How Comfortable is Naturalism with Highly Atypical Events?

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There are numerous definitions of naturalism. Here is one definition with some additional observations from infidels.org:

As defined by philosopher Paul Draper, naturalism is “the hypothesis that the natural world is a closed system” in the sense that “nothing that is not a part of the natural world affects it.” More simply, it is the denial of the existence of supernatural causes. In rejecting the reality of supernatural events, forces, or entities, naturalism is the antithesis of supernaturalism.

As a substantial view about the nature of reality, it is often called metaphysical naturalism, philosophical naturalism, or ontological naturalism to distinguish it from a related methodological principle. Methodological naturalism, by contrast, is the principle that science and history should presume that all causes are natural causes solely for the purpose of promoting successful investigation. The idea behind this principle is that natural causes can be investigated directly through scientific method, whereas supernatural causes cannot, and hence presuming that an event has a supernatural cause for methodological purposes halts further investigation.

http://infidels.org/library/modern/nontheism/naturalism/

For the purposes of this discussion, I’m not going to be too insistent on particular definitions, but it seems to me this captures the essence of naturalism: “More simply, it [naturalism] is the denial of the existence of supernatural causes.”

Personally, I’d be on the side of naturalists or at least agnostic if I felt the origin of life question were satisfactorily resolved. So although I have sympathy for the naturalistic viewpoint, I find insistence on it too closed-minded. I don’t think reality operates in a completely law-like, predictable fashion, it only does so mostly, but not always.

The word “natural” can be equivocated to death and is often equated with “ordinary” or “typical” when it should not be. So if someone insists that naturalism is true but wishes to also be fair with the facts and avoid such equivocations, when they comment on the origin of life, they might say:

The origin of life was an atypical and unique event far from ordinary expectation, but many of us presume it happened naturally since supernatural events are not observed in the lab.

That would be the an accurate way to characterize the state of affairs, but this not what is usually said by advocates of naturalistic origins of life. Most origin-of-life proponents insinuate that the origin of life event was not terribly extraordinary, that OOL fits well within “natural” expectation, even though by accepted laws of physics and chemistry and current knowledge, such an event violates the ordinary (dare I say “natural”) expectation that non-living things stay non-living.

Turning to evolution, if someone insists on naturalism, but is at least fair with our present day knowledge, they might say:

It is NOT typical for something as complex as an animal to emerge from a single-celled organism, but we presume it happened naturally since animals share some DNA with single celled creatures.

Again, that would be the an accurate way to characterize the state of affairs, but this is not what is usually said by advocates of naturalistic evolution of life from the first cell. Evolutionists insinuate that the necessary events to evolve an animal from a single cell must not have been terribly extraordinary because animals and single-celled creatures share some similar DNA — the idea is insinuated even though it is a non-sequitur because something can share DNA via extraordinary or atypical events, at least in principle.

Darwin and his supporters argue that most evolution of complex function proceeded via a mechanism which Darwin labeled “natural selection”. However, if Darwin’s claims actually entail highly atypical events rather than ordinary ones, then his label of “natural selection” for how things evolved would be a false advertising label. If major evolutionary changes require highly atypical events, then “highly atypical events almost indistinguishable from miracles” would be a far more appropriate label for Darwin’s proposed mechanism of evolution. Instead, Darwin’s label of “natural” is presumptuous and unproven at best and completely false at worst. For all we know, natural selection prevents major evolutionary change. Michael Lynch points out:

many genomic features could not have emerged without a near-complete disengagement of the power of natural selection

Michael Lynch
opening, The Origins of Genome Architecture

Many? How about most? No one knows for sure, and thus Darwin’s label of “natural” for “natural selection” is presumptuous. For all we know the correct theory of evolution could be “evolution of significant novel forms by highly exceptional events”.

Animals and single-celled creatures share some DNA, but from all that we know, the transition from single-celled creatures to something as complex as a multi-cellular animal is highly atypical and so far from natural expectation that something of that order of change might likely not happen again in the history of the universe.

If naturalism can accommodate any atypical or extraordinary event as a matter of principle, no matter how improbable, then naturalism can accommodate events that would otherwise be indistinguishable from miracles.

Whether there is a theological dimension with atypical events is a separate question. Can there be an event atypical enough that it warrants supernatural explanations? That’s a philosophical question with probably no formal resolution.

Proponents of naturalistic emergence of biological complexity desperately pretend the sequence of necessary events are not atypical, but rather within the realm of ordinary expectation. Hence they try to render the question of supernatural origins as moot as the question of whether supernatural causes are needed to make ice melt on a hot day.

But imho, efforts to characterize emergence of biological complexity as “not that out of the ordinary” are failing. The more we learn of life’s complexity the more it seems highly atypical events were involved to create them. Perhaps these events were so atypical that they are virtually indistinguishable from miracles of supernatural creation.

I’m certainly not alone in those sentiments:

If we do not accept the hypothesis of spontaneous generation, then at this one point in the history of evolution we must have recourse to the miracle of a supernatural creation

Ernst Haeckel, 1876

Pasteur’s experiments and those followed from 1862 disproved spontaneous generation. Ernst Haeckel’s 1876 quote shows how false ideas like spontaneous generation die a slow death. Haeckel’s quote symbolizes how naturalism seems inherently uncomfortable with anything that suggests a highly atypical event actually happened somewhere in the past.

530 thoughts on “How Comfortable is Naturalism with Highly Atypical Events?”

  1. DNA_Jock,

    So long as they are fractionally less crappy than their crappy cousin, they will win out.

    If the genetic information starts to degrade in the population doesn’t the population move toward extinction? If you don’t agree, why not?

    If we disabled DNA repair and started a bacteria culture could it survive? If yes, how would it stop rapidly moving toward non function?

  2. Allan Miller:
    phoodoo,

    OK, you can have it back if you want. I find the spectacle of a Creationist thinking it worth considering that an OoL produced a perfect replicator first time off to be a bit of a novelty, but … yeah! It was soooo lucky it wasn’t too perfect to evolve! Another bullet dodged by our ancestor.

    I have no idea what on Earth you are getting at. How is it not lucky that DNA copies itself badly, but not too badly. Do water molecules form well, but not too well? Does sodium sometimes have 11 electrons, sometimes 13, maybe 14?

    The luck of copying not too good is just as lucky as the luck of not copying too badly.

    How lucky. Well, this gives some idea:

    For a cell to divide, it must first replicate its DNA.[10] This process is initiated at particular points in the DNA, known as “origins”, which are targeted by initiator proteins.[3] In E. coli this protein is DnaA; in yeast, this is the origin recognition complex.[11] Sequences used by initiator proteins tend to be “AT-rich” (rich in adenine and thymine bases), because A-T base pairs have two hydrogen bonds (rather than the three formed in a C-G pair) and thus are easier to strand separate.[12] Once the origin has been located, these initiators recruit other proteins and form the pre-replication complex, which unzips the double-stranded DNA.
    Elongation

    DNA polymerase has 5′-3′ activity. All known DNA replication systems require a free 3′ hydroxyl group before synthesis can be initiated (note: the DNA template is read in 3′ to 5′ direction whereas a new strand is synthesized in the 5′ to 3′ direction—this is often confused). Four distinct mechanisms for DNA synthesis are recognized:

    All cellular life forms and many DNA viruses, phages and plasmids use a primase to synthesize a short RNA primer with a free 3′ OH group which is subsequently elongated by a DNA polymerase.
    The retroelements (including retroviruses) employ a transfer RNA that primes DNA replication by providing a free 3′ OH that is used for elongation by the reverse transcriptase.
    In the adenoviruses and the φ29 family of bacteriophages, the 3′ OH group is provided by the side chain of an amino acid of the genome attached protein (the terminal protein) to which nucleotides are added by the DNA polymerase to form a new strand.
    In the single stranded DNA viruses — a group that includes the circoviruses, the geminiviruses, the parvoviruses and others — and also the many phages and plasmids that use the rolling circle replication (RCR) mechanism, the RCR endonuclease creates a nick in the genome strand (single stranded viruses) or one of the DNA strands (plasmids). The 5′ end of the nicked strand is transferred to a tyrosine residue on the nuclease and the free 3′ OH group is then used by the DNA polymerase to synthesize the new strand.

    The first is the best known of these mechanisms and is used by the cellular organisms. In this mechanism, once the two strands are separated, primase adds RNA primers to the template strands. The leading strand receives one RNA primer while the lagging strand receives several. The leading strand is continuously extended from the primer by a DNA polymerase with high processivity, while the lagging strand is extended discontinuously from each primer forming Okazaki fragments. RNase removes the primer RNA fragments, and a low processivity DNA polymerase distinct from the replicative polymerase enters to fill the gaps. When this is complete, a single nick on the leading strand and several nicks on the lagging strand can be found. Ligase works to fill these nicks in, thus completing the newly replicated DNA molecule.

    The primase used in this process differs significantly between bacteria and archaea/eukaryotes. Bacteria use a primase belonging to the DnaG protein superfamily which contains a catalytic domain of the TOPRIM fold type.[13] The TOPRIM fold contains an α/β core with four conserved strands in a Rossmann-like topology. This structure is also found in the catalytic domains of topoisomerase Ia, topoisomerase II, the OLD-family nucleases and DNA repair proteins related to the RecR protein.

    The primase used by archaea and eukaryotes, in contrast, contains a highly derived version of the RNA recognition motif (RRM). This primase is structurally similar to many viral RNA-dependent RNA polymerases, reverse transcriptases, cyclic nucleotide generating cyclases and DNA polymerases of the A/B/Y families that are involved in DNA replication and repair. In eukaryotic replication, the primase forms a complex with Pol α.[14]

    Multiple DNA polymerases take on different roles in the DNA replication process. In E. coli, DNA Pol III is the polymerase enzyme primarily responsible for DNA replication. It assembles into a replication complex at the replication fork that exhibits extremely high processivity, remaining intact for the entire replication cycle. In contrast, DNA Pol I is the enzyme responsible for replacing RNA primers with DNA. DNA Pol I has a 5′ to 3′ exonuclease activity in addition to its polymerase activity, and uses its exonuclease activity to degrade the RNA primers ahead of it as it extends the DNA strand behind it, in a process called nick translation. Pol I is much less processive than Pol III because its primary function in DNA replication is to create many short DNA regions rather than a few very long regions.

    In eukaryotes, the low-processivity enzyme, Pol α, helps to initiate replication because it forms a complex with primase.[15] In eukaryotes, leading strand synthesis is thought to be conducted by Pol ε; however, this view has recently been challenged, suggesting a role for Pol δ.[16] Primer removal is completed Pol δ[17] while repair of DNA during replication is completed by Pol ε.

    As DNA synthesis continues, the original DNA strands continue to unwind on each side of the bubble, forming a replication fork with two prongs. In bacteria, which have a single origin of replication on their circular chromosome, this process creates a “theta structure” (resembling the Greek letter theta: θ). In contrast, eukaryotes have longer linear chromosomes and initiate replication at multiple origins within these.>[18]
    Replication fork
    Scheme of the replication fork.
    a: template, b: leading strand, c: lagging strand, d: replication fork, e: primer, f: Okazaki fragments
    Many enzymes are involved in the DNA replication fork.

    The replication fork is a structure that forms within the nucleus during DNA replication. It is created by helicases, which break the hydrogen bonds holding the two DNA strands together. The resulting structure has two branching “prongs”, each one made up of a single strand of DNA. These two strands serve as the template for the leading and lagging strands, which will be created as DNA polymerase matches complementary nucleotides to the templates; the templates may be properly referred to as the leading strand template and the lagging strand template.

    DNA is always synthesized in the 5′ to 3′ direction. Since the leading and lagging strand templates are oriented in opposite directions at the replication fork, a major issue is how to achieve synthesis of nascent (new) lagging strand DNA, whose direction of synthesis is opposite to the direction of the growing replication fork.
    Leading strand

    The leading strand is the strand of nascent DNA which is being synthesized in the same direction as the growing replication fork. A polymerase “reads” the leading strand template and adds complementary nucleotides to the nascent leading strand on a continuous basis.
    Lagging strand

    The lagging strand is the strand of nascent DNA whose direction of synthesis is opposite to the direction of the growing replication fork. Because of its orientation, replication of the lagging strand is more complicated as compared to that of the leading strand. As a consequence, the DNA polymerase on this strand is seen to “lag behind” the other strand.

    The lagging strand is synthesized in short, separated segments. On the lagging strand template, a primase “reads” the template DNA and initiates synthesis of a short complementary RNA primer. A DNA polymerase extends the primed segments, forming Okazaki fragments. The RNA primers are then removed and replaced with DNA, and the fragments of DNA are joined together by DNA ligase.
    Dynamics at the replication fork
    The assembled human DNA clamp, a trimer of the protein PCNA.

    As helicase unwinds DNA at the replication fork, the DNA ahead is forced to rotate. This process results in a build-up of twists in the DNA ahead.[19] This build-up forms a torsional resistance that would eventually halt the progress of the replication fork. Topoisomerases are enzymes that temporarily break the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix; topoisomerases (including DNA gyrase) achieve this by adding negative supercoils to the DNA helix.[20]

    Bare single-stranded DNA tends to fold back on itself forming secondary structures; these structures can interfere with the movement of DNA polymerase. To prevent this, single-strand binding proteins bind to the DNA until a second strand is synthesized, preventing secondary structure formation.[21]

    Clamp proteins form a sliding clamp around DNA, helping the DNA polymerase maintain contact with its template, thereby assisting with processivity. The inner face of the clamp enables DNA to be threaded through it. Once the polymerase reaches the end of the template or detects double-stranded DNA, the sliding clamp undergoes a conformational change that releases the DNA polymerase. Clamp-loading proteins are used to initially load the clamp, recognizing the junction between template and RNA primers.[2]:274-5
    DNA replication proteins

    At the replication fork, many replication enzymes assemble on the DNA into a complex molecular machine called the replisome. The following is a list of major DNA replication enzymes that participate in the replisome:[22]

    There is much more to it than this of course, but space is limited.

  3. phoodoo,

    I have no idea what on Earth you are getting at. How is it not lucky that DNA copies itself badly, but not too badly.

    I have already conceded that one could call it ‘luck’ if one wishes. That can be ascribed to any outcome of any stochastic process: ‘luck’. The thing I find amusing is that you wish to circumscribe the range of fidelity in the upward direction too, as if that makes any serious difference to the likelihood of an OoL, by narrowing the bounds of acceptable fidelity. I was more than happy to concede to the Creationist that an early replicator is almost certainly highly imperfect. But you wondered why I would make that concession, so I withdrew it, and you still aren’t happy!

    The luck of copying not too good is just as lucky as the luck of not copying too badly.

    What, it is just as probable that a replicator is perfect than that it can’t replicate at all? I think you might seek the views of your Creationist colleagues on that one. You’d certainly not take it from me, though my left eyebrow is presently much higher than my right, in reflection of my dubiousness on the claim.

    How lucky. Well, this gives some idea: [ snip massive irrelevant C&P dump]

    Thanks, I’m familiar with the biochemistry of modern replication. I skip past Sal’s C&P’s too. Yet you think it was ‘lucky’ that this was not all available at the start to assist in perfect replication! You are having a battle with yourself, unknowing. I’ll pull up a chair.

  4. Alan Fox,

    I realise Sal, Mung, Colewd and phoodoo find evolutionary theory and a “naturalistic” explanation for the origin of life unbelievable. Let me add that I am far less optimistic than some regarding ever establishing an explanation for the origin of life on Earth (find evidence or echos of evidence of life elsewhere and everything changes 🙂 ). Until then, I’m content to concede we really don’t have anything approaching a complete explanation.

    I am curious as to what those that mock attempts at scientific hypotheses think happened. There appears to be no hypothesis attributable to the “Intelligent Design” movement that could be stretched to any sort of explanation for the origin and subsequent diversity of life on Earth. Have our Evolution Skeptics any positive ideas of their own they’d like to share?

    Sal? Mung? Colewd? phoodoo? Anyone? Is there a thread topic there?

    This is a very fair question.

    As Herbert Yockey said in his 1979 paper “the origin of life is as difficult as the origin of matter” this came from his calculation of the size of sequence space of a “simple” life form.

    The point I have been trying to make is that “simple” and life are opposite concepts and this makes it very hard to conceptualize a purely natural origin. So maybe one of the possibilities that the key component of life, genetic information, originated from the same place matter did.

    So here is the first swag at a wild hypothesis.

    The origin of matter, and the origin of genetic information came from outside of space-time prior to the big bang.

  5. Why do these people think anyone here believes life started by the replication of DNA? And not just here, I don’t think I’ve ever come across a publication wherein somebody suggests life started by the spontaneous emergence of a self-replicating system with a DNA-based genome.

    The point, as usual, is just that “there’s a simpler way to get it to work”. That simpler way is usually worse than the more complex way, but it still works.
    That’s it, that’s the point. It isn’t “so life could have started with DNA being replicated by DNA polymerase”, the point is “much of this stuff we see today, strictly isn’t needed”.

  6. Rumraket: Why do these people think anyone here believes life started by the replication of DNA?

    Who are “these people”?

    We have no idea what form a spontaneous appearance of life might take. Not you, not me, not Allan. So how do we “know” it probably wouldn’t survive?

  7. Flint: Someone who knows orders of magnitude mopre than you about this tries to explain, but you won’t understand because understanding would dispel what is obviously very comfortable ignorance.

    Now that’s funny, I don’t care who you are.

  8. phoodoo:

    DNA_Jock: As others have noted, there is a Goldilocks range of mutation rates.
    [Emphasis in original]

    What do you think I said, for crying out loud??

    Yes, lucky evolution, it just so happens to get the exact Goldilocks range it needs. Just like ALL THE OTHER LUCK it got!

    Just another coincidence!

    What you actually wrote:

    phoodoo: So it sure is a good thing that evolution is sloppy, or it wouldn’t be very good at all. The goldilocks of evolution. Sloppy JUST RIGHT!

    Nothing about a range.

    As Allan has tried to point out to you, “too accurate” is not a problem.

    DNA polymerase (without proof-reading) has an error rate of about 10^-5. Proofreading and error repair add ~two orders of magnitude apiece, yielding an overall error rate of 10^-9. That’s great for mammals and salamanders, but really not necessary for “life”: RNA replication has error rates between 7.2 x 10^-5 (influenza) and 1.5 x 10^-3 (Qbeta).

    So the “Goldilocks range” for extant beasties covers 5 to 6 orders of magnitude. Early replicators could have been somewhat worse that Qbeta.
    “Sloppy JUST RIGHT!” is a strange way to characterize something with a million-fold leeway.

  9. colewd: So here is the first swag at a wild hypothesis.

    The origin of matter, and the origin of genetic information came from outside of space-time prior to the big bang.

    All science so far

  10. Alan Fox: I realise Sal, Mung, Colewd and phoodoo find evolutionary theory and a “naturalistic” explanation for the origin of life unbelievable.

    Evolutionary theory does not explain the origin of life, and there are no naturalistic explanations for the origin of life. It’s a mystery. Perhaps one day it will no longer be a mystery. But until then, the anti-ID types ought to show a bit more reticence about making broad sweeping statements that assume that we know things that we just don’t know. Is there an OP in that, perhaps?

  11. Mung: Evolutionary theory does not explain the origin of life, and there are no naturalistic explanations for the origin of life. It’s a mystery. Perhaps one day it will no longer be a mystery. But until then, the anti-ID types ought to show a bit more reticence about making broad sweeping statements that assume that we know things that we just don’t know. Is there an OP in that, perhaps?

    Anti-ID. ROTLFLMAO

  12. colewd: The point I have been trying to make is that “simple” and life are opposite concepts..

    We get the point every time you make it. You just never get around to actually demonstrating the truth of your claim.

    So maybe one of the possibilities that the key component of life, genetic information, originated from the same place matter did. The origin of matter, and the origin of genetic information came from outside of space-time prior to the big bang.

    That’s outright ridiculous. What the hell are you even saying here, that DNA formed in the big bang?

  13. Mung: Evolutionary theory does not explain the origin of life, and there are no naturalistic explanations for the origin of life.

    Technically there are, we just don’t know if they’re true.

  14. Allan Miller: I can think of, and have presented, several objections to this line of reasoning, which seem to being being met with a rearguard squirm as if I had been the one advancing an argument, as opposed to addressing one.

    My only objection was that you claimed to have knowledge of probabilities. You don’t.

  15. Kantian Naturalist: This goes to the point I was making earlier: we don’t have the relevant background knowledge necessary to determine whether abiogenesis was extremely unlikely, or extremely likely, or anywhere in between.

    But we claim to know that abiogenesis has ceased, or that if it hasn’t ceased it’s getting eaten, or that it’s less probable now than in the past. All I want is to see the actual probability calculations. Don’t people here appreciate irony?

  16. Mung: We have no idea what form a spontaneous appearance of life might take.

    Oh, then how the fuck can you even argue that it is unlikely or lucky or required design?

  17. Rumraket,

    That’s outright ridiculous. What the hell are you even saying here, that DNA formed in the big bang?

    First, I stated this as a wild hypothesis so just roll with it. Alan asked for new ideas.

    That matter and DNA sequences were and are formed outside of space-time. Forget when for now.

    If new DNA information is downloaded into an existing animals reproductive cells then its off spring can evolve into a new animal.

    We know cells have the ability to take existing information and modify DNA (DNA repair). We also know that proteins react to specific optical frequencies.

  18. Mung,

    We have no idea what form a spontaneous appearance of life might take. Not you, not me, not Allan. So how do we “know” it probably wouldn’t survive?

    Revelation. Or … because we ‘know’ that organic molecules routinely get hoovered up by prokaryotes, and adapted organisms outcompete the less well adapted.

    We also ‘know’ that primitive life is likely to be shit at it. It’s all you guys ever say, ferchrissakes! So no, it almost certainly would not survive, though I concede we can never ‘know’ with quite the certainty you seem to require.

    This is the bizarre doublethink that I mentioned. It’s not just different ‘doubters’ having contradictory notions, it’s the same doubter having contradictory notions. Life is impossible to get going, but there is nothing to stop it happening again and again and again …

  19. Rumraket: Oh, then how the fuck can you even argue that it is unlikely or lucky or required design?

    I think you’re jumping to conclusions about what I am arguing. I realize it’s not easy to track who said what and why they said it.

    🙂

  20. Rumraket,

    We get the point every time you make it. You just never get around to actually demonstrating the truth of your claim.

    100% of the observed evidence of life on earth supports this claim. The OOL claims are the opposite. 0% of observed evidence supports OOL.

  23. Mung,

    My only objection was that you claimed to have knowledge of probabilities. You don’t.

    Yes I do. It is more probable that a repeat inception of an organic-polymer replicator will struggle on a populated earth. I don’t have to know the precise probablities to be able to have a high degree of confidence in that position.

    It is absurd to deny it, unless you also deny all of ecology as a matter of routine.

  24. colewd:
    Rumraket,

    First, I stated this as a wild hypothesis so just roll with it.Alan asked for new ideas.

    That matter and DNA sequences were and are formed outside of space-time. Forget when for now.

    If new DNA information is downloaded into an existing animals reproductive cells then its off spring can evolve into a new animal.

    We know cells have the ability to take existing information and modify DNA (DNA repair).We also know that proteins react to specific optical frequencies.

    So much crackpottery in such few words.

  25. Allan Miller,

    This is the bizarre doublethink that I mentioned. It’s not just different ‘doubters’ having contradictory notions, it’s the same doubter having contradictory notions. Life is impossible to get going, but there is nothing to stop it happening again and again and again …

    Yep. One amazing design 🙂

  28. colewd: If new DNA information is downloaded into an existing animals reproductive cells then its off spring can evolve into a new animal.

    Same question again: is this “new information” added in a way that it’s gradual, making it indistinguishable to standard evolution? Or does the “new information” inserted in reproductive cells make animals give birth to entirely different animals than can’t reproduce with the members of it’s own population?

    Use your fucking brain

  29. Alan Fox,

    Dazz: So much crackpottery in such few words.

    I guess this is why the other guys won’t share new ideas. I guess this is the culture of TSZ.

  30. colewd,

    If new DNA information is downloaded into an existing animals reproductive cells then its off spring can evolve into a new animal.

    I should forget this one right off the bat. It is supported by 0% of the available evidence.

  31. colewd:

    DNA_Jock,

    So long as they are fractionally less crappy than their crappy cousin, they will win out.

    If the genetic information starts to degrade in the population doesn’t the population move toward extinction? If you don’t agree, why not?

    If we disabled DNA repair and started a bacteria culture could it survive? If yes, how would it stop rapidly moving toward non function?

    To answer your second question first, yes: most of the bacteria grown in labs are deliberately made defective in one or two DNA repair pathways, for reasons of biosafety (prevent recombination) and convenience (facilitate certain manipulations). I don’t know what would happen if you knocked them ALL out in one strain; I suspect you would get a rather sickly strain that would be very sensitive to mutagens. So what?
    Your first question still reveals your “Twas ever thus” thinking. Well, that or it’s incoherent. I will try to explain.
    Imagine an early replicator with a RdRPol error rate of 10-3.
    Suppose it has a 1,000 base genome.
    On average, 36% of its replications will be error-free. That’s pretty good…
    OTOH suppose it has a much larger genome, of which 4,000 nucleotides are absolutely essential. Now it faces a tougher battle, since only 1.83% of its replications will correctly reproduce all 4,000 essential nucleotides. It’s bloody inefficient (but not mind-numbingly inefficient). However, if it’s better than its cousins, it will quietly plug away for months on end, generating some viable offspring amongst all the dross. All it needs to do is produce (on average) 1.0001 viable offspring before it succumbs, result happiness. 0.9999 viable offspring, result misery. It’s a very low hurdle…

  32. Allan Miller,

    So you think it both impossible and routine?

    I think outside of space-time it may be designed to very reliably self replicate. Its generation inside of space-time is whats impossible.

  33. colewd:
    Alan Fox,

    Dazz: So much crackpottery in such few words.

    I guess this is why the other guys won’t share new ideas.I guess this is the culture of TSZ.

    New ideas? We all noticed you’re just trying to reformulate the good old “goddidit” nonsense in your own weird way.

  34. colewd,

    I think outside of space-time it may be designed to very reliably self replicate. Its generation inside of space-time is whats impossible.

    Apart from the fundamental incoherence on display, you appear not to agree with what you agreed with – the sentence to which you responded ‘Yep […]’.

  35. DNA_Jock,

    Suppose it has a 1,000 base genome.
    On average, 36% of its replications will be error-free. That’s pretty good…
    OTOH suppose it has a much larger genome, of which 4,000 nucleotides are absolutely essential. Now it faces a tougher battle, since only 1.83% of its replications will correctly reproduce all 4,000 essential nucleotides. It’s bloody inefficient (but not mind-numbingly inefficient). However, if it’s better than its cousins, it will quietly plug away for months on end, generating some viable offspring amongst all the dross. All it needs to do is produce (on average) 1.0001 viable offspring before it succumbs, result happiness. 0.9999 viable offspring, result misery. It’s a very low hurdle…

    In any scenario this looks like rapid extinction to me. DNA repair is a sophisticated design using design concepts that humans only recently developed. If you were, through experiment, to become convinced that it was mission critical for life to be sustainable would that start you thinking that the design inference might have some merit?

  36. Allan Miller,

    Apart from the fundamental incoherence on display, you appear not to agree with what you agreed with – the sentence to which you responded ‘Yep […]’.

    Fundamental incoherence ? Not sure what your point is.

  37. colewd,

    Apart from the fundamental incoherence on display, you appear not to agree with what you agreed with – the sentence to which you responded ‘Yep […]’.

    Let me try to respond. A cell phone is amazingly repeatable at direct dialing people yet it does not spontaneously generate. A cell phone can be designed inside space-time but not on its own.

  38. There is an Improbability Bubble that grows out of a quantum event. Occasionally it invades the macro world and affects molecules, sometimes reaching out and affecting entire houses before collapsing back and leaving the occupants slightly bemused by an unexpected turn of events. Outside it, things happen according to the basic rules of probability. Inside, those rules are suspended. We can’t make or get inside such bubbles – their weirdness can only be encountered if they expand to engulf us. They always collapse back and the outer normality re-establishes itself (from inside the bubble, of course, the outer world looks weird). There is no net change in the overall probability of the universe – when an improbability bubble grows in one place, another elsewhere has someone bemused because something they were absolutely certain of didn’t happen. Thus probabilities continue to add up to 1 – the Law Of Conservation Of Probability.

    ‘Twas in just such a bubble, 3.8 billion years ago, that the first replicator emerged. Buy My Book!

  39. colewd,

    In any scenario this looks like rapid extinction to me.

    The value of the exponent is the vital difference. Anything >1 is not headed for extinction.

  40. Allan Miller,

    <

    t;I should forget this one right off the bat. It is supported by 0% of the available evidence

    There is some evidence that supports this concept.
    -DNA repair
    -DNA replication
    -Protein reacting (changing shape) to outside optical signals

  41. colewd,

    A cell phone is amazingly repeatable at direct dialing people yet it does not spontaneously generate. A cell phone can be designed inside space-time but not on its own.

    You misunderstood. People who think the OoL impossible are also saying that it should keep happening – not that the original lineage should keep replicating, but that new ones should as well, as if the first were not there. They seem immune to the idea that the probability of detection may be a dependent one, to get a bit Bayesian.

  42. colewd,

    There is some evidence that supports this concept.
    -DNA repair
    -DNA replication
    -Protein reacting (changing shape) to outside optical signals

    They support The Improbability Bubble more.

  43. Allan Miller,

    You misunderstood. People who think the OoL impossible are also saying that it should keep happening

    I think the OOL problem is actually the same as the evolution problem. The origin of functional genetic information that indeed does very complex things like cell division, repair, apoptosis, splicing, cell differentiation.

    None of us have a clue how we could generate these sequences from scratch.
    We also know that the sequence space is too large for trial and error.

    The sequences must be generated with the knowledge of how the DNA sequences map to proteins that fold to function.

    If we have a design function with all this knowledge outside space time and the ability to down load then OOL is easy. Multiple OOL is easy. What is hard is OOL without the design function.

  44. Allan Miller:
    There is an Improbability Bubble that grows out of a quantum event. Occasionally it invades the macro world and affects molecules, sometimes reaching out and affecting entire houses before collapsing back and leaving the occupants slightly bemused by an unexpected turn of events. Outside it, things happen according to the basic rules of probability. Inside, those rules are suspended. We can’t make or get inside such bubbles – their weirdness can only be encountered if they expand to engulf us. They always collapse back and the outer normality re-establishes itself (from inside the bubble, of course, the outer world looks weird). There is no net change in the overall probability of the universe – when an improbability bubble grows in one place, another elsewhere has someone bemused because something they were absolutely certain of didn’t happen.Thus probabilities continue to add up to 1 – the Law Of Conservation Of Probability.

    ‘Twas in just such a bubble, 3.8 billion years ago, that the first replicator emerged. Buy My Book!

    Still better than Lost

  45. colewd,

    I think the OOL problem is actually the same as the evolution problem. The origin of functional genetic information that indeed does very complex things like cell division, repair, apoptosis, splicing, cell differentiation.

    Apart from cell division, the rest of your list seems heavily biased towards multicellularity and eukaryotes. So not ‘the same as the evolution problem’ at all.

    None of us have a clue how we could generate these sequences from scratch.

    Indeed. But I tried stepping outside spacetime to try it, and that was even worse. You would not believe what’s out there!

    We also know that the sequence space is too large for trial and error.

    No we don’t.

    The sequences must be generated with the knowledge of how the DNA sequences map to proteins that fold to function.

    Not at all.

    If we have a design function with all this knowledge outside space time and the ability to down load then OOL is easy. Multiple OOL is easy. What is hard is OOL without the design function.

    Can I interest you in my book The Improbability Bubble: What You Thought Was Hard Is Sometimes Easy?

  46. colewd: 100% of the observed evidence of life on earth supports this claim.

    No, the way life that exists now is =/= evidence it could not be simpler.

    Sorry, you don’t understand how evidence works.

  47. Mung: I think you’re jumping to conclusions about what I am arguing. I realize it’s not easy to track who said what and why they said it.

    Fair enough, and you’re right I mistook you for colewd and phoodoo. The fact that we’re all active in like 4 or 5 threads simultaneously doesn’t make it any easier.

  48. colewd:
    colewd,

    Let me try to respond.A cell phone is amazingly repeatable at direct dialing people yet it does not spontaneously generate.A cell phone can be designed inside space-time but not on its own.

    Still with the same dumbfuckery – trying to support his claims on biological life by using analogies to human designed equipment.

  49. Allan Miller,

    Indeed. But I tried stepping outside spacetime to try it, and that was even worse. You would not believe what’s out there!

    Hey Mung. The first serious competition for the humor of the year award 🙂

  50. colewd:
    Allan Miller,

    None of us have a clue how we could generate these sequences from scratch.
    We also know that the sequence space is too large for trial and error.

    Evolution doesn’t have to search the entire sequence space. Each generation only searches in the immediate neighborhood of its existing working form. This process goes all the way back to the very first prebiotic imperfect self-replicators.

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