall, Dobzhansky says in the complete quote that Schramm correctly used the term natural selection in his paper. This takes the teeth out of the creationist’s use of Dobzhansky’s remark, it seems to me.

    I’m not aware of any good online source of scientific quotes. If I use a quote, I usually try to get it from the primary source if at all possible.

    As for the RNA world, I’m familiar with some of it (the literature on the subject is enormous). One thing I have found, though, is that the most productive work on the plausibility of the RNA world has come by abandoning certain restrictive assumptions. For example, regarding RNA itself, The traditional view is that the ribose sugar and its other components formed separately, and then combined. This assumption led the experimental work down a path of reactions which were ultimately found to be implausible. However, recent work has shown that thsi basic assumption may be incorrect–at least for the pyrimidine bases cytosoine and uracil. Using a set of far more plausible reactions for prebiotic conditions, the building blocks of RNA for pyrimides, at least, have been experimetally assembled via a chemical intermediate. Recent Nobel laureate Jack Szostak wrote a summary of this work in the May 2009 issue of Nature.

  30. Nakashima,

    Here is the full text of the article

    http://nar.oxfordjournals.org/...../37/8/2574

    It is interesting but looks like we have just built a couple screws when it is the space shuttle that is the objective. There is still the information building that is necessary. They still have to overcome those nasty probabilities.

  31. vjtorley: All in all, it’s entirely reasonable to say that there’s at least a 1% chance that the Big Bang theory is wrong.

    We can almost guarantee that any scientific theory will be supplanted by a new theory as more is learned. But in the case of the Big Bang, any new theory would almost certainly incorporate cosmic expansion.

    GilDodgen: All of modern Darwinian theory is fundamentally based on the presupposition that the first living cell came about by stochastic chemical processes.

    Sorry, though biologists would like to see a unified theory that encompasses the origin of life, such a theory doesn’t exist.

    Stephen C. Meyer: First, for strands of RNA to perform enzymatic functions (including enzymatically mediated self-replication), they must, like proteins, have very specific arrangements of constituent building blocks (nucleotides in the RNA case). Further, the strands must be long enough to fold into complex three dimensional shapes (to form so called tertiary structures). Thus, any RNA molecule capable of enzymatic function must have the properties of complexity and specificity exhibited by DNA and proteins.

    Scientists regularly find ribozymes (catalytic RNA) in random sequence libraries.

  32. Miller-Urey?

    Their experiment did not match any primordial Earth and the results show that toxins were also produced.

  33. vivid,

    The empirical data from COBE and other experiments suggests that the belief the universe was always as it is now is extremely untenable. As a matter of fact, the best evidence suggests that the universe used to be extremely hot and dense.

    Now if you think that requires less mental gymnastics than contemporary biology, I really have nothing to say to you. There is substantial empirical evidence that the universe, (eg, COBE, WMAP, Boomerang) and not just the earth, was at one point in time unsuitable for life.

  34. vjtorley,

    Even if the current model is mistaken, how do you get around the observations regarding the cosmic microwave background radiation?

    So perhaps the details aren’t ironed out, but why prefer the idea that the universe has always been suitable for life when the data from COBE and others suggests completely the opposite?

    So what if particular details about the theory are mistaken? You still need to establish that a theory which claims that the universe has always been suitable for life is easier to fit with our observations than not.

  35. Mr. Nakashima and Dave Wisker:

    Thank you both for your posts. As you are both aware, I make no claim to any expertise in biochemistry, so it is difficult for me to respond to your arguments in favor of the RNA world. As luck would have it, I came across this letter to The Times (December 9, 2009) while I was pondering how I would reply. The author is John Walton, a chemist and professor at the University of St Andrews. He wrote a letter in defense of philosopher Thomas Nagel, who was lambasted by another chemist, Dr. Stephen Fletcher, of Loughborough University, for recommending Dr. Stephen Meyer’s Signature in the Cell in The Times‘s Books of the Year. Here is Dr. Walton’s letter, complete and unabridged:

    Sir, – The resilience of the “prebiotic soup” myth, in spite of torrents of counter-evidence, is truly astonishing. Even professionals such as Stephen Fletcher (Letters, December 4), criticizing Thomas Nagel’s recommendation of Signature in the Cell by Stephen C. Meyer (Books of the Year, November 27), apparently still believe in it. Fletcher asserts that “Natural selection is in fact a chemical process as well as a biological process, and it was operating for about half a billion years before the earliest cellular life forms appear in the fossil record”.

    Actually the operation of neoDarwinian natural selection depends on the prior existence of entities capable of self-replication. Variants are produced in their genetic material by mutations, the variants are copied by the organism’s biochemical machinery, and then natural selection ensures the most “fit” survive. Before the arrival of organisms capable of reproduction, this process could not operate. In the words of the renowned evolutionist Theodosius Dobzhansky: “Prebiological natural selection is a contradiction in terms”. It follows that, even in principle, some quite different explanation is required to account for the origin of life. Fletcher is pinning his hopes on a supposed RNA world. He tells us: “Indeed, before DNA there was another hereditary system at work, less biologically fit than DNA, most likely RNA (ribonucleic acid)”.

    It is an amusing irony that while castigating students of religion for believing in the supernatural, he offers in its place an entirely imaginary “RNA world” the only support for which is speculation! Intense laboratory research has failed to produce even one nucleotide (RNA component) under geologically plausible conditions. As for the chains of nucleotides required for the RNA world, there are insuperable problems associated with their information content, as well as the chemical selectivity needed for their assembly. Furthermore, the earth’s oldest Precambrian rocks show very good evidence that life was present from the start, so the half-billion years Fletcher counts on were actually not available for chemical evolution.

    Rather than just kowtowing to the creaky naturalist “prebiotic soup” scenario, Meyer engages with the whole range of origin of life problems. Anyone interested in discovering where the evidence leads will find this a fascinating book.

    JOHN C. WALTON
    School of Chemistry, University of St Andrews, North Haugh, St Andrews.

    Well, that’s what a chemistry professor says. If he likes Dr. Stephen Meyer’s book, then I think his arguments deserve careful scrutiny.

    Mr. Nakashima:

    I’m greatly heartened to hear that you’re reading Dr. Meyer’s book. I’m sure his arguments against the RNA world in his book are a lot more sophisticated than those in the brief two-page critique he wrote, as part of his 2007 paper, DNA and the Origin of Life: Information, Specification and Explanation, which I recommended to you earlier.

    By the way, my tactical preference for an eternal universe is a hypothetical one. If I were an atheist (which, as you know, I’m not), that’s the argumentative strategy I’d adopt. At the present time, the scientific arguments that the universe had a beginning are highly suggestive but not compelling, whereas the probabilistic argument that life could not have evolved in the space of a few hundred million (or even a few billion) years is much more mathematically rigorous.

    Another attraction of the “eternal universe” scenario is that it leaves open the possibility of top-down explanations; there’s no need to boil everything down to physics and chemistry. (If, hypothetically speaking, I were an atheist, I’d definitely want to retain my belief in libertarian freedom. For to seriously suppose that my reasons for acting persuade me by virtue of the chemical processes occurring in my brain while I cogitate, is to undermine the validity of rational thought itself. A chemical process may be efficacious, but that doesn’t make it rational.)

    As you point out, given the infinite probabilistic resources of an eternal universe, one might argue that life could have originated from non-living matter, but why bother? Wouldn’t it be simpler to just say it was always there? (By the way, there are some philosophers who would dispute your implicit assumption that anything can happen, given enough time.)

    You may be wondering why I proposed the eternal universe scenario. Well, you might say I was fishing: I was curious as to whether any of the atheists would bite. None did. That tells me something.

    What it suggests to me is that dyed-in-the-wool atheists are not content to have a self-sufficient universe, where God is absent; rather, what they want is a bottom-up, reductionist, materialistic universe, which precludes the very possibility of a theological explanation of anything, on principle. In other words, they want a universe in which God is an “un-thought,” a meaningless concept.

    I am not accusing skeptics of having a hostile, anti-theistic motivation, you understand. The underlying motivation is not to exclude God, but to exclude certain ways of explaining reality: top-down explanations are a no-no, and teleological explanations are an even bigger no-no. It seems to me that many scientifically-minded atheists are hooked on “bottom-up” explanations, to the extent that they cannot conceive of any other kind. That kind of tunnel vision strikes me as dangerous. After all, does the world have to be bottom-up? And if so, why? Might it not be a brute fact that there are different levels of explanation in the universe, with no possibility of reducing one level to another?

    Faced with these arguments, atheists typically fall back on two lines of defense: (i) “Scientific reductionism has worked well so far; why shouldn’t it explain the origin of life too?” and (ii) a bottom-up explanation is the only kind of explanation that really explains anything.

    Neither line of defense works.

    Statement (i) is an inductive argument. Now, the inductive approach is quite appropriate when one has reason to believe that there may be an underlying law which grounds the regularity that one observes. If falling objects on Earth accelerate at 9.8 meters per second per second (unless buffeted by air currents), you might well think there’s a law that covers all these falling objects. But a grand master law covering all scientific explanations? (As in: It is a law that all explanations have to be reductive explanations.) That doesn’t even make sense. Laws cover classes of events, not explanations.

    Statement (ii) is sadly revealing. What it boils down to is: “I can’t get my head around non-reductive explanations, so I’ll stick to formulating reductive ones, and carry on in the hope that the universe conforms to my cognitive limitations.” Well, why should it? The universe doesn’t care a fig about us and what our minds can do, if it’s godless.

    Dave Wisker:

    Thanks for your comments. I just came across The Alfred Russel Wallace Page , and of course I was already aware of The Complete Work of Charles Darwin Online . What do you think of the idea of creating similar pages for 20th century evolutionary biologists? Just a thought. (Copyright might be a problem, but even if some of their older works could be made available online, that would be a useful resource.) On top of that, you’d need a master page linking to all of them, for ease of reference.

  36. Mr Jerry,

    Thank you for the reference to the full text.

    They still have to overcome those nasty probabilities.

    I think they already have shown the path forward on that.

    Of the original 10^-164, 45 orders of magnitude was from producing only peptide bonds, and templating on RNA supports that. Another 74 orders of magnitude was functional specificity, and the RNA was functionally specific for arginine-arginine sequences while the polypeptide showed enzymatic activity for the associated RNA. (The remaining 45 orders of magnitude were chirality, which this experiment does not address.)

    Also, the length of RNA and AA polypeptide are much smaller than 150 AAs, and yet they still have some function. The presence of a metal ion also catalyzes the reaction, a factor not considered in the original improbability calculation.

  37. Mr Joseph,

    Their experiment did not match any primordial Earth and the results show that toxins were also produced.

    Indeed, but as a refutation of Mr Dodgen’s position that basic chemistry defeats abiogenesis, that is acceptable.

  38. Would it be possible to focus on Gil’s OP and (try to) list what is required for the origin of living organisms?

    For example:

    1- Parts- as in what parts are required and how can they be produced:

    a
    b
    c
    d
    e

    2- Localization (getting the parts in one area)

    3- Configuration

    4- Cross reactions

    5- ?

    This is just the basic DCO (discrete combinatorial object) stuff discussed in “No Free Lunch”.

  39. A recent culmination of research provided the following paper:

    Self-Sustained Replication of an RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce.

    It was touted as evidence for self-replicating RNA and “evolution in a bottle” (SciAm).

    The research is leading edge stuff and should give us a glimpse at the reducibility of living organisms.

    If this paper is any indication, origin of life research isn’t looking so good.

    I say that because all the synthesized RNA did was make- catalyze- ONE connection.

    It took two pre-synthesized sections and joined them together.

    The “evolution” came with variance of sequence but the new sequences still performed the same function (the original sequence “died out”).

    This is a start and I hope they continue to see how far they can go-

    Sooner or later the “mainstream” will come to realize what IDists have been telling them- living organisms are not reducible to matter, energy, chance and necessity.

  40. Nakashima-san,

    Had they actually produced a living organism it would refute Gil.

  41. Mr Vjtorley,

    How felicitous that as you were thinking how to respond, you came across a letter on the exact subject, containing the exact phrase you had Googled earlier. The world is a remarkable place.

    Dr Walton’s letter glosses over exactly the same issues as Dr Meyer does in his paper. When he says:

    As for the chains of nucleotides required for the RNA world, there are insuperable problems associated with their information content, as well as the chemical selectivity needed for their assembly.

    He is merely repeating Dr Meyer’s mistake of ignoring direct templating and the stereochemical theory. When he insists that natural selection only occur based on genetics, he is overstepping the bounds of Dobzhansky’s quote. As a chemist he should know that if two reactions are going on in the same flask, using the same feedstocks, there will be a natural selection of the faster reaction, and the faster reaction’s end products will dominate over the reaction products of the slower reacton. This is all that is meant by chemical or molecular evolution.

  42. Nakashima:

    If we didn’t know that templates to assist protein self assembly existed in nature, your point that proteins can’t self assemble would have more force.

    This is quite an optimistic statement in reference to Miller-Urey. Were any proteins self-assembled? You’re crediting the experiment with an outcome that it didn’t produce, based only on your personal conviction that one day some evidence will justify your extrapolation.

    Not that it matters. If, if you could solve the problem of “protein self-assembly,” that only leads to the next question – what templates cause proteins to assemble into even the simplest living organisms?

    I don’t have a problem with all the research to determine if this is possible, although I’m sure there are better uses of public funding.

    What irks me is the blatantly non-scientific assumption of the outcome. Every experiment is spoken of as progress toward determining how abiogenesis occurred, which presumes that it did.

    There’s nothing wrong with faith and hope. But they’re as far from science as the sunrise is from the sunset.

  43. vjtorley,

    I’m afraid I have to concur with Nakashima’s assessment of John Walton’s remarks, especially this:

    Intense laboratory research has failed to produce even one nucleotide (RNA component) under geologically plausible conditions.

    I suggest this paper (to which I indirectly referred to earlier):
    Powner MW, BG Gerland & JD Sutherland (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature 459:239-242

    Here we show that activated pyrimidine ribonucleotides can be formed in a short sequence thatbypasses free ribose and the nucleobases, and instead proceeds through arabinose amino-oxazoline and anhydronucleoside intermediates.The starting materials for the synthesis—cyanamide,cyanoacetylene, glycolaldehyde, glyceraldehyde and inorganicphosphate—are plausible prebiotic feedstock molecules12–15, and the conditions of the synthesis are consistent with potential early-Earth geochemical models. Although inorganic phosphateis only incorporated into the nucleotides at a late stage of the sequence, its presence fromthe start is essential as it controls three reactions in the earlier stages by acting as a general acid/base catalyst, a nucleophilic catalyst, a pH buffer and a chemical buffer. For prebiotic reaction sequences, our results highlight the importance of working with mixed chemical systems in which reactants for a particular reaction step can also control other steps.

    Jack Szostak, in his summary of this paper in the same issue of Nature, writes:

    One of the goals of those developing theories of prebiotic chemistry is to identify geochemically
    plausible means of purifying key intermediates away from contaminants that might cause trouble in later reactions. The remarkable volatility of 2-aminooxazole suggests that it could be purified by sublimation, as it undergoes cycles of gentle warming from the sun, cooling at night (or at higher altitudes) and subsequent
    condensation. The compound would thus behave as a kind of organic snow, which could accumulate as a reservoir of material ready for the next step in RNA synthesis.

    Phosphate continues to have several essential roles in the remaining steps of Powner and colleagues’
    pathway, in one case causing depletion of an undesired by-product, and in another saving a critical intermediate from degradation. The penultimate reaction of the sequence, in which the phosphate is attached to the nucleoside, is another beautiful example of the influence of systems chemistry in this set2 of interlinked reactions. The phosphorylation is facilitated by the presence of urea4; the urea comes from the phosphate-catalysed hydrolysis of a by-product from an earlier reaction in the sequence. The authors wrap up their synthetic tour de force by using ultraviolet light to clean up the reaction mixture. They report that ultraviolet irradiation destroys side products while simultaneously converting some of the desired ribocytidine product to ribouridine (the second pyrimidine component of RNA). The development of this complex photochemistry required remarkable mechanistic insight from Powner and colleagues, who not only correctly predicted that ultraviolet irradiation would destroy the majority of the by-products, but also that the desired ribonucleotides would
    withstand such treatment. The authors’ careful study2 of every potentially relevant reaction and side reaction in
    their sequence is a model of how to develop the fundamental chemical understanding required for a reasoned approach to prebiotic chemistry. By working out a sequence of efficient reactions, they have set the stage for a more fruitful investigation of geochemical scenarios compatible with the origin of life.

  44. Nakashima’s behavior is an example of the faith based beliefs of Darwinists. Like members of most religions they are hoping for something to some day appear to validate their commitment to their beliefs. Unlike those who profess belief in God and a particular religion, those who search for a naturalistic approach to OOL and evolution and the universe will not admit the faith they hold.

    They will not admit what weird untruth they believe in. It would be a shame at the end of the day, Nakashima learned that all these properties were part of the fine tuning which he denies. Just tweak one or two variables a hair either way and maybe the stereochemistry would not work. I believe Mike Gene has brought up that evidence for design is in the properties of amino acids. They are an amazing triumph of design.

    The outcome of this is that Darwinist’s outward but false cocksureness is leading many people to believe they actually know something.

  45. Nakashima,

    I don’t believe you have even began to dent to mass probabilities needed to form the proteins/polymers necessary for a working cell. How did a ribosome or ATP synthase come about?

  46. Gage:

    While its true that Darwin’s text dealt with the origin of species (not life), the atheistic worldview his theory so strongly supported requires an abiotic OOL.

    What’s atheism got to do with it? Atheism doesn’t need anything beside itself; rejection of supernature is all it takes. But as soon as the inability of supernature to explain anything in this world is recognized, it is of course easily understood that science does.

  47. Be patient, this debate will soon be filed away as another myth debunked. Only this morning; I am sorry I can’t remember just where, I read about a number of successful OOL experiments.

    It seems to me that George M. Whitesides may be somewhat behind the times WRT the current standing of OOL research.

  48. Mr Jerry,

    Thank you for criticising my beliefs and expectations, rather than my citations. Now I know I’m on the right track.

  49. Mr ScottAndrews,

    You are conflating two of my comments which had different subjects.

  50. vjtorley,

    I’ll answer that with a quote from an evolutionary biologist whose academic credentials are impeccable:

    Natural selection is differential reproduction, organism perpetuation. In order to have natural selection, you have to have self-reproduction or self-replication and at least two distinct self-replicating units or entities. Prebiological natural selection is a contradiction in terms. — T. Dobzhansky, “Synthesis of Nucleosidase and Polynucleotide with Metaphosphate Esters,” in The Origins of Prebiological Systems (1965), pp. 299, 310. (Emphasis mine – VJT.)

    A typical response, presenting a forty year old reference as if that had settled some controversy. Am I to believe that was the final and decisive word on that subject?

  51. JDH,

    Therefore Darwinian evolution must insist on life starting by chance.

    Of course not, we have no means of knowing the mind of the designer. Nothing says he couldn’t have set it up to look the way it looks.

    The evidence for evolution is obvious; what went before is not detectable in the same way although abiogenesis as a natural phenomenon seems the most reasonable option. We know no reason why it could not be the result of natural processes. It may be a little premature to write it off yet.

    As soon as we invoke a designer we open a Pandora’s box of possibilities: He may have set it up any way he wants; even to create the world 6000 years ago making it look like it is 4.6 billions.

  52. jerry,

    The outcome of this is that Darwinist’s outward but false cocksureness is leading many people to believe they actually know something.

    That’s what you say. I however tend to believe the “Darwinists” really are on to something while cocksureness and letting on knowing something seems to be no less of a virtue in ID circles.

    I suggest more relevant arguments be used.

  53. Cabal: George Whitesides is at the cutting edge (if there is one) of OOL chemistry, not “behind the times” as you assume based only on the way overly optimistic appraisals of those who desperately want life-from-chemicals to be true. The difference between Whitesides and the more optimistic Darwinists is that he is brutally honest about what we know and what we don’t know. In every area of chemistry, he sets the “we understand this” bar very high, and rightfully so. He is honest enough to not substitute imagination for evidence.

  54. Cabal:
    Only this morning; I am sorry I can’t remember just where, I read about a number of successful OOL experiments.

    If there were one such successful experiment, you wouldn’t need to remember where you read it. It would be the headline of every newspaper and new site everywhere.

    But I know what you mean. It’s progress in that direction.
    Sort of like driving a car and saying you’re getting closer to Chicago. Except there’s no evidence there is or ever was a Chicago, and if there is, no one knows where. You can’t say you’re getting closer unless you assume it’s there and you know where it is.

    Such assumptions, confidently waiting for evidence to confirm them, are articles of faith.

    No one is criticizing you for holding fast to your beliefs. You see the world a certain way, and you need to believe that it’s true. We all do it. The problem is that your religion includes the self-referential belief that it’s not a religion.

  55. Cabal: Since I’m sure you are not familiar with Professor Whitesides’ qualifications in OOL chemistry, I should have added that he is part of the Harvard origin of life project.

    http://origins.harvard.edu/

    I think its safe to assume that he keeps up with the subject, to put it mildly.

  56. Nakashima,

    I bet I know your profession based on some of your vocabulary. Where did you first hear the word “dispositive?” I heard it first in law school.

  57. Mr Collin,

    Not me, a friend of mine!

  58. Give my condolences to your friend (for being a lawyer, not for being your friend, haha).

  59. Cabal,

    Forgive me, but I think you missed the entire point. Here it is shorter.

    1. A pillar of Darwinian theory is unguided natural selection.
    2. As soon as you allow the first cell to have DNA chosen as the method of inheritance – you are restricted to producing life forms that can proceed on the given machinery.
    3. This is going to favor some evolutionary paths over others.
    4. Therefore, evolution begun by anything else other than chance and necessity is no longer unguided.

    This is why Darwinian theory is absolutely linked to OOL by chance and necessity. Darwinian theory can not be scientifically honest, and divorce itself from OOL.

  60. JDH,

    Well said.

  61. To JDH: What a confused mess. What is this ‘first cell’ thing ? No one is claiming life started as a ‘first cell’. It is presumed to have started as extremely primitive compounds that dont have DNA as we know it. There may have been some other completely different scheme for reproduction, that later evolved into the DNA we see now. It is then possible to evolve into some other scheme again in the future.

    Regarding the origin, it is possible that God could have kicked off the process at any stage whatsoever, and the current thinking regarding evolution would be completely unnafected. In fact, if God/Creator/Designer were sufficiently clever, he could do this and leave absolutely no trace. He could have created the unsiverse last Tuesday, creating us with all our memories, etc, so we have simply no basis whatever for distinguising this from any other miraculous intervention.

  62. Graham,

    He could have created the unsiverse last Tuesday, creating us with all our memories, etc, so we have simply no basis whatever for distinguising this from any other miraculous intervention.

    You all read from the same playbook don’t you? I had a professor in college make the same inane argument. It was then, and it is now.

  63. Whats inane about it ? If you postulate an ‘agent’ capable of creating all life on earth, then why stop there ? Why could he not have created us yesterday ? Do you know the mind of the creator ? Do you have some insight into his big plan ? If you do, I wish you could share it with us.

  64. Graham #61
    “There may have been some other completely different scheme for reproduction, that later evolved into the DNA we see now.”

    Would you mind providing some kind of empirical evidence to substantiate this speculation? Fascinating that those of your persuasion ( I assume here that you subscribe to evolution by means of random mutation and natural selection ). You might as well be talking about the flying spaghetti monster here. Where are your naturalistic processes in this scenario?

  65. Mr. Nakashima

    I would like to ask you a simple question: are you a chemist of some sort?

    I respect people’s right to privacy, and I’m not asking you to reveal your identity. But the fact is that you have made several posts in this thread, attempting to rebut assertions by researchers – including chemistry professors such as Dr. Walton – that the origin of life through undirected processes is massively improbable, and that the RNA world scenario is simply not feasible. The question I have to ask myself is: should I believe you, and if so, why?

    You may respond that you shouldn’t have to identify yourself; your arguments stand or fall on their own merits. That would be fair enough, except for one small problem: I simply don’t understand your arguments. To me, they read like so much gobbledygook, because of the technical jargon they employ. Although I have studied a little chemistry at university level (two years of undergraduate chemistry, WAY back in 1979-80, and it was mostly inorganic chemistry at that), I am NOT a chemist. My background is in philosophy. So when I come across an argument which I cannot fully understand, in which you contradict a chemistry professor, I’m inclined to believe the professor. To overcome this natural bias in my belief-forming system, you’ll have to either raise your credibility (e.g. “I am a senior chemist with 20 years’ research experience,” or “I’m not a chemist, but a chemist who is a friend of mine, Dr. X, has vetted my post and vouches for its accuracy”) OR make your arguments a lot clearer.

    Take this statement of yours, attacking Dr. Stephen Meyer’s probability calculations for the origin of life:

    Of the original 10^-164, 45 orders of magnitude was from producing only peptide bonds, and templating on RNA supports that. Another 74 orders of magnitude was functional specificity, and the RNA was functionally specific for arginine-arginine sequences while the polypeptide showed enzymatic activity for the associated RNA. (The remaining 45 orders of magnitude were chirality, which this experiment does not address.)

    With regard to “templating on RNA,” I have to say that your statement sounds rather vague. (The link you provided to an article entitled Direct templating of amino acids on RNA wasn’t much clearer, either: it spoke of a “simple model system,” based on “the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides.” The rest went over my head.) Are you asserting that the peptide problem has been solved, and we can all go home now? If not, how much work remains to be done? Could we have a progress metric, please?

    The same goes for your remarks on functional specificity. Functional specificity, as Meyer uses the term, is something you can quantify. Can you quantify the degree of specificity found for arginine-arginine sequences and compare it with that required for the synthesis of RNA? In other words, how far along the road are we?

    Yes, you can talk of progress, but one step on a thousand mile journey would hardly count as significant progress. And what if the journey I thought was a thousand miles long suddenly turned out to be two thousand miles, due to an unexpected roadblock?

    I’d like to return to the journey metaphor. When people embark on a journey, they usually have a good idea where they want to go, how far they will have to travel, and how long it will take them to get there. If they’ll be stopping at a couple of places along the way, they also know the relative distances between these places – i.e. which leg of the trip will be the longest, and which will be the shortest.

    All right. Let’s go with that. At the moment, the most promising naturalistic model for the origin of life is something like this: simple organic chemicals (e.g. amino acids) => RNA => (DNA and protein) => first cell. Sorry for skipping over so many vital steps, but I can only keep a limited number of things in my head at once (four’s about the limit, I’m afraid), and those are the key steps.

    I’ve identified three steps: (1) amino acids to RNA, (2) RNA to DNA and proteins, and (3) DNA & proteins to first cell. What I want to know is this:

    (1) Which of the three steps is the most difficult to achieve, and which is the least, in a given time period, under plausible prebiotic conditions? This is a qualitative statement. If you cannot even answer this question, then how can I possibly trust your quantitative assertions, in which you critique Dr. Meyer’s probability estimates?

    (2) At the present time, can scientists quantify the relative probabilities of the steps involved (e.g. step 2 is 1,000,000 times harder to achieve, over a given time period, than step 1)?

    (3) At the present time, can scientists quantify the probabilities of any of the key steps in absolute terms, given plausible assumptions about the prebiotic Earth and the amount of time over which they took place (say, 500 million years)?

    (4) Breaking it down into small steps, suppose we follow the long path from amino acid to first cell, focusing on the largest chemical molecule at each stage along the way, and tracking its growth as it gets bigger and more complex. For simplicity’s sake, we’ll ignore all the other molecules that it must have reacted with. We’re just looking at the most direct chemical pathway from amino acids to the first cell. Using this metric, how many chemical steps were there from amino acid to first cell, to the nearest order of magnitude? 10,000? 1,000,000? 1,000,000,000? More?

    (5) Typically, journeys have a known distance. The relevant analogue to distance here might be the estimated probability of getting from amino acid to first cell, or the number of steps that must have been traversed. Newspapers always report breakthroughs in origin-of-life research, but they never reported unexpected roadblocks: that doesn’t sell with the reading public, who only want to hear about progress. So I would like to ask: has the estimated probability of life arising by undirected natural processes risen or fallen over the past 15 years? Ditto for the number of steps required. Now that would be a valid measure of whether abiogenesis is more difficult to achieve than scientists had first anticipated, or whether it is easier than they first thought.

    Now, I respect honest ignorance, and it may be that no-one in the world knows the answers to any of these questions (although I very much doubt it). In that case, proponents of aabiogenesis should have the intellectual honesty to admit their ignorance, and then maybe we can all return to this discussion in 20 years’ time. But if that’s the case, then it would not be fair of you to criticize researchers who identify problems in abiogenesis, by downplaying the improbabilities involved. Instead, a more appropriate response would sinply be: we don’t know. Which brings me to question (6):

    If we don’t know, then when will we?

    And if we don’t know that, then we really are up salt creek without a paddle. If our ignorance is that severe, then scientists are in no position to affirm that abiogenesis is scientifically possible. A non-quantifiable possibility is mere hand-waving.

    But suppose you have some answers to my first five questions, and suppose that your answers are significantly at variance with Dr. Meyer’s. Here’s my suggestion. Let’s have an online debate – or series of debates – between opposing teams of biochemists. I for one would like to get to the bottom of this.

    After all, the question of whether life on Earth could have arisen by undirected natural processes during the time available is an important one. It’s a question with philosophical and theological implications, and it affects how we live our lives.

    Over to you, Mr. Nakashima.

  66. …we have no means of knowing the mind of the designer.

    What designer?

    Nothing says he couldn’t have set it up to look the way it looks.

    Well that’s pretty obvious, since the way it looks is the way it looks.

    …abiogenesis as a natural phenomenon seems the most reasonable option.

    Why? What’s reasonable about it?

    We know no reason why it could not be the result of natural processes.

    Is this why you think “abiogenesis as a natural phenomenon” is reasonable, because you know of no reason why it is not reasonable? Seriously?

    We know no reason why it could not be the result of natural processes.

    Do you know of a reason why it could be the result of natural processes?

    Usually, for a belief to be reasonable, it needs to have some basis in reason.

    It may be a little premature to write it off yet.

    Most lenders write off bad debts after a reasonable amount of time has passed. I think we’re at the point now where we’re asking for the debt to be paid. Consider it notice. If it continues to be unpaid, we have every right to “write it off.”

    As soon as we invoke a designer we open a Pandora’s box of possibilities:

    What designer?

    As soon as we invoke a designer we open a Pandora’s box of possibilities:

    Not knowing anything about the designer, making assumptions about what the designer is capable of is a bit premature, don’t you think?

    He may have set it up any way he wants; even to create the world 6000 years ago making it look like it is 4.6 billions.

    So what? We deal with the world as it appears to us. If it was created 6000 years ago how will that change they way that it looks to us and “put an end to science”?

    Your objection is irrelevant.

  67. vjt:

    I can only keep a limited number of things in my head at once (four’s about the limit, I’m afraid), and those are the key steps.

    I consider it a design flaw that I can keep more things on my head at one time than I can keep in my head.

    (1) amino acids to RNA

    This should be nucleic acids to RNA.

    Amino acids are the constituents of protein molecules. Nucleic acids for RNA and DNA.

  68. I seem to have a bizarre talent for instigating long threads. Perhaps it’s because I know how to touch sensitive nerves.

    The bottom line is that the phenomenon of life coming from life, and not from non-life, is as close as anything we know to a universal law of nature.

    Those who assert that life can come from purely materialistic causes should be required to provide evidence that their thesis is defensible, in contradiction of this observational universal law.

    Go ahead: Attempt to defend spontaneous generation, but let’s see some evidence that this discredited hypothesis has modern scientific support.

    The burden of proof clearly rests on the shoulders of the spontaneous-generation crowd.

  69. Kevlar (#34)

    Thank you for your post. You write:

    Even if the current model is mistaken, how do you get around the observations regarding the cosmic microwave background radiation?

    I don’t. My whole point was that the total number of possible theories which scientists could formulate in order to explain the development of the cosmos is very large, and that to date, only a handful of theories have actually been formulated by scientists. The fact that the Big Bang theory is far and away the best of these paltry few, doesn’t make it true.

    You also wrote:

    So perhaps the details aren’t ironed out, but why prefer the idea that the universe has always been suitable for life when the data from COBE and others suggests completely the opposite?

    It certainly does seem to suggest that – although I should add that the COBE data only applies to the observable universe. At the present time, we don’t know how big the universe is, so we can’t say if the rest of it was hot or cold, ten billion years ago.

    Now, I believe in God, so I’m quite happy if research points to the universe having a beginning. My point was simply that an atheist, confronted with evidence that abiogenesis was astronomically improbable, would be rational to propose the least improbable scenario for how we got here today. Let me illustrate.

    About 100 years ago, the world’s leading physicist, Lord Kelvin, confidently pronounced that the Earth was 20 to 40 million years old. What did sensible Darwinists do? They knew perfectly well that this was not enough time for life to have arisen naturally, so they took a scientific gamble that Kelvin was wrong. They knew that it would have been silly to accept Kelvin’s physics, and then propose a “mud-to-man” scenario occurring over a mere 20 million years.

    As it happened, their gamble paid off. We now know the Earth is 4,540 million years old. But there’s a new problem. Getting from “mud” to the first cell appears far more difficult than Darwin envisaged. Once again, the time span appears insufficient: 500 million years doesn’t seem to be enough. There are several independent reasons – discussed at length in Dr. Stephen Meyer’s Signature in the Cell – for thinking that barring a miracle, life could not have arisen naturally on Earth over that time period. (If you’re wondering whether to believe the claims made in Dr. Meyer’s book, just have a look at the Reviews page on his Web site, and see how many chemistry and biology professors loved it.)

    To make matters worse, the world’s top cosmologists and physicists are now claiming that 13.7 billion years ago, the entire Universe was unimaginably hot and dense, precluding the possibility of life. What’s a Darwinist to do?

    Well, if I were one, I’d either question the physics (are we sure the Big Bang happened?), or endeavor to minimize it (maybe it happened, but it was only local). The last thing I would want to do is suppose that massively improbable events occurred. That would be too miraculous – and Darwinists don’t believe in miracles, do they?

    That was the point of my earlier posts, in which I was arguing (in devil’s advocate fashion) for an eternal universe. I don’t believe in an eternal universe any more than you do.

    Finally, you conclude:

    You still need to establish that a theory which claims that the universe has always been suitable for life is easier to fit with our observations than not.

    First, I don’t need to establish anything – after all, I’m not an atheist, am I?

    Second, I hope it is clear now that what a smart atheist would need to establish is that the probability that some part of the universe was not hot and dense 13.7 billion years ago is significantly greater than zero, leaving the door open for life to have either existed eternally or evolved over a much longer time period, thereby giving the atheist some breathing space. That was all I really wanted to say.

  70. Graham objects to my statement of there being a “first cell”.

    Maybe a philosopher like vjtorley can help me out, but I guess Graham’s denial of the first cell only allows for two other possibilities.

    Cells always existed or no cells have existed. Which option does Graham believe?

    Note: I reject the idea of many cells popping into existence at once because of the difficulty of establishing the idea of simultaneous events due to the effects of quantum phycics E* delta t > hbar. And the special theory of relativity. ( Whether events are simultaneous or not depends on your inertial frame of reference )

  71. vjtorley,

    You wrote
    “If our ignorance is that severe, then scientists are in no position to affirm that abiogenesis is scientifically possible. A non-quantifiable possibility is mere hand-waving.”

    Given that you believe the universe-and life-had a beginning, then at some point, wether here on earth, or somewhere else, non-life became life. Some scientists are doing good work trying to figure out how that happened. They don’t know, probably aren’t close to knowing, and may not ever know. But that doesn’t change the fact that abiogenesis isn’t just likely, it is certain to have happened. Life exists.

  72. vjtorley:

    If you’re wondering whether to believe the claims made in Dr. Meyer’s book, just have a look at the Reviews page on his Web site, and see how many chemistry and biology professors loved it.

    No doubt a random sample of chemistry and biology professors.

  73. Mung (#66)

    In your response to Cabal regarding the reasonableness of assuming abiogenesis occurred naturally, you wrote…

    Do you know of a reason why it (life) could be the result of natural processes?

    And by that I assume you meant that the alternative–namely that life is the result of non-natural processes–is just as reasonable a statement to make.

    However, that statement is not only not reasonable, it is non sensical. A “process” is by definition natural. If you are going to argue that life could have happened non-naturally, then you are going to have to come up with some alternative language so as to allow it to make sense.

  74. lryna,

    What of Phil Skell’s qualifications are you calling into question? Is it that he is an emeritus prof at Penn State, or is that he is a member of the National Academy of Sciences?

    What about Norman Nevin, emeritus prof at Queens College? Or Edward Peltzer at Scripps? Do they have something in their background that should disqualify them from voicing an opinion in favor of Meyer’s book?

    What is the actual point of your comment? Is it that there can be no dissenting opinions? How exactly does that work in science?

    Are you simply suggesting we should consider the Alfred Wegener argument for consensus in science? The Georges Lemaître/Gregor Mendel law of group approval, perhaps?

  75. Gil,

    In what way would origin of life through intelligent design (not to call it creation) be observably different from spontaneous generation?

    And to cut the likes of Mung off at the pass: I am not referring to researchers who might eventually produce life in the laboratory. You know what I am talking about: the origin of life without human interference. What would it look like, if not the presence of life where shortly before there wasn’t any?

    fG

  76. Mung writes:

    (1) amino acids to RNA

    This should be nucleic acids to RNA.

    Amino acids are the constituents of protein molecules. Nucleic acids for RNA and DNA.

    RNA and DNA are nucleic acids. They are composed of monomers called nucleotides

  77. Graham:

    No one is claiming life started as a ‘first cell’. It is presumed to have started as extremely primitive compounds that dont have DNA as we know it. There may have been some other completely different scheme for reproduction, that later evolved into the DNA we see now. It is then possible to evolve into some other scheme again in the future.

    The point is there isn’t any evidence for any of that.

  78. Dave Wisker,

    The first clue should have been RNA = Ribonucleic acid and the second DNA = dioxyribonucleic acid.

    But anyway… (shrug, sigh)

  79. vjtorley: But the fact is that you have made several posts in this thread, attempting to rebut assertions by researchers – including chemistry professors such as Dr. Walton – that the origin of life through undirected processes is massively improbable, and that the RNA world scenario is simply not feasible.

    An appeal to authority is valid when

    * The cited authority has sufficient expertise.
    * The authority is making a statement within their area of expertise.
    * The area of expertise is a valid field of study.
    * There is adequate agreement among authorities in the field.
    * There is no evidence of undue bias.

    The scientific consensus of those in the field is that life arose spontaneously, but that there are yet many questions and no adequate theory. The vast majority of scientists in the relevant fields of study also strongly support the Theory of Evolution. Abiogenetics has been a fruitful area of research.

    The proper argument against a valid appeal to authority is to the evidence.

  80. Mr Vjtorley,

    My apologies. I was in the middle of composing a long reply and my browser crashed. I will attempt to reply later.

  81. Vjtorley,

    The earth is 4.5 Billion, not million years old. But I agree with your point, even in that length of time, evolution is unlikely.

  82. joseph,

    I was simply correcting a simple error on Mung’s part. I’m so pleased that you know what RNA and DNA stand for.

  83. This is a quote from wikipedia:

    “The details of the origin of life are unknown, but the broad principles have been established.”

    Hahahahahahaha! How do they know that their broad principles are correct? I’m sure that their belief is sincere and I shouldn’t mock it. But it isn’t science.

  84. Collin (#78)

    Thank you for your vote of support. By the way, 4,540 million years (the figure I quoted for the age of the Earth in #69) is equivalent to the figure you quote of 4.5 billion years, so we are in agreement. (To be precise, 4,540 million years is 4.54 billion years.) 1,000 million equals 1 billion.

  85. To those who may be interested (Mr. Nakashima and Dave Wisker, I presume):

    Recently, I emailed Professor John Walton and asked him for his comments about the paper by Powner MW, BG Gerland & JD Sutherland (2009), entitled “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions” in Nature 459:239-242. Professor Walton was courteous enough to reply. I hope he won’t mind if I quote an extract from his response:

    I have seen previous papers by Sutherland and co-workers on supposed prebiotically plausible syntheses. The Nature paper you mention is of much the same kind. It’s nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input. Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable. They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order. What they show is that with intelligent chemists supervising each step of the process, nucleotides can be accessed from some simple molecules. It is good evidence of intelligent design at work.

    I especially like that last sentence.

  86. Dave Whisker: You suggested the paper by Sutherland and co-workers: “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions”, Nature, 459:239-242 (2009) as a refutation of my statement that: “Intense laboratory research has failed to produce even one nucleotide (RNA component) under geologically plausible conditions.”

    Professor Sutherland and his group certainly deserve full credit for designing a viable route through the maze from some possible prebiotic precursors to pyrimidine ribonucleotides. They can also be congratulated for their literary acumen in crafting a title likely to persuade the editor of the journal Nature to publish their article, and to bring the naturalist claque on to their side. Theirs is nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input of each stage. They isolate their reactions in nice clean compartments. None of these conditions pertain to the prebiotic earth. Although they claim their route is plausible under prebiological conditions, nothing in their paper makes this believable. Their claim will remain wildly optimistic until they demonstrate their preparative sequence taking place, on its own, in some unsupervised corner of mother nature. (It is of course debatable if “mother” is an appropriate descriptor for prebiological nature!) They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order. What their work actually shows is that with intelligent chemists supervising each step of the process, nucleotides can be accessed from some simple molecules. Their paper, and others like it, provide good examples of intelligent design at work.

  87. vjtorley: Recently, I emailed Professor John Walton and asked him for his comments about the paper by Powner MW, BG Gerland & JD Sutherland (2009), entitled “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions” in Nature 459:239-242.

    Walton: Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable.

    Walton doesn’t bother to explain why it’s not plausible, ignoring the supporting cites.

    Walton: They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order.

    The study doesn’t intend to address anything more than the narrow issue of the plausible synthesis of ribonucleotides.

  88. Vjtorley,

    Sorry, I thought the comma was a decimal point.

  89. Mr Vjtorley,

    Dr Walton’s views are in consonance with those already expressed in much the same terms via ID-friendly outlets such as ENV. As with the improbability argument and the Dobzhansky quote, he isn’t bringing his own qualifications as a chemist to bear on the issues. As such, I would be careful of a credentials based preference for his opinion. This is a small part of the larger response I was trying to give to a previous post of yours. I fear it will have to come in disjoint segments. My apologies.

  90. vjtorely,

    Frankly, I was disappointed in Professor Walton’s response. Perhaps it was too much to expect specific objections to the paper, or the work it cited from him, other than they carefully controlled certain parameters of the work, which he uses, oh-so-cleverly, as an excuse to dredge up the old, tired ID bromide of “they used a laboratory and test tubes and stuff, therefore it was all Intelligent Design!”

    He fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelieveable? Walton doesn’t even attempt to address them. His reaction, I’m afraid, is much like Michael Behe’s reaction to the immune system literature at the Dover trial: non-specific dismissal.

    Do you really find this kind of response useful?

  91. lastyearon,

    However, that statement is not only not reasonable, it is non sensical. A “process” is by definition natural. If you are going to argue that life could have happened non-naturally, then you are going to have to come up with some alternative language so as to allow it to make sense.

    A process only means a sequence of events, whether they be physical or metaphysical. The word “process” does not necessitate “natural process”. And, to be quite honest, if you want to talk about proper definitions, we don’t have a proper definition of natural or non-natural. This is where the real problem lies. One must take it for granted that they “understand” the “natural” world, when in reality they don’t, for through science we can get descriptions of nature, but not explanations of why nature is the way it is, nor can we get an explanation of why it couldn’t have been otherwise. Therefore, we cannot use descriptions as normative explanations against anything non-natural, because descriptions are not explanations. You have to have an explanation before you can explain why it’s counterpart is ruled out. You cannot judge that which is non-natural until you can explain (not just describe) that which is natural. The truth is that nature is just as baffling and wanting of an explanation as is anything non-natural. We don’t understand the basis of nature, and cannot rule-out non-natural by comparison. If anything “non-natural,” to you, is crazy, I think you’ve forgotten just how crazy “natural” things are. They are equally baffling concerning an explanation. All we could hope to do by comparison of the two would be to compare both of their descriptions. But descriptions (which is all we can ever have in science and the study of nature) are not an argument against proscriptions.

  92. lastyearon,

    Given that you believe the universe-and life-had a beginning, then at some point, wether here on earth, or somewhere else, non-life became life. Some scientists are doing good work trying to figure out how that happened. They don’t know, probably aren’t close to knowing, and may not ever know. But that doesn’t change the fact that abiogenesis isn’t just likely, it is certain to have happened. Life exists.

    But that begs the question doesn’t it, for that is the question at hand, and asserting it as the answer is begging the question.

  93. Clive,

    Thank you for knowing what begging the question means. It does not mean implying a question like so many others think.

  94. The following sequence by Zachriel seems to be a complaint, followed by a refutation of the complaint, followed by an excuse.

    Walton doesn’t bother to explain why it’s not plausible, ignoring the supporting cites.

    Walton: “They haven’t solved the stereoselectivity problem. They haven’t solved the problems of chemoselectivity in assembly of the pyrimidine ribonucleotides and they don’t address the problem of the information needed to assemble the nucledotides in the right order.”

    The study doesn’t intend to address anything more than the narrow issue of the plausible synthesis of ribonucleotides.

    And then, Dave Whisker chimes in. He seemingly misses the point that one of the central reasons the synthesis is not considered plausible is because of the intense investigator manipulation to control the unfolding of a planned chemical event. Not seeing the forest for the trees, Dave states:

    He fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelieveable?

    Again, investigator input is simply ignored for the obvious reasons of design. In Dave’s case, he goes further and takes the opportunity to have a couple cheap shots at one of the chief villains in his play, Michael Behe. This reaction can virtually always be counted on when the design argument hits its target.

    In any case, Prof Walton’s critique of Sutherland’s work is in good company.

    “Although as an exercise in chemistry this represents some very elegant work, this has nothing to do with the origin of life on Earth whatsoever” … “the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely”

    - Robert Shapiro, Prof Emeritus NYU

  95. And, to be quite honest, if you want to talk about proper definitions, we don’t have a proper definition of natural or non-natural. This is where the real problem lies.

    Indeed. What is a natural thing? That which is not a supernatural thing. What is a supernatural thing? Why, it is that which is not a natural thing.

    If you ask me, everything that exists has a “nature” or “essence” and anything which does have a “nature” or “essence” is therefore, by definition, natural.

    Take a being who by it’s very nature cannot not exist. Why, such a being would be the most natural thing possible.

    So here’s my attempt at a definition of natural. A natural thing is a thing which is contingent. It can exist or not exist, come into being and cease to exist. Now, this obviously excludes God as conceived above, but does it also give away the store?

    The natural world, in order to be natural, must be contingent.

  96. Behe tried it, Walton tried it, and Sharpiro apparently tried it too.

    What is the it? Perhaps it is the professional discipline to not trample the evidence.

  97. Upright BiPed,

    Correct me if I am wrong, but it seems that according to your reasoning it is impossible that intelligent scientists ever demonstrate experimentally plausible chemical pathways of abiogenesis. After all, experiments are always designed by intelligent humans. What kind of experiment would it take to convince you of the plausibility of “unguided” abiogenesis?

    Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?

  98. Mr Vjtorley,

    My reply, all together again! I hope writing it twice made it better.

    I would like to ask you a simple question: are you a chemist of some sort?

    No, but I know how to find the work of respected chemists on the Internet! ;)

    I respect people’s right to privacy, and I’m not asking you to reveal your identity. But the fact is that you have made several posts in this thread, attempting to rebut assertions by researchers – including chemistry professors such as Dr. Walton – that the origin of life through undirected processes is massively improbable, and that the RNA world scenario is simply not feasible. The question I have to ask myself is: should I believe you, and if so, why?

    I’d say you have to ask yourself the same question about Dr Walton. A Ph.D in Chemistry doesn’t make him an expert in OOL. His letter does not quote any substantive or relevant work of his own, it just puts forward a talking point you could have heard from Casey Luskin just as easily.

    You may respond that you shouldn’t have to identify yourself; your arguments stand or fall on their own merits. That would be fair enough, except for one small problem: I simply don’t understand your arguments. To me, they read like so much gobbledygook, because of the technical jargon they employ.

    That is a problem. Since you began participating in this thread, you’ve made several references to your own lack of understanding of the subject you chose to talk about. I’ve gone back and forth on whether you are actually expressing ignorance or are displaying a rhetorical stance. Because I respect your integrity, I will take your words at face value.

    Although I have studied a little chemistry at university level (two years of undergraduate chemistry, WAY back in 1979-80, and it was mostly inorganic chemistry at that), I am NOT a chemist. My background is in philosophy. So when I come across an argument which I cannot fully understand, in which you contradict a chemistry professor, I’m inclined to believe the professor.

    As someone trained in philosophy, I’m surprised your approach is not more nuanced. I have a citation, he has an assertion. Credential fail.

    To overcome this natural bias in my belief-forming system, you’ll have to either raise your credibility (e.g. “I am a senior chemist with 20 years’ research experience,” or “I’m not a chemist, but a chemist who is a friend of mine, Dr. X, has vetted my post and vouches for its accuracy”) OR make your arguments a lot clearer.

    I am abashed, and will try harder. Thank you for sticking with me.

    Take this statement of yours, attacking Dr. Stephen Meyer’s probability calculations for the origin of life:
    Of the original 10^-164, 45 orders of magnitude was from producing only peptide bonds, and templating on RNA supports that. Another 74 orders of magnitude was functional specificity, and the RNA was functionally specific for arginine-arginine sequences while the polypeptide showed enzymatic activity for the associated RNA. (The remaining 45 orders of magnitude were chirality, which this experiment does not address.)
    With regard to “templating on RNA,” I have to say that your statement sounds rather vague. (The link you provided to an article entitled Direct templating of amino acids on RNA wasn’t much clearer, either: it spoke of a “simple model system,” based on “the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides.” The rest went over my head.)

    I wouldn’t conflate my vagueness with the article’s technicality. I know you’ve followed cosmology for a long time, and even though you are not a cosmologist, feel confident assessing arguments in that area. I’m sure you are capable of doing the same in chemistry. Gambatte!

    The direct templating idea is simply that nucleotide sequences (RNA) has a surface whose physical contour and arrangement of electric charges allows some amino acids to attach directly. A made up example: triplet GAC will let AA1 attach for 1 second, AA2 attach for 2 seconds, … , AA20 attach for 0.005 seconds. The preferences are not perfect. Why triplets? I don’t know, maybe they are the same basic size as amino acids.

    A further development has been the discovery that if two amino acids attach, the alignment brought about makes it easy for their peptides to connect (ligate, in chemical jargon, but if you know Latin that is obvious).

    Are you asserting that the peptide problem has been solved, and we can all go home now? If not, how much work remains to be done? Could we have a progress metric, please?

    Yes, basically. Not that ‘the peptide problem’ has been a great concern. I’ve never seen it raised in OOL discussions outside of Dr Meyer’s improbability argument.

    The same goes for your remarks on functional specificity. Functional specificity, as Meyer uses the term, is something you can quantify. Can you quantify the degree of specificity found for arginine-arginine sequences and compare it with that required for the synthesis of RNA? In other words, how far along the road are we?

    We can also reference Szostak for a definition of functional specificity, and many ID friendly people are happy to do so. If some RNA strand prefers to ligate Arg-Arg, and Arg-Arg enhances ribozyme activity, that is functional specificity. Yes, it can be measured and quantified.

    It is true that in modern biology, enzymes are large proteins with highly functional, highly specific attributes. It would be a mistake to assume the same had to be true in the distant past. Functional specificity is a metric that can be applied to a broad hill as well as a narrow peak.

    When you say, ‘compared to the synthesis of RNA’, it isn’t clear to me that that is a valid comparison to ask for. The abiotic environment is going to continue making RNA, nucleotide by nucleotide until something changes. I would put the burden on proteins to push the synthesis of nucleotides until much further in the development of early life.

    Yes, you can talk of progress, but one step on a thousand mile journey would hardly count as significant progress.

    That is equivocating on the meaning of significant. The Wright Flyer and Neil Armstrong hopping off the ladder onto the Moon were single steps, and yet they were significant. We choose to celebrate our first or last steps on a journey, yet each has significance in the sense that you would not arrive without them!.

    And what if the journey I thought was a thousand miles long suddenly turned out to be two thousand miles, due to an unexpected roadblock?

    What of it? The world is joyously more complicated than we have ever expected.

    I’d like to return to the journey metaphor. When people embark on a journey, they usually have a good idea where they want to go, how far they will have to travel, and how long it will take them to get there. If they’ll be stopping at a couple of places along the way, they also know the relative distances between these places – i.e. which leg of the trip will be the longest, and which will be the shortest.

    Yes, most trips over known territory are like that. Journeys of exploration, such as Columbus or Lewis and Clark, are not. This is the limit of your analogy.

    All right. Let’s go with that. At the moment, the most promising naturalistic model for the origin of life is something like this: simple organic chemicals (e.g. amino acids) => RNA => (DNA and protein) => first cell. Sorry for skipping over so many vital steps, but I can only keep a limited number of things in my head at once (four’s about the limit, I’m afraid), and those are the key steps.
    I’ve identified three steps: (1) amino acids to RNA, (2) RNA to DNA and proteins, and (3) DNA & proteins to first cell. What I want to know is this:

    Let’s stop here and rewrite the steps in slightly more realistic and well agreed form.

    1 – the abiotic synthesis of amino acids, nucleotides, and lipid membranes, faster than these structures can degrade in the environment

    2 – the confinement of these components in close physical proximity and concentration (at this point, molecular evolution starts working)

    3 – the elaboration of metabolism in the confined environment

    4 – the replacement of confinement with containment by lipid vesicles

    5 – the ability of these protocells to reproduce themselves to an agreed level of fidelity to allow natural selection at the cellular level (biology per se begins)

    We have no idea when DNA entered the picture, and it is unecessary to get to 5.

    (1) Which of the three steps is the most difficult to achieve, and which is the least, in a given time period, under plausible prebiotic conditions? This is a qualitative statement. If you cannot even answer this question, then how can I possibly trust your quantitative assertions, in which you critique Dr. Meyer’s probability estimates?

    To answer the last first, I don’t see the force of your question. If we read over this reasoning into the field of cosmology, would you agree with it? If someone refused to listen to your interpretation of COBE data because you hadn’t explained how to tie QM and GR together, or whether the curvature of the universe is positive, negative or 0, would that be an appropriate response? No.

    To return to the first question, of the items in 1, nucleotides have been the hardest to synthesize. 2 is easy to acheive in the lab, and pumice, sand, ice, mud and other similar confining physical compartments are expected to have been available on the early Earth. I think 3 is the area where the least experimental work has been done, even though we have Kaufman’s autocatalytic networks and Eigen’s hypercycles as guidance. Dr Meyer in Signaure in the Cell correctly identifies hypercycles as an explanation of development, not origination of early life.

    (2) At the present time, can scientists quantify the relative probabilities of the steps involved (e.g. step 2 is 1,000,000 times harder to achieve, over a given time period, than step 1)?

    For chemists, nucleotides have been hard, much harder than amino acids (which you can find if you crack open a meteorite!). Step 3, I have no data on.

    (3) At the present time, can scientists quantify the probabilities of any of the key steps in absolute terms, given plausible assumptions about the prebiotic Earth and the amount of time over which they took place (say, 500 million years)?

    1a and 1c are pretty certain – probability approaching 1.

    (4) Breaking it down into small steps, suppose we follow the long path from amino acid to first cell, focusing on the largest chemical molecule at each stage along the way, and tracking its growth as it gets bigger and more complex. For simplicity’s sake, we’ll ignore all the other molecules that it must have reacted with. We’re just looking at the most direct chemical pathway from amino acids to the first cell. Using this metric, how many chemical steps were there from amino acid to first cell, to the nearest order of magnitude? 10,000? 1,000,000? 1,000,000,000? More?

    I’d guess between 1 and 10 million. We know that bacteria such as M. genitalium have very small genomes and protein sets. So you are asking how many steps to build a 600,000 base pair genome. There are slightly less than 300,000 different RNA sequences that are only 9 bases long. So you could easily generate many copies of every possible sequence and confine these in a small space. The research I cited shows that there is some functional specificity even for such short sequences and the proteins that can template directly on them. So the most direct route that you are asking for is going to be some sequence of combining small sequences like this. Starting from this collection of random snippets, by the most direct route you will need 599,999 events to connect them into the genome of M. gen, so guessing 10 million allows a fair bit of backing and filling in the estimate.

    So if we could get just one of those events to happen every thousand years or so, we’d be happy.

    (5) Typically, journeys have a known distance. The relevant analogue to distance here might be the estimated probability of getting from amino acid to first cell, or the number of steps that must have been traversed. Newspapers always report breakthroughs in origin-of-life research, but they never reported unexpected roadblocks: that doesn’t sell with the reading public, who only want to hear about progress. So I would like to ask: has the estimated probability of life arising by undirected natural processes risen or fallen over the past 15 years?

    Again, exploratory journeys do not have a known distance. Lewis and Clark did not know that hundreds of miles of mountainous terrain lay on the other side of the Continental Divide. Columbus did not know the width of the Atlantic Ocean.

    Having said that, I would say the circle of our ignorance is shrinking, and therefore that the probability is rising over the last 15 years.

    Ditto for the number of steps required. Now that would be a valid measure of whether abiogenesis is more difficult to achieve than scientists had first anticipated, or whether it is easier than they first thought.

    Or a measure of analogical failure, as the case might be.

    Now, I respect honest ignorance, and it may be that no-one in the world knows the answers to any of these questions (although I very much doubt it). In that case, proponents of aabiogenesis should have the intellectual honesty to admit their ignorance, and then maybe we can all return to this discussion in 20 years’ time. But if that’s the case, then it would not be fair of you to criticize researchers who identify problems in abiogenesis, by downplaying the improbabilities involved. Instead, a more appropriate response would sinply be: we don’t know.

    Again, I’m happy to share an admission of ignorance, but arguments from implausibility aren’t admissions of ignorance. They are claims to sufficient knowledge to make the calculation. If those that make a calculation have such knowledge they should share it, or stop making claims (of improbability) based on ignorance.

    Which brings me to question (6):
    If we don’t know, then when will we?
    And if we don’t know that, then we really are up salt creek without a paddle. If our ignorance is that severe, then scientists are in no position to affirm that abiogenesis is scientifically possible. A non-quantifiable possibility is mere hand-waving.

    Heavier-than-air powered flight may be an interesting analogy here. During the late 19th century, there were people who argued that it was impossible for humans to construct such devices. However, those working on the problem had the feeling of a race to solve the problem, that the solution was imminent. Even as they solved the puzzle step by step, I’m not sure that the Wright Brothers would have been able to offer you the estimate you are asking for. Yet the Wright Brothers knew birds could fly, and birds were heavier than air. They knew the goal was acheivable. Similarly, we know living cells exist.

    But suppose you have some answers to my first five questions, and suppose that your answers are significantly at variance with Dr. Meyer’s. Here’s my suggestion. Let’s have an online debate – or series of debates – between opposing teams of biochemists. I for one would like to get to the bottom of this.

    This is a geat idea, and I’ve picked out a name for this grand debate: PubMed.

    After all, the question of whether life on Earth could have arisen by undirected natural processes during the time available is an important one. It’s a question with philosophical and theological implications, and it affects how we live our lives.

    It does, and it is the grand intellectual challenge of the age.

    Over to you, Mr. Nakashima.

    And return!

  99. lryna,

    I think your question to me has already been on the table for those who are in a much better position to answer it. I am not limited in my ability to see rational significance in the variance of degree. You should try it.

    If you look at the reasoned objections of trained chemists over the measure of investigator input in reaching a result, and then feel the need to throw up your arms and say “then we can never prove our case”. Then perhaps the problem is the case you are trying to prove.

  100. ????,

    The burden to demonstrate the power of chance is on the “chance worshippers”—those indoctrinated in materialism.

    But mainly—way off topic here—I just wanted to see if a non-Latin script comes through. I see it now—will I in a moment?

  101. Nakashima,

    Your comparison of Columbus, Lewis and Clark with scientific research is apt. They had to have had a high amount of confidence and maybe even some arrogance to accomplish what they did. They didn’t know what was out there, but they had faith in their idea and were able to discover, not what they sought, but something far better.

    But it may be that our modern biological explorers will end up finding a whole new world that they never expected to find.

    Here’s an interesting quote from Columbus’ diary: “It was the Lord who put it into my mind … the fact that it would be possible to sail from here to the Indies.” His deity seemed to give him promise of something that would never happen, yet it led to something far more important than spice trading. Maybe that is analogous to what we will find with OOL.
    See http://endtimepilgrim.org/columbus.htm for columbus diary quote.

  102. Upright BiPed:

    I think your question to me has already been on the table for those who are in a much better position to answer it.

    Then you could have repeated their answer. Instead, you are silent. Maybe you friends don’t know the answer either. Here, let me repeat one of my questions:

    Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?

    If you look at the reasoned objections of trained chemists over the measure of investigator input in reaching a result, and then feel the need to throw up your arms and say “then we can never prove our case”. Then perhaps the problem is the case you are trying to prove.

    The case is that unguided chemical evolution led to life. Let me ask you this then: do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no? Please explain your answer.

  103. IrynaB,

    one of the interesting things about these kinds of discussions is that people forget that there are two propositions and that disproving one does not prove the other.

    It is the scientists’ burden to prove that their theories are correct and it is beneficial to be skeptical and critical in order to find the truth.

    But if you are saying that Upright Bipedal does not have a very good alternative in OOL, you are right. Nevertheless, that does not do anything for the weakness in mainstream OOL.

    I’m beginning to believe that all scientific endeavor is faith-based. That’s not bad! But just because you’ve made discoveries before does not mean that you will tomorrow. Yet you keep searching, hoping that you will find more knowledge. It is a noble endeavor, but let’s get real. It’s based on faith and hope and that’s just fine.

  104. Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?

    1.) Guided abiogenesis.
    2.) Life never had a start. Life has always existed.

    … and how would you test that proposal?

    1a.) Evaluate the results of guided abiogenesis experiments.
    1b.) Evaluate the results of unguided abiogenesis experiements.

    2.) Evaluate attempts to show that life can be produced from non-life, guided or not.

  105. Hi everyone,

    It’s interesting to compare the responses of various contributors to the experiments reported by Sutherland et al.: “Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions”, Nature, 459:239-242 (2009)

    chemstandup (#86)

    It’s nice chemistry, carried out with the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input. Although they claim their route is plausible under prebiotic conditions, nothing in their paper makes this believable.

    Dave Wisker (#90)

    He [Professor Walton - VJT] fails to address their incorporation of UV light, nor the simulation of periodic light/day via sublimation. Or having phosphate present from the beginning. How exactly, are these features of the work so unbelievable?

    What this exchange of views tells me (and it’s obvious in retrospect) is that any realistic probability assessment for a model of how life could have originated naturally, is incomplete without a computation of the probability of the prebiotic conditions invoked by the model. Sutherland et al. are to be commended for including UV light and phosphates, and for simulating light and day. However, the wording in chemstandup’s post suggests that several parameters in their experiment (pH, temperature, reaction medium, reaction mixture, contact time, and energy input) were tightly controlled. That suggests to me that the results they achieved would have been highly improbable on the early Earth.

    Mr. Nakashima (#98) estimates that between 1 and 10 million sequential steps would have been required to get from simple organic chemicals to the simplest bacterium, M. genitalium, the synthetic version of which has 582,970 base pairs, according to this press release by the J. Craig Venter Institute. If many of these 1 million-plus steps were highly improbable steps, then the likelihood is abiogenesis is rendered extremely remote: it dies the death of a million cuts.

    Just to set the achievements of Sutherland et al. in perspective: The longest of the various chemical pathways leading to ribo-cytidine phosphate, the molecule they synthesized, has only four steps, as readers can verify from this linkto an article in The New York Times (May 13, 2009) by Nicolas Wade, entitled “Reconstructing the Master Molecules of Life.”

    The synthetic M. genitalium I mentioned above has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons. Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages. By contrast, the RNA nucleotide which Sutherland et al. manufactured (ribo-cytidine phosphate) has a molecular weight of less than 360 daltons: less than a millionth that of the simplest bacterium.

    Four steps versus 1 million plus steps. That’s something like the distance from New York to Atlanta, if you want a visual metaphor. Some progress! Abiogenesis fans are crowing about the highly artificial synthesis of a molecule which is one million times smaller than the simplest bacterium.

    May I respectfully suggest that their excitement is a little premature?

  106. Mr Vjtorley,

    How about we circle back to the improbability concerns raised earlier. To someone flogging those as an impossiblity proof, even one counter-example is significant. That is the relevance of very small first steps.

  107. Mr. Nakashima & IrynaB:

    Mr. Nakashima, you wrote:

    How about we circle back to the improbability concerns raised earlier.

    An excellent idea. I shall spend my Christmas / New Year vacation boning up on biochemistry. I have taken your “Gambatte” (Go for it!) to heart.

    To someone flogging those as an impossiblity proof, even one counter-example is significant.

    Quite so. However, I never said that abiogenesis was impossible. All I ever said was that it was astronomically improbable, through undirected natural processes. By all means let’s make the probability estimates more precise.

    IrynaB, you asked:

    What kind of experiment would it take to convince you of the plausibility of “unguided” abiogenesis?

    Speaking for myself: a computer simulation, starting with plausible prebiotic conditions and simple organic molecules and ending with a self-replicating life-form. Of course, I’d have to see the program code to make sure it wasn’t rigged. And of course, you’d need a very, very fast computer to perform such a simulation of the early Earth. Maybe the advent of quantum computing will make it possible to perform these calculations some day.

    In the meantime, origin-of-life research could still make some very interesting discoveries in the lab (see below).

    You also asked:

    Do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no? Please explain your answer.

    Realistically, I don’t think it at all likely that experiments will reveal an unguided mechanism, although theoretically speaking, they could surprise us all.

    What I think more likely, though, is that the universe itself might have been extraordinarily fine-tuned, both in its carbon chemistry and in its initial conditions, such that the emergence of life through natural processes was inevitable. Professor Michael Behe entertains this hypothesis in The Edge of Evolution when he discusses the possibility that an uberphysicist may have set up the universe so as to ensure the emergence of life, in the beginning. For those who dislike acts of Divine intervention, that’s a possibility to be considered.

    The late astronomer Sir Fred Hoyle once predicted that predicted that the carbon-12 nucleus would have a certain energy level (or resonance) to enable helium to undergo fusion. Likewise, scientists, using a process of reverse engineering, may one day discover that carbon compounds have certain surprisingly fine-tuned chemical properties which would have favored the emergence of life, and that these properties, in conjunction with a very specific set of initial conditions, could explain the origin of life. That kind of research I would encourage.

    But I would call that evidence for directed evolution. Wouldn’t you?

  108. vjtorley,

    Just to set the achievements of Sutherland et al. in perspective: The longest of the various chemical pathways leading to ribo-cytidine phosphate, the molecule they synthesized, has only four steps, as readers can verify from this linkto an article in The New York Times (May 13, 2009) by Nicolas Wade, entitled “Reconstructing the Master Molecules of Life.”

    The synthetic M. genitalium I mentioned above has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons. Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages. By contrast, the RNA nucleotide which Sutherland et al. manufactured (ribo-cytidine phosphate) has a molecular weight of less than 360 daltons: less than a millionth that of the simplest bacterium.

    Methinks you are making an inappropriate comparison. The number of steps in the chemical pathway may only be four, but that doesn’t mean that pathway only resulted in one single molecule. It produced many ribo-cytidine phosphate molecules. That is, it produced one of the four basic types of ribonucleotides:, those with the base cytosine (the letter “C” in the RNA sequence), and lots of them.. In other words, it generated lots of “C’s”. However, one key finding of the paper was that the irradiation step, which generated the cytosine needed for steps further down the path also generated uracil, (found in the ribonucleotide for the letter “U”). This is probably because uracil and cytosine are similar chemically (they are in the class of molecules known as pyrimidines). The authors used cytosine for the rest of the work, but there is no reason to think the path would be much different for uracil because of the similar chemistry of the two. So in reality, the authors found a simple path that can generate one, and most likely two of the four different ribonucleotides found in RNA. Now, when you talk about the number of letters in an organism’s genome, you are actually counting the physical number of nucleotides, the building blocks of DNA . But you have to keep in mind in any genome there are only four different types of nucleotides in DNA and ribonucleotides in RNA, only four different “letters”. In DNA, those letters are “A”, “T”, “C” and “G”, and in RNA, “A”, U”, C” and “G”. So, to put the paper in perspective, it describes a simple 4-step pathway capable of generating at least one quarter and likely one-half of the kinds of ribonucleotides necessary to build an RNA genome.

  109. I need to correct the above. Not only did the irradiation step generate ctosine and uracil, it also converted some of the ribocytidine (the “C” letter” to ribouridine, (the “U” letter”). So the pathway described by the authors is capable of producing one-half of the types of ribonucleotides needed to synthesize RNA.

  110. 110

    lryna,

    you could have repeated their answer. Instead, you are silent.

    The direct answers to the questions given by two profs of chemistry were just a few inches away based on my 21” monitor. I hardly think I needed to re-copy their words – did you not see them? In any case, suggesting silence is a wee bit petty, since it was one of my posts (containing the words from one of the quoted profs) to which you responded.

    Maybe you friends don’t know the answer either.

    When the chemistry professor emeritus of NYU says “the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely then I think he is meaning to say that the chances that blind, undirected, inanimate chemistry would go out of its way in multiple steps and use of reagents in just the right sequence to form RNA is highly unlikely. His opinion seems to dovetail perfectly with the opinions of others whom are well-credentialed in the field. It was pointed out that the researchers used “the best reagents and lab equipment, supervised by intelligent chemists. They use pure components, separate and purify products using the most up to date methods. They control the pH, temperature, reaction medium, reaction mixture, contact time, and energy input of each stage. They isolate their reactions in nice clean compartments. None of these conditions pertain to the prebiotic earth.”. I don’t think the professors are saying that demonstrating a pathway is impossible, but they question the pathway being demonstrated.

    If you are suggesting that if any pathway is demonstrated, it therefore cannot be challenged, then please just say so.

    If that is not your position, then the alternative position is that the pathway can indeed be questioned, and that the objections of the many biologists, chemists, physicists (and others) who question it may be accepted for their content. Indeed, they may even be viewed for the level of consistency among their objections.

    Since you seem to rule out unguided abiogenesis, how do you propose that life got started, and how would you test that proposal?

    First it’s fair to remember we are talking about a momentous event (regardless of your perspective) that took place billions of years ago in an environment that we can only speculate about. I am not certain anything can be “tested” in the sense of certainty, if that is the point of your question. However, it is a question I have some familiarity with. I asked the same of Cornell Prof Allen MacNeil regarding the testability of assuming purely unguided processes in nature, and he did a series of fanciful pirouettes just in order to exit stage left. You may be able to shed some light on it if you wish – how would you test the assumption of purely unguided processes in the existence of life on this planet?
    To answer your question: In place of certainty, we have the evidence of life as we know it. We may investigate that by appropriate reasoning.

    Let me ask you this then: do you or do you not agree that experiments performed by intelligent scientists could indicate plausible unguided pathways to life? Yes or no?

    I believe I have answered this. Do I think it is conceptually possible that scientists could demonstrate a plausible pathway to abiogenesis by purely unguided processes (yes or no)? Yes. But that is not the question. In fact, that is not even a question; it’s a rather junior debating point. The question is – did life result from purely unguided processes? If those processes will allow life to organize without agency input, then logically, scientists should be able to demonstrate it. If those processes will not allow life to organize without agency input, then scientists will not be able to demonstrate it can.

    Given the testability issues either way, this is where priori assumptions come into the picture. Science has operated with the assumption that purely unguided processes led to life for well over 100 years. It is the central theme in every textbook and is spoken to the public (to which science has a responsibility) on a daily basis, ranging from unabashed proclamations made on television and in newspapers, to popular books written by scientists using their status as a means to further the assumption. Do you think that science has provided the evidence that life came about by purely unguided processes?

    “Yes or no?”

  111. vjtorley:

    What I think more likely, though, is that the universe itself might have been extraordinarily fine-tuned, both in its carbon chemistry and in its initial conditions, such that the emergence of life through natural processes was inevitable.

    You may be right, but it contradicts your earlier claim that natural emerge of life is astronomically improbable.

    But I would call that evidence for directed evolution. Wouldn’t you?

    No, I wouldn’t. I would call it directed setup of initial conditions. The subsequent evolution of life by natural processes would be undirected, and it’s a big question to what extent the detailed properties of such life are predictable (Gould’s famous tape being played twice). After all, it took several billion years for multicellular life to evolve after the first microbes arrived on the scene. That’s longer than the evolution of life itself. Apparently, that major transition is not highly probable to occur.

  112. #111

    After all, it took several billion years for multicellular life to evolve after the first microbes arrived on the scene. That’s longer than the evolution of life itself. Apparently, that major transition is not highly probable to occur.

    That is a good point that is easily overlooked. Any theory that suggests that multicellular or eukaryotic life could arise easily from prokaryotic life is implausible. It has to be a very infrequent series of events.

    If life was designed then you have to wonder why the designer waited so long to implement this important stage. But then we again run up against the problem that it is impossible to critique a design hypothesis without saying something about the designer’s motives and powers. Maybe it wanted to delay for reasons unfathomable.

  113. vjtorley: What this exchange of views tells me (and it’s obvious in retrospect) is that any realistic probability assessment for a model of how life could have originated naturally, is incomplete without a computation of the probability of the prebiotic conditions invoked by the model.

    The authors cite studies concerning the prebiotic Earth.

    vjtorley: However, the wording in chemstandup’s post suggests that several parameters in their experiment (pH, temperature, reaction medium, reaction mixture, contact time, and energy input) were tightly controlled. That suggests to me that the results they achieved would have been highly improbable on the early Earth.

    Because the primordial Earth didn’t have pH, temperature, energy or time?

    vjtorley: Abiogenesis fans are crowing about the highly artificial synthesis of a molecule which is one million times smaller than the simplest bacterium.

    RNA World hypotheses predict a natural pathway to the synthesis of nucleotides. This experiment provides evidence of such a pathway. It doesn’t purport to provide a complete history of abiogenesis.

    -

    We apologize for the long, and heretofore unexplained moderation delay.

  114. … and how would you test that proposal?

    Mung: 1a.) Evaluate the results of guided abiogenesis experiments.
    1b.) Evaluate the results of unguided abiogenesis experiements.

    Could you possibly be more vague?

  115. Mark,

    Actually, I think it would not be hard to fathom.

    First bacteria and plants as the means, (ramping up and completing the atmospheric cycle), then animals as the end goal. Note neither bacteria nor plants are dependent upon animals for survival but the converse is not true. Hence, the Cambrian explosion.

    Makes perfect design sense.

    “If life was designed then you have to wonder why the designer waited so long to implement this important stage. But then we again run up against the problem that it is impossible to critique a design hypothesis without saying something about the designer’s motives and powers. Maybe it wanted to delay for reasons unfathomable.”

  116. Mark Frank:

    If life was designed then you have to wonder why the designer waited so long to implement this important stage.

    Oramus beat me too it, but that explanation works.

    But then we again run up against the problem that it is impossible to critique a design hypothesis without saying something about the designer’s motives and powers.

    One doesn’t have to know the motivations to critique the design.

  117. IryanB,

    If scientists did manage to create “life in a test tube” so to speak we would need to find out what level of intervention was required.

    Then we start backing off that intervention one step at a time.

  118. Dave Wisker,

    I know you were correcting Mung.

    My point was that his “answer” was contained in RNA and DNA.

  119. But anyways, even given all the parts there still isn’t any evidence those parts can configure themselves in such a way as to give rise to a living organism.

    If blind and undirected processes could give rise to semi-conductors does that mean blind and undirected processes can give rise to a PC?

  120. Vjtorley,

    Sutherland et al. are to be commended for including UV light and phosphates, and for simulating light and day. However, the wording in chemstandup’s post suggests that several parameters in their experiment (pH, temperature, reaction medium, reaction mixture, contact time, and energy input) were tightly controlled.

    That is because they are trying to fully understand the chemistry involved (per a personal note from John Sutherland). This is important as the next step will be to determine the pathway(s) to purine ribonucleotide synthesis, which will probably be a more difficult nut to crack.

    That suggests to me that the results they achieved would have been highly improbable on the early Earth.

    I agree, but what they achieved has enabled origin of life workers to overcome what was seen as a very difficult problem– getting pyrimidine ribonucleotides at all. Their out-of-the box thinking produced a fairly simple pathway to pyrmidines under conditions that better approached the early Earth than before. If they can find a way to produce purine ribonucleotides and understand that chemistry thoroughly, then the next logical step is to try and simulate the early Earth conditions even more exactly and let the system run by itself without such strict controls. That seems to me to be a coherent, logical, and methodical research plan.

  121. 121

    lryna,

    Above you asked me a yes or no question. I gave you the answer (yes) but simply questioned the value of the question to begin with.

    I then asked you a yes/no question which you chose to ignore.

    I asked:

    Given the testability issues either way, this is where priori assumptions come into the picture. Science has operated with the assumption that purely unguided processes led to life for well over 100 years. It is the central theme in every textbook and is spoken to the public (to which science has a responsibility) on a daily basis, ranging from unabashed proclamations made on television and in newspapers, to popular books written by scientists using their status as a means to further the assumption. Do you think that science has provided the evidence that life came about by purely unguided processes?

    “Yes or no?”

    I was wondering, in fairness, what your answer is. You can certainly answer it – then choose to question its value in return.

    :)

  122. Dave Wisker (#108, #109)

    You made a substantive point in your recent post. I’d like to respond at length.

    First, here’s the relevant extract from my post (#105):

    Just to set the achievements of Sutherland et al. in perspective: The longest of the various chemical pathways leading to ribo-cytidine phosphate, the molecule they synthesized, has only four steps, as readers can verify from this link to an article in The New York Times (May 13, 2009) by Nicholas Wade, entitled “Reconstructing the Master Molecules of Life.”

    The synthetic M. genitalium I mentioned above has a molecular weight of 360,110 kilodaltons (kDa), or 360,110,000 daltons. Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages. By contrast, the RNA nucleotide which Sutherland et al. manufactured (ribo-cytidine phosphate) has a molecular weight of less than 360 daltons: less than a millionth that of the simplest bacterium.

    You replied (#108, #109):

    Methinks you are making an inappropriate comparison. The number of steps in the chemical pathway may only be four, but that doesn’t mean that pathway only resulted in one single molecule. It produced many ribo-cytidine phosphate molecules. That is, it produced one of the four basic types of ribonucleotides: those with the base cytosine (the letter “C” in the RNA sequence), and lots of them.. In other words, it generated lots of “C’s”….

    Not only did the irradiation step generate cytosine and uracil, it also converted some of the ribocytidine (the “C” letter) to ribouridine, (the “U” letter)….

    Now, when you talk about the number of letters in an organism’s genome, you are actually counting the physical number of nucleotides, the building blocks of DNA . But you have to keep in mind in any genome there are only four different types of nucleotides in DNA and ribonucleotides in RNA, only four different “letters”. In DNA, those letters are “A”, “T”, “C” and “G”, and in RNA, “A”, “U”, “C” and “G”…

    So the pathway described by the authors is capable of producing one-half of the types of ribonucleotides needed to synthesize RNA. (Emphasis mine – VJT.)

    First of all, I’d like to begin by citing an earlier part of my post, which you omitted in your response:

    Mr. Nakashima (#98) estimates that between 1 and 10 million sequential steps would have been required to get from simple organic chemicals to the simplest bacterium, M. genitalium, the synthetic version of which has 582,970 base pairs, according to this press release by the J. Craig Venter Institute.

    This is a vitally important point. In an earlier post (#65) to Mr. Nakashima, I asked him for an estimate of how many steps were required to get from the simplest organic compounds to the first cell, by the most direct pathway, ignoring side-reactants and focusing on the largest chemical molecule at each stage along the way, as it gets bigger and bigger. Mr. Nakashima was gracious enough to reply: he estimated between 1 and 10 million steps.

    That number provides me with a progress metric for origin-of-life research. In my post #105, I generously adopted the lower figure of 1,000,000 steps.

    Sutherland et al. managed to synthesize ribo-cytidine phosphate, via a four-step chemical process. You have kindly informed me that they also generated ribouridine, so let’s make that eight steps for argument’s sake. That’s eight steps along a 1,000,000-step journey – which, as I wrote above, is about the distance from New York to Atlanta.

    That’s very modest progress, to put it mildly.

    You think this is an unfair analogy. You seem to be arguing that half of the RNA molecule is made of these two ribonucleotides, so basically we’re half-way to building one. I know you don’t actually say that; but that’s the rhetorical implication of your words, which a non-specialist reading your post might draw. In essence, you’re saying: Sutherland et al. have already generated half the basic ingredients; once we’ve got the other half, all we have to do is put them all together.

    But that’s precisely the problem: putting them all together. As you know perfectly well, RNA is not a repetitive polymer, like polythene. You don’t get the same pattern repeating itself again and again and again. The sequencing is highly specific. And that’s what scientists have to figure out. That’s where the really hard work begins.

    Allow me to cite the Wikipedia article on RNA:

    RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but there are numerous modified bases and sugars in mature RNAs. Pseudouridine (Psi), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T), are found in various places (most notably in the T-Psi-C loop of tRNA). Another notable modified base is hypoxanthine, a deaminated adenine base whose nucleoside is called inosine (I). Inosine plays a key role in the wobble hypothesis of the genetic code. There are nearly 100 other naturally occurring modified nucleosides, of which pseudouridine and nucleosides with 2′-O-methylribose are the most common. The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that in ribosomal RNA, many of the post-transcriptional modifications occur in highly functional regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal function.

    The functional form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable “domains” of secondary structure like hairpin loops, bulges and internal loops. Since RNA is charged, metal ions such as Mg2+ are needed to stabilise many secondary structures.

    Like DNA, most biologically active RNAs, including mRNA, tRNA, rRNA, snRNAs and other non-coding RNAs, contain self-complementary sequences that allow parts of the RNA to fold and pair with itself to form double helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, their structures do not consist of long double helices but rather collections of short helices packed together into structures akin to proteins. (Emphases mine – VJT.)

    See what I mean?

    Allow me to conclude with a little anecdote, and I hope it conveys my incredulity when I hear people say we’ve made substantial progress towards solving the origin-of-life problem.

    A few months ago, my wife and I went shopping at the local mall. Actually, we were looking for a suitable birthday present for a nephew of ours, but our four-year-old son (who was with us) indicated that he wanted a little present too, so we thought, “Why not?” He pointed to a plastic model kit, containing 170 pieces, of six different kinds. The plastic kit was a model of a shark – just the thing a four-year-old boy would like. I should add that each kind of piece had its own specific shape. These pieces weren’t Duplo blocks; they were designed to fit together in a particular way, although of course you could make all sorts of things with them, if you wanted. In other words, the geometry of the little pieces constrained the ways in which they could join together, but did not in any way dictate the 3D form of the creature that they were used to make. It’s already starting to sound like DNA and RNA, isn’t it – except that there are six letters, not four!

    When I got home, the first thing I did was sort all the pieces into their different kinds. I put them in six little plastic bags, and I thought to myself: “Piece of cake. All I have to do was follow the instructions.” Boy was I wrong!

    Even with instructions, putting the shark together was not easy. At certain key points (especially the vertices), the diagrams were not detailed enough for me to figure out exactly which piece was meant to fit which. On top of that, it was not easy to make the different sides of the model shark join up properly: I had to virtually wrestle them into shape.

    Now, before I go on, let me ask you a question: what would be a good progress metric here? Would it make sense to say: well, he’s got all the pieces, so basically his job’s done? Of course not. You’d naturally say: how far along is he? How many pieces of the shark has he put together so far? That would be a good progress metric.

    Well, I never did finish that shark. I managed to put about 30 pieces together, so that my son could see the shark’s face and a bit of its side. That’s a miserable 30 pieces out of 170 – less than 20% completed. That’s how we can gauge success or failure. I guess the manufacturers of the shark kit didn’t realize that they’d have to make their instructions clearer for a dumb Dad like me.

    Fortunately, my son (who has about 300 toys – I’ve lost count) was not at all upset by my failure. Playing with the pieces was still an enjoyable experience for him. And fortunately, too, I can at least draw a realistic picture of a shark, even if I can’t put a model of one together.

    The moral of the story is: pieces don’t make a structure. Life is defined by its structure, and it’s not a repetitive structure, but a highly specific one, which has to support all sorts of complex metabolic functions. Oh – and it has to be able to make a copy of itself. And it has to be capable of evolving – or else it would be unable to cope with environmental change. Quite a tall order – and far harder than making a model shark.

    Let’s go back to Sutherland et al. They’ve done some excellent work. But what have they made? Two ribonucleotides. How many steps did that take, altogether, if we follow the longest path for each ribonucleotide they made? Eight or thereabouts. How many more steps do they need to complete before they’ve built the simplest kind of cell in existence (M. genitalium)? 999,992.

    Now do you see why I am underwhelmed?

    Eight steps along the road to Atlanta. You’ve got a long, long way to go.

  123. Mr Vjtorley,

    I think Mr Wisker is making a different point, that the kind of steps you are comparing are not in fact comensurable.

    Counting the reaction steps, and assuming you get to append the result to a growing chain would be 4*600,000 reactions + 600,000 appends = 3,000,000 “steps”.

    My estimate (which Mr Wisker is free to criticise or reject) of 1-10 million steps does bracket that number, but that process is hardly the one I had in mind. My estimate was devloped from the idea that the genome as a single molecule would grow through fusion events of smaller RNAs together. Fusion provides the selectable benefit of a better guarantee of having all of the instructions and components needed when you need them. I assumed random short mers of RNA were the “simple organic chemicals” available as starting points. Mers of 10-20 nucleotides in length could form abiotically and without selection on surfaces, and then become available to participate in organic chemistry leading to a first cell.

    Since I was starting with larger units (much larger than the inputs to the reaction pathways of Sutherland et al) I could have been extreme in my dependence on your wording and stated that between 100-500,000 events was sufficient, but I’d rather leave a few orders of magnitude wiggle room in in a SWAG like this.

    Actually, it is possible that a protocell could become self reproducing long before all of these RNAgenes linked up into one molecule. Then your question about number of steps to the longest molecule would be even shorter. But i think that would not be reflective of the actual size of the issue.

  124. vjtorley,

    Before I reply further (which may take some time as I have other pressing things to get done this afternoon), I would like to point out that I was reacting specifically to your mentioning of the molecular weight differential between one nucleotide and the entire genome of M. genitalium. Somehow it seemed to me you were tying the number of chemical steps with the number of nucleotides, which didn’t make sense. My apologies for misconstruing your argument– I’m glad the error was on my part.

    As for the number of actual chemical steps and pathways, it is important to keep in mind the kinds of initial assumptions being made. Early on in our discussion here I mentioned that Sutherland’s work was important because it threw out some initial assumptions that rendered the synthesis of ribonucleotides nearly impossible to achieve under pre-biological conditions. I think, as the work proceeds on abiogenesis, that other assumptions will be thrown out as well. I will mention a few in a subsequent comment.

  125. Mr Nakashima,

    I think Mr Wisker is making a different point, that the kind of steps you are comparing are not in fact comensurable.

    Yes, that was what I was trying to address, but now I don’t think that was what vjtorley was trying to argue. At least, I hope not.

  126. 126

    vjt,

    “How many more steps do they need to complete before they’ve built the simplest kind of cell in existence (M. genitalium)? 999,992.”

    Whatever the numbers, this seemingly misses the point. Life is not the collection of its parts (ask a physiologists) as you acknowledge.

    Life is the intricate coordination of those parts into a function.

    Let’s assume the synthesis of every part of an organism (after all, they do exist already). Take the M. genitalium you mention – what is its proteome count up to now – over a couple thousand for the smallest bacterium? (http://www.strgen.org/proteome/).

    A complete demonstration of the assumption that unguided processes lead to living organisms is not just getting to the synthesis of the nucleic acids, its the getting to those nucleic acids embedded with the instructions for the development of a proteome and metabolome and coordinating those into function and replication with the capacity of inheritance (without unwarranted investigator input).

    The work that has been done is incredibly interesting and will pay fantastic dividends (and is a heck of a testament to intelligent beings doing what intelligent beings do), but it does not demonstrate what is essential to life. It’s not even close.

    I think this is why many ID proponents are perhaps happy that all this research is being done. The sooner we get past the parts and the entrenched ideology; we can get down to the idea that it doesn’t just coordinate itself. This is most likely to become apparent when we try to do it ourselves.

  127. Mr BiPed,

    Yes, if we can get past the synthesis of the physical components, things will be prepared to challenge the next level – whether or not autocatalytic sets actually form as predicted by mathematical models.

  128. Upright BiPed:

    Sorry for the delay. I didn’t ignore your question — I was just too busy furthering our knowledge of the natural world.

    Given the testability issues either way, this is where priori assumptions come into the picture. Science has operated with the assumption that purely unguided processes led to life for well over 100 years. It is the central theme in every textbook and is spoken to the public (to which science has a responsibility) on a daily basis, ranging from unabashed proclamations made on television and in newspapers, to popular books written by scientists using their status as a means to further the assumption. Do you think that science has provided the evidence that life came about by purely unguided processes?

    No.

    Let me clarify a bit: science cannot rule out that evolution (or anything else for that matter) is somehow guided. Unless you would care to be more specific about how the guidance takes place, with sufficient detail to allow some testable predictions to be made.

    It is therefore also incorrect to say that science “assumes” unguidedness. “Guidance” is so ill-defined that it cannot be incorporated in scientific models in a useful way. That’s not the same as denying that guidance exists.

  129. 129

    lryna,

    So, I asked if science had proven the assumption and you said “no”.

    You then went on to deny that such an assumption is real within the sciences. Your denial falls with the sound of a thud against what is verifiably true. As if the constant pronouncement coming from science to the public is not real, does not exist, cannot be demonstrated, is a thing of fiction. How disingenuous can you be?

    Let’s look:

    “science cannot rule out that evolution (or anything else for that matter) is somehow guided.”

    Firstly, this thread isn’t about evolution and I am not certain if the word had even come up until you yourself brought it up. We were talking about a demonstration surrounding theories regarding the beginning of life on this planet. Why the change of topic?

    In any case, your comment is completely false. Science makes judgments about guided things all the time. (Forensics, SETI, historical sciences, etc). The reason that the methodologies of these disciplines are withheld from the biological sciences is for nothing but the protection of the core assumption, which of course, you deny exists.

    Even more interesting is how a question about science providing some empirical basis for its metaphysical assumption of unguided-ness morphed into a safehouse statement about an inability to disprove guided-ness regarding an issue not even under discussion. It’s awash in political maneuver. Just butt the tactical answer given to the simply question asked, and take it for a drive:

    Do you think that science has provided the evidence that life came about by purely unguided processes? Science cannot rule out that evolution is guided.

    (smirk)

    “It is therefore also incorrect to say that science “assumes” unguidedness.

    Really? Lets both start typing. You type all the quotes from science that proves your point and I’ll do the same for those that prove my point. Let’s see who dies typing.

    “Guidance is so ill-defined that it cannot be incorporated in scientific models in a useful way.”

    We’ve now moved away from the fact that science has failed to provide empirical evidence for an entrenched assumption, and we’ve all but forgotten that the assumption is peddled to the public every single day. We are now squinting our eyes and moving into the illogical justifications for ignoring the previous facts.

    The website you are on is dedicated to the proposition that we can make rational inferences to design from the observable evidence (in DNA, for instance) using the same explanatory techniques used within the other historical sciences, as well as forensics, and even the search for extraterrestrial life.

    “That’s not the same as denying that guidance exists.”

    Sure, whatever. But hey, thanks for confirming the evidence for the materialist’ assumption has not been provided.

    ;)

  130. By “guidance”, you mean a miracle, right? No one can ever prove or disprove the existence of miracles.

    Anyone is free to maintain that absent a sufficiently detailed explanation for the emergence of the first living organisms, (or any natural event) they’ll continue to believe that it was a miracle. That is the very essence of a god-of-the-gaps position. The weakness of that position is that no matter where you make a stand you’ll eventually have to move.

  131. Clive Hayden,

    The great thing about language is that we can make anything have a counterpart, just put the prefix “non” in front of it.

    There is no utility in trying to compare the natural and the non natural. Simply chalk the concept of the later up to the generous ‘nature’ of language and the creative abilities of the human mind.

  132. Mung, you said…

    If you ask me, everything that exists has a “nature” or “essence” and anything which does have a “nature” or “essence” is therefore, by definition, natural.

    So nothing non natural exists.

  133. Upright BiPed, Dave Wisker, Mr. Nakashima, IrynaB and Mark Frank:

    First of all, Upright BiPed is perfectly correct to point out that my “steps-along-the-road” metaphor fails to adequately convey the real difficulty of undirected abiogenesis. The main reason why I used the “steps along the road” metaphor is that ordinary people (including myself) are psychologically wedded to it. Discuss any outstanding problem at work with your boss, and he/she will ask you when you’re on track to finish. And when people read articles in The New York Times suggesting that progress has been made in discovering how life evolved, their natural response is: “Well, how far along the road are we?” The purpose of the “steps” metaphor was to lend a sense of perspective to the issue. We are nowhere close to finding out how life evolved. The “size” metaphor ws intended for the same purpose. People want to know stuff like that, because that’s how they think. Ordinary people (including myself) appreciate vivid visual metaphors. Telling people that scientists have made a molecule that’s 1,000,000 times smaller than the simplest cell immediately conveys that progress achieved to date has been very limited. That’s why popular science magazines pushing abiogenesis never mention these awkward facts.

    But UprightBiPed hit the nail on the head with his comments. For, as he correctly observes, life is not just a collection of parts, but the intricate coordination of those parts into a function. In other words, the defining feature of life consists in its form, not its matter. Mr. Nakashima acknowledges the same point when he suggests that we need to get past the synthesis of the physical components, and move up to the next level.

    Nothing we see in the world is totally unstructured. We can speak of a form-matter spectrum, for the sake of convenience. Although it represents a geneuine advance, the foregoing discussion of ribonucleotide synthesis by Sutherland et al., is much closer to the “matter” end of the spectrum than the “form” end, as far as life is concerned.

    With life, we see layer upon layer of complexity. The rich 3D structure of life is a marvel that we are struggling to explain. When I narrated my story of making a model shark, I remarked that it was very hard to fit the pieces into the right 3D shape. But assembling an RNA molecule would be incomparably more difficult: as I remarked in my previous thread, it has a rich 3D structure.

    Mark Frank: the reason why the development of metazoans took so long was that it was a much bigger jump, in terms of complexity. You might like to have a look at these pages, which will answer your questions:

    http://www.darwinsdilemma.org/.....losion.php

    http://www.darwinsdilemma.org/pdf/faq.pdf

    As to the late emergence of animals: maybe the reason was that the early Earth needed to be stabilized first (think of climate systems etc).

    It has been a pleasure exchanging views with you all. Bye for now.

  134. Mr Vjtorley,

    I respect your exit from the conversation for now, and I hope you do not feel chased by a bear! Enjoy your vacation reading as much as you can!

    Here is an article that sketches the origin of the RNA World in a way similar to that which I laid out above. I offer it with compliments and a hope you enjoy Christmas and New Years.

  135. lastyear,

    There is no utility in trying to compare the natural and the non natural. Simply chalk the concept of the later up to the generous ‘nature’ of language and the creative abilities of the human mind.

    Then call it super instead of non natural. It doesn’t much matter. We don’t know what nature is, and cannot rule out super or non natural things.

  136. Oramus 115, Joseph 116, vjtorley 133

    You are right! I had not thought about the requirement to create an oxygen rich atmosphere to sustain multicellular life.

    I do disagree with Joseph’s line in #116

    One doesn’t have to know the motivations to critique the design

    If you don’t know what the design is intended to do – how can you know if it does it well?

  137. Mr Nakashima,

    That was a good reference. Tied in with the following article, we can begin to see how tRNAs (which are actually very small)could form from random RNA sequences. This then ties in well with the stereochemical hypothesis for the origin of the genetic code.

    Nagaswamy U & GE Fox (2003). RNA ligation and the origin of tRNA. Origins of Life and Evolution of the Biosphere 33: 199-209

    A straightforward origin of transfer RNA, (tRNA), is difficult to envision because of the apparently complex idiosyncratic interaction between the D-loop and T-loop. Recently, multiple examples of the T-loop structural motif have been identified in ribosomal RNA. These examples show that the long-range interactions between the T-loop and D-loops seen in tRNA are not an essential part of the motif but rather are facilitated by it. Thus, the core T-loop structure could already have existed in a small RNA prior to the emergence of the tRNA. The tRNA might then have arisen by expansion of an RNA that carried the motif. With this idea in mind, Di Giulio’s earlier hypothesis
    that tRNA evolved by a simple duplication or ligation of a minihelix RNA was re-examined. It is shown that an essentially modern tRNA structure can in fact be generated by the ligation of two 38-nucleotide RNA minihelices of appropriate sequence. Although rare, such sequences occur with sufficient frequency, (1 in 3 × 107), that they could be found in a standard in vitro RNA selection experiment. The results demonstrate that a series of RNA duplications, as previously proposed, can in principal account for the origin of tRNA. More generally, the results point out that RNA ligation can be a powerful driving force for increased complexity in the RNA World.

  138. vjtorley,

    I would like to echo Mr Nakashima’s comments and say this discussion has been a pleasure.

  139. Clive Hayden

    We don’t know what nature is, and cannot rule out super or non natural things.

    That is correct. There’s all manner of things that we cannot rule out. But just because something cannot be ruled out doesn’t mean it has any merit or even makes sense.

  140. Mr Nakashima & vjtorley, you both might enjoy this article as well:

    Costanzo G, S Pino, F Ciciriello, & E Di Mauro (2009). The generation of long RNA chains in water. The Journal of Biological Chemistry 284: 33206-33216.

    The synthesis of RNA chains from 3?,5?-cAMP and 3?,5?-cGMP was observed. The RNA chains formed in water, at moderate temperatures (40–90 °C), in the absence of enzymes or inorganic catalysts. As determined by RNase analyses, the bonds formed were canonical 3?,5?-phosphodiester bonds. The polymerizations are based on two reactions not previously described: 1) oligomerization of 3?, 5?-cGMP to ?25-nucleotide-long RNA molecules, and of 3?,5?-cAMP to 4- to 8-nucleotide-long molecules. Oligonucleotide A molecules were further extended by reciprocal terminal ligation to yield RNA molecules up to >120 nucleotides long and 2) chain extension by terminal ligation of newly polymerized products of 3?,5?-cGMP on preformed oligonucleotides. The enzyme- and template-independent synthesis of long oligomers in water from prebiotically affordable precursors approaches the concept of spontaneous generation of (pre)genetic information.

  141. Mr Frank,

    If the atmosphere became oxygenated 2.4 billion years ago, and metazoa appeared 600 million years ago, there is still a vast gulf of time not explained by that hypothesis.

    Somewhere in that gap, life invented and refined the idea of sexual reproduction. Judging by memories of my own teenage years, I am not at all surprised if this took a billion years to figure out! ;)

  142. #141

    Yes – but this diagram on Wikipedia suggested to me that the oxygen content was low until just before the Cambrian – mind you it is in German so maybe I don’t understand it!

  143. lastyear,

    That is correct. There’s all manner of things that we cannot rule out. But just because something cannot be ruled out doesn’t mean it has any merit or even makes sense.

    Nor does it mean that it doesn’t make sense. We cannot make sense of nature, therefore we have no real basis for comparison when comparing nature to super or non natural things. If we don’t understand the rule, we cannot rule out the exception.

  144. Mr Frank,

    The Wiki (English) entry for “Oxygen catastrophe” has a clearer and more detailed image.

    While I can imagine a link between oxygen levels and a motile, carnivorous lifestyle, just being multicellular could apply to plants as well.

    On a related note, I wonder if anyone has studied the timing of the endosymbionic events for chloroplasts and mitochondria.

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