How Comfortable is Naturalism with Highly Atypical Events?

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. stcordova: Please tell the readers where you and the intelligently designed PCR industry got their polymerases. I seem to recall a Nobel Prize was awarded for the ingenious intelligently designed method of PCR not to mention the polymerases came from pre-existing organisms.

    Who the hell cares that a PCR machine is intelligently designed? Strictly speaking, it isn’t needed.

    Again, all it takes to replicate DNA is a cycling temperature and a single enzyme, DNA polymerase.

    Do temperatures cycle in nature? Yeah, yeah they do.

    How do they manufacture (ugh, you mean as in intelligently create) polymerases or do they extract them from genetically engineered (uhg, as in intelligently designed) God-made living creatures. Or do they take them from God made creatures without any modification.

    All of this is:
    1. Question-begging (the whole God-made shit).
    2. Irrelevant (that DNA-polymerase comes from a pre-existing life-form).

    Your claim was that DNA replication requires lots of fancy molecular machinery. It doesn’t. It just requires cycling temperature and DNA polymerase.

    In any case, you should save your accusations of me not thinking for yourself.

    No, you’re in need of hearing this. STOP MAKING BASIC FALLACIES IN LOGIC.

    The point is what will replicate DNA in a living context not in an intelligently designed purposeful laboratory context like you in a PCR lab experiment.

    The living context you are providing is how life is today, now. Not how it was when life first originated. You don’t know how life was when it first originated, or even how life was when DNA first evolved, which could be signficantly later.

    Again, things are some particular way now =/= they must have always been so and no simpler form is possible or ever existed.

    IT DOESN’T FOLLOW.

    I was talking OOL, not PCR which generates non-living DNA.

    No, you weren’t talking OOL, you were talking life AS IT IS NOW.

    Oh, maybe I need to point out to you, DNA by itself is customarily not thought as a living cell.

    I could not possibly be any less interested in if DNA by itself is thought to be alive or not, I’m interested in CONCEPTS, not LABELS.

    If life originated by “naked” DNA evolving (I don’t believe it did, but for the sake of making a point), then whether some random creationist four thousand million years in the future wants to call that evolving DNA for “life” is completely and utterly irrelevant. Labels don’t decide what can or can’t happen. Labels are for communication, not for dictating what happens, or can happen in reality.

    The issue isn’t replication alone, but replication machine like a living cell and whether emergence of such a machine is far from ordinary expectation.

    No that isn’t the issue at all, that’s what you’re NOW CHANGING the issue to be instead.

    The replication machinery in extant cells (and back in the universal common ancestor) is the product of biological evolution. As in, mutations in the RNA and later DNA-based genomes living replicating cells, filtered by natural selection and genetic drift.

    And neither is the issue merely making replicators, it is the fact the replication machine is extravagant, perhaps more so than absolutely necessary for mere replication.

    Extravagant? How.. interesting! And amazing!

    You misstating the problem.

    No, I’m responding directly to what you wrote, which was that DNA replication required a substantial list of enzymes and complex molecular machines.

    You were wrong.

    You are framing it solely in terms of achieving replication simply

    Yes, because that’s what you directly stated to begin with. And that’s what you’re now trying to make appear is the only possible way for life to exist.

    Of course, you’ve now also deceptively constructed a way out for yourself, by just declaring that some kind of mere DNA replication alone isn’t life.
    Well, if it isn’t, it’s irrelevant, because IF such a system of simple replication (of DNA, or RNA or even something simpler, who knows? Not you) can lead to cellular life as we know it, then whatever you want to call it is completely without consequence.

    whereas I’m pointing out the extravagance of a machine that maybe has more parts that it needs to get the job done — you know, a Rube Goldberg Machine.

    The problem of extravagance bothered Darwin.

    Bla bla it’s so complicted, man is it complicated. Ohh, ahh, it’s so complicated. Also, new fancy word: Rube Goldberg Machine. PRAISE THE LORD! Also Darwin had doubts, was bothered, awoke every night from nightmares about his Soon-to-be-failing(TM) just-a-theory and recanted on his deathbed. Also, he smelled and was an awful person. And Nazi’s and Hitler and Marxism.

    Pictured below is the one component replicator of replication system that really bothered him, so much so it made him sick since it highlighted complexity that should be selected against, not for, and hence was strong evidence against his falsely labeled theory of “natural” selection.

    Who are you writing this nonsense for? It can’t be anyone here, because there’s not a single person on this site who is not aware that Darwin had no idea about DNA or genome-replication. So who are you writing these lies for?

    What the actual flying fuck are you on about?

    Not that you really had a valid point, but if you did find a way to implement a DNA-RNA-protein replication cycle simply, it doesn’t solve why there exists some that are so much more complex and involve more steps then absolutely needed

    Could it be because they had higher fitness? Large parts of the replication machinery in complex life is to ensure high-fidelity replication of large(ish) genomes. High-fidelity replication is known to have higher fitness than low-fidelity replication. It is also known that there’s a slope for selection to climb between the two outermost extremes. Very error-prone replication, in so far as it isn’t so error-prone it is lethal, has lower fitness than ever-so-slightly less error-prone replication and detectably so(by natural selection). And so on. In this particular case, there really provably is selection for better and better replication all the way up the slope.

    (like say a eukaryotic replicator, or a sexually reproducing eukaryotic multicellular animal), since natural selection should select against wasteful inefficiencies that seem to be just there to make Rube Goldberg machines that show off ingenuity of the designer.

    They seem to be that, aye? Cool story bro.

    You really aren’t realizing the problem of OOL

    YOU aren’t realizing the problem of the OOL, because you’re assuming life originated with something at least as complex as any contemporary bacterium.

    and supposed subsequent evolution of biological complexity is the problem of God-made extravagant DNA replicators like a Peacock/Peafowl, not your relatively trivial (by comparison) man-made and intelligently designed PCR amplifications.

    Halleluja the LAWD is so great compared to us puny, unworthy humans. Particularly Darwin, that old fart.

    Pictured below is one part of that DNA replicator that made Darwin sick.

    He also traveled to the Galapagos for bestiality and sex-tourism. He longed for the emission of warm horse-semen on his satanic beard. Or something. I should note here, a creationist actually wrote this to me once when he got mad. Apparently thinking I had some sort of emotional connection to a man that lived one and a half century before my own birth. What an idiot.

    Look, Sal. This Darwin-bashing stuff, I really don’t care. I know you people have your authorities and your God that must be worshipped and defended from all criticism or doubt. It’s not like that on my side of the fence, so if you’re trying to somehow work me up or insult me by piling shit on Darwin you’re wasting your time. I’m not saying it because I want you to stop, by all means keep it up, I could ask for no better an advocate for my position than having yours defended by infantile lies and insults. I’m just saying.. you could use your time better than this.

  2. colewd:
    Kantian Naturalist,

    KN:If I showed you 6 objects.3 were the product of human design and 3 were not, do you think you could pick the 3 that were the product of human design out?Would it always be the three most complex?

    Probably, and no, respectively.

    The products of human design are specified to the needs and interests of human beings. Since I have a good deal of background knowledge about what human beings are like, I think it’s likely that I could figure out which ones are most likely human artifacts.

    What the IDist always wants to do here is say, “sure, but organisms are even more complex that artifacts, so they were probably designed by something even more intelligent than we are!”

    To which the response has always been, “sure, maybe — that’s a hypothesis worth investigating. How do you propose to investigate it?”

    And to that the IDist response is always one of the following:

    “We don’t need to do any empirical science — look, we have calculations of probability, and that’s almost like science, right?”

    or

    “We really want to do the empirical science, but we can’t because that conspiracy of Darwinists always getting in the way!”

    or

    “We’ve done the science, and it’s been published in our journal that we set up ourselves and pay for ourselves!”

  3. FierceRoller:

    I have never heard that argument, and I am trying to distinguish whether it is something that an evolutionary biologist has actually said or a strawman.

    So would you be willing to say, “evolution of animal multicellularity isn’t terribly extraordinary”. So now I can quote a real evolutionary biologist as saying so. Or you could say, “evolution of animal multicelluarity is terribly extraordinary”. Or you could say what you really think, and I’ll quote you.

    That said:

    At least in developmental terms, the transition from uni- to multicellular organization may be easy.

    Thus, the transition to multicellularity is relatively easy—a minor major transition.

    Finally, we turn to the question posed by Szathm´ary &Wolpert (2003, p. 301):

    Is then the evolutionary transition to multicellularity a difficult one or not? The blunt answer is: not at all, since multicellularity has arisen more than twenty times in evolution

    http://www-eve.ucdavis.edu/grosberg/Grosberg%20pdf%20papers/2007%20Grosberg%20&%20Strathmann.AREES.pdf

    Do you think my “evolution of animal multicellularity isn’t terribly extraordinary” is too much of an over-interpretation of such sentiments?

    But gee, talk about circular reasoning! The reasoning is “It’s easy (aka not out of the ordinary event) since it happens so often.” So if miracles that violate mathematical expectation happen frequently, they are natural. Doesn’t matter if the miracles don’t align with natural mathematical expectation.

    But anyway, would you feel better if I used those words verbatim:

    Is then the evolutionary transition to multicellularity a difficult one or not? The blunt answer is: not at all, since multicellularity has arisen more than twenty times in evolution

    So how do you know it evolved? Uh, some phylogenetic comparison I guess. So how do you know it was easy? Because it evolved. Since it evolved the transition was easy, not hard. Goodness, that’s not too far from what I said:

    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.

    But since you don’t like my choice of words, I’ll use and honest-to-Darwin evolutionary biologists words in the future. Besides, the real thing says it better than my second-hand characterization:

    Is then the evolutionary transition to multicellularity a difficult one or not? The blunt answer is: not at all, since multicellularity has arisen more than twenty times in evolution

    NOTE:
    Btw, I saw this guy in person at the 2013 international creation conference, Erik Hanchen who studies evolution of multicellularity. He was laughed of the stage when he said something to the effect “I’m not here to talk about science.”

    https://www.researchgate.net/profile/Erik_Hanschen

    He authored this study and says RB proteins are the driving force of multicellularity:
    https://www.sciencedaily.com/releases/2016/05/160505105021.htm

  4. Hey Sal, I was wondering, do you teach online courses in creationist quote-mining? I think I’ve run into one of your pupils a couple of times. He’s so dead-set on cherry-picking quotes from the scientific literature, at one point he was referencing the RNA-world-paper:
    The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others).
    but he had cut out the last part of the paper’s title, so it just read
    “The RNA World-hypothesis: the worst theory for the early evolution of life”.

    Hilarious!

    Then he had deceptively lifted out the “list” of common objections to the RNA world found in the abstract:
    (i) RNA is too complex a molecule to have arisen prebiotically;
    (ii) RNA is inherently unstable;
    (iii) catalysis is a relatively rare property of long RNA sequences only; and
    (iv) the catalytic repertoire of RNA is too limited.
    .. and basically this was what amounted to his “argument” against the RNA-world hypothesis, together with a couple of really old quotes from Leslie Orgel and Bob Shapiro talking about the conflict between the formose-reaction and formation of the glycosidic-bond, in the 1970’s.

    You taught him to do this shit, didnt’ you? It smelled too familiar.

  5. Rumraket:

    1. Question-begging (the whole God-made shit).
    2. Irrelevant (that DNA-polymerase comes from a pre-existing life-form).

    Uh, you mean that the DNA-polymerase that you (a living creature) use to replicate DNA comes from a creature that has all those fancy-schmancy things that I diagramed? So in effect you (who has all those fancy-shmancy DNA replication systems) use a polymerase that is extracted from a fancy-schmancy organism, to argue that you don’t need a fancy-shmancy system to replicate DNA.

    Don’t you see you’ve sort of left out some important details of what actually causes your PCR experiment to work, namely you had to use the product of something that would likely not be there if there was not a living organism with all those fancy-shmancy systems to replicate DNA, and not only that, code a protein called a Polymerase.

    You can’t conduct the PCR experiment unless you have a living creature from which you can harvest the necessary ingredients like pfu or Taq polymerases from thermophillic archea or bacteria or genetically engineered organisms.

    Your claim was that DNA replication requires lots of fancy molecular machinery.

    In existing cells it does. But you’re PCR illustration does too, you just don’t realize it since you failed to consider where you got those polymerases that allow you to conduct your PCR amplifications in the first place. Kind of not very meticulous on your part.

    Depicted below is an example of a pfu Polymerase such as used by humans to conduct PCR amplifications which you says don’t need complex machinery. The problem is this polymerase has to be synthesized by living organisms or by intelligently designed, genetically engineered living organisms. For example this describes a little part of the procedure:
    http://barricklab.org/twiki/bin/view/Lab/ProtocolsReagentsPhusion

    The pfu Polymerase has over 760 amino acids according to the Uniprot database. Biologists say polymerases are highly “conserved”, thus one might argue a lot of those amino acids are pretty important for function, thus they would not easily form by random assembly in a pre-biotic chemical mixture.

  6. stcordova,

    Biologists say polymerases are highly “conserved”, thus one might argue a lot of those amino acids are pretty important for function, thus they would not easily form by random assembly in a pre-biotic chemical mixture.

    I think ‘proteins-first’ is indeed a non-starter. But still, conservation is not a reliable guide to the bitwise necessity of every acid for primitive function. There are many things pinning a peptide structure in place beyond catalysis and optimal reaction kinetics. All one can really deduce from widespread conservation is that the modern structure had been significantly fixed by LUCA’s time, with most amendments since being selectively ‘downhill’.

  7. stcordova,

    Thanks (sincerely) for allowing contrary views here.

    …since multicellularity has arisen more than twenty times in evolution

    is a different argument from

    …because animals and single-celled creatures share some similar DNA.

    Yes, your strawman draws the same conclusion as Grosberg (multicellularity is not difficult to evolve), but for completely different reasons. (I say strawman provisionally, since I don’t think you’ve yet given an example of an evolutionary biologist saying that multicellularity is easy because animals and unicells share some similar DNA)

    …would you feel better if I used those words verbatim?

    It’s your blog, and I’m a guest here; I don’t get to tell you what to write. But since you asked, I would feel better if you used those words or another fair characterization of your opponents’ arguments.

  8. FierceRoller,

    It’s your blog, and I’m a guest here; […].

    It’s actually Elizabeth Liddle’s site – most members can author an OP, including Sal.

  9. FierceRoller: It’s your blog, and I’m a guest here;

    The site owner is Dr Elizabeth Liddle. She set up TSZ to enable and encourage communication across wide differences of view. You can get more of an idea from the Rules page. We invite contributions from all members who have a valid point to make.

  10. stcordova,

    Do you think my “evolution of animal multicellularity isn’t terribly extraordinary” is too much of an over-interpretation of such sentiments?

    Not at all; that is a totally fair summary of Grosberg’s conclusion. But the reason he gives

    …since multicellularity has arisen more than twenty times in evolution.

    is not the reason you gave:

    …because animals and single-celled creatures share some similar DNA.

    They are completely different arguments. So if it’s Grosberg you had in mind, I think it’s fair to say that you have mischaracterized his argument.

  11. stcordova: Uh, you mean that the DNA-polymerase that you (a living creature) use to replicate DNA comes from a creature that has all those fancy-schmancy things that I diagramed? So in effect you (who has all those fancy-shmancy DNA replication systems) use a polymerase that is extracted from a fancy-schmancy organism, to argue that you don’t need a fancy-shmancy system to replicate DNA.

    And I’m right, since the polymerase and the cycling temperatures alone do the job just fine.

    Don’t you see you’ve sort of left out some important details of what actually causes your PCR experiment to work

    No, they don’t cause the PCR to work. They’re the source of the polymerases we use, that doesn’t mean they’re “causing PCR to work”. Complete gibberish.

    The fact that that is how we got them =/= they cause PCR to work.

    Once again, it doesn’t follow.

    namely you had to use the product of something that would likely not be there if there was not a living organism with all those fancy-shmancy systems to replicate DNA, and not only that, code a protein called a Polymerase.

    I don’t deny that DNA-polymerase is itself a complex molecule and wouldn’t just pop out of nowhere as if by magic. Well, fuck me, that’s what you believe.

    But just because how we get polymerases now is from extant life, doesn’t mean there was not a simpler form of life without all the additional replication machinery, and it also doesn’t mean we can conclude that DNA-polymerase itself could not have, or did not, evolve.

    It doesn’t follow.

    Depicted below is an example of a pfu Polymerase such as used by humans to conduct PCR amplifications which you says don’t need complex machinery.

    Which would be absolutely correct. PCR amplifications don’t need all that other shit from your list to replicate DNA.

    The problem is this polymerase has to be synthesized by living organisms or by intelligently designed, genetically engineered living organisms.

    As above, again, the fact that that is how we get them does not mean they couldn’t evolve, or that DNA replication requires anything other than DNA-polymerase and cycling temperatures.

    There doesn’t need to be a factory next door, continously producing DNA-polymerases, for PCR to work.

    It’s basically like a person asking what it takes to tighten a bolt, and upon hearing someone answer “a wrench” you immediately start blathering about factories that make tools, and also you need the metals for the tools, so you need to mine ores, and to mine ores you need mining equipment, and to process and refine the ores also takes place in factories with more tools and knowledge and intelligent design, and people to operate the equipment, and people require food and sleep and bla bla bla. Talk about a complete red herring.

    The question addressed was what it takes to replicate DNA, just like what it takes to tighten or loosen a bolt. Not “how did everything come to exist?”.

    The pfu Polymerase has over 760 amino acids according to the Uniprot database. Biologists say polymerases are highly “conserved”, thus one might argue a lot of those amino acids are pretty important for function, thus they would not easily form by random assembly in a pre-biotic chemical mixture.

    And I’d be the first to agree with all of that and on that basis conclude that life highly probably didn’t start by a process involving anything like proteins spontaneously coalescing from random mixtures of amino acids.

  12. FierceRoller:

    that is a totally fair summary of Grosberg’s conclusion.

    Thank you. 🙂

    But the reason he gives

    …since multicellularity has arisen more than twenty times in evolution.

    is not the reason you gave:

    …because animals and single-celled creatures share some similar DNA.

    They are completely different arguments. So if it’s Grosberg you had in mind, I think it’s fair to say that you have mischaracterized his argument.

    I don’t think so. How does he know they evolved? Single celled-creatures have a different morphology than multicellular animals. I presume if they don’t have the same morphology, the next recourse is DNA similarity to “prove” common descent. So I don’t think I’m off the mark. I would be off the mark if I said, “morphology” rather than “DNA”.

  13. Kantian Naturalist,

    nd to that the IDist response is always one of the following:

    “We don’t need to do any empirical science — look, we have calculations of probability, and that’s almost like science, right?”

    or

    “We really want to do the empirical science, but we can’t because that conspiracy of Darwinists always getting in the way!”

    or

    “We’ve done the science, and it’s been published in our journal that we set up ourselves and pay for ourselves!”

    Thank you for your response. I think we are basically on the same page here. Design is an interesting observation but lacks meat on the bone at this point. Also, thank you for your continuing interesting posts on philosophy. I have learned a lot from your comments.

  14. Rumraket:

    The video explains what enzymes are used for chromosomal replication during meiosis, this is not the same as saying all of these enzymes are strictly necessary for any and all DNA replication and-must-have-been-present-since-the-origin-of-life. We know that they aren’t, otherwise PCR would not be possible.

    As I pointed out PCR (as in POLYMERASE chain reaction) is possible because polymerases from living creatures, not random chemicals from failed OOL experiments.

    So the irony is that your claim that you can do PCR amplification without all that machinery sort of illegitimately compartmentalizes and hides the fact you were relying on living creatures for the key ingredient in your PCR amplification, namely, the polymerase enzyme. That polymerase enzyme wouldn’t be in your lab if all those other enzymes I talked about in DNA replication weren’t doing their job.

    Your comment reminds me of the girl who complained “why do people have to kill animals for meat, why don’t they get their meat from the grocery store?” Why do we have to get polymerases from living things, why don’t we get it from bio-online instead? 🙄

    The video explains what enzymes are used for chromosomal replication during meiosis, this is not the same as saying all of these enzymes are strictly necessary for any and all DNA replication

    Ahem, I said this:

    DNA replication doesn’t have to happen exactly with these enzymes any more than there is only one way to implement a lock-and-key system in the world of man-made affairs. But a such a replication machines made of proteins are still far from natural expectation from random sequences of amino acids.

    How Comfortable is Naturalism with Highly Atypical Events?

    So you apparently disregarded what I said and then accused me of imply the opposite. Not a good show on your part.

    No that isn’t the issue at all, that’s what you’re NOW CHANGING the issue to be instead.

    No I’m not. Before you went on your tirade I explicitly said:

    DNA replication doesn’t have to happen exactly with these enzymes any more than there is only one way to implement a lock-and-key system in the world of man-made affairs. But a such a replication machines made of proteins are still far from natural expectation from random sequences of amino acids.

    DNA replication doesn’t have to happen exactly with these enzymes

    I said that, you ignored it and went on your tirade. Do you like shouting down things I didn’t say?

    I also said (before you last few tirades):

    The calculation of odds of OOL of some life (not one specific life) is about calculating the deviation from natural expectation of coordinated events or parts.

    At issue is how far from natural expectation the origin of life is. The issue is not about how probable a replicator is. Salt crystals “replicate”. The issue is why should something as coordinated as the living cells on Earth emerge. It’s not something that should be expected anymore than an airplane (doesn’t have to be a 747) to emerge from a junkyard when a tornado hits it.

    How Comfortable is Naturalism with Highly Atypical Events?

    Again I’ll repeat it since you seem to miss it: “The calculation of odds of OOL of some life (not one specific life) ”

    So we have extant life. How did that originate? It’s not very helpful to define OOL in terms of origin of life we have zero data on (like hypothetical RNA world creatures, or proteins first creatures, or metabolism first creatures, etc.) and which we already know won’t work.

    From the OOL researchers themselves in 2014:

    Proposed Open Questions in OQOL2014
    The following is the 15 open questions for your vote.

    01. How can we make ordered sequences of amino acids, or mononucleotides by prebiotic means?

    This question is in fact never asked in the modern research on the origin of life. Do you agree then that we do not know how to make macromolecular sequences in many identical copies under prebiotic conditions? Do we have to wait for this orderly sequence until the genetic code has been developed?

    02. Why is the origin of life still a mystery?
    Premise: Why is the origin of life still a mystery? The turning point nonlife-life has never been put into one experimental set up-actually it has never be clarified from a conceptual point of view either. There are of course several hypotheses, and this plethora of ideas means already that WE DO NOT HAVE A CONVINCING ONE! The most popular is with the RNA-world prebiotic scenario, which has the advantage of providing on paper a theoretical series of IMAGINARY events, each however with an UNINAMIGINABLY SMALL PROBABILITY (be the prebiotic production of a self-replicating RNA, and its eventual transformation into a catalyst for DNA and independently for protein synthesis)

    Why should this happen, and what about the genetic code? Aside from the problem of experimental implementation, don’t you think we lack (until now) the capability of intellectually conceiving how the turning point really happened?

    03. Is the molecular crowding critical for the beginning of life?
    Quite a dense concentration of macromolecules in cells: Is it an essential condition for origin of life? If so, how was the concentration acquired before the origin of life? Or, was it a result of the evolutionary process?

    04. Can Artificial Life or Synthetic Biology contribute to the origin of life?
    Artificial life deals with life as it might have been. UP UNTIL NOW THESE EFFORTS HAVE NOT BEEN VERY SUCCESSFUL, and IT ALMOST APPEARS THAT THERE ARE NO FORMS OF LIFE SIMPLER THAN “OUR” LIFE.

    Do you have any data that imply alternative forms of life (still within the general category of metabolism + self-reproduction + evolvability) with molecules different from the biological ones? Or, do you think that synthetic biology research can provide a model or theory for the origin of life study?

    05. Can catalysts come out from the free ticket of thermodynamics?

    06. Can we construct real RNA world and RNA-based biological systems in a test tube?
    At the early stage of RNA world, RNA molecules should have no functional property. What physical or chemical process mediates the selection of specific RNA? Even when functional RNA enzymes are generated, it still remains a challenge to construct sustained self-replication and metabolic system in which multiple RNA molecules function cooperatively. Once we can construct the precursor of a replication system by a set of RNA molecules, is it possible to emulate another path of evolution in a test tube?

    07. What is the origin of genetic code?: Investigating DESIGN PRINCIPLE of aa-tRNA and aa-RS?
    The genetic code is most essential part for the genetic systems. In the context of the origin of life, a major issue on the genetic code is to understand how the materials relevant to genetic code that can translate the sequence of four bases into a polypeptide. … Can we find or design simple aa-RS and aa-tRNA from the cocktail of molecules (e.g., amino acid, tRNA(-like) molecule, and ATP), which might be relevant to the origin of translation and genetic code? What features are required as a mechanism that ensures robust translation?
    08. Prior to genetic code: Is the notion of prebiotic cells conceivable?
    The simplest cells on our Earth contain at least 500–600 genes, and more generally several thousand. This observation elicits the question, whether this high complexity is really necessary for the simplest form of cellular life, also in view of the fact that early cells in the origin of life and evolution could not have been as complex as modern cells…. Do you think it is possible to construct in the laboratory, models of early cells, displaying a kind of primitive cellular life (self-maintenance + self-reproduction + evolvability), based on a number of genes which is one order of magnitude smaller than the present day simplest cells. Say a living cell with 30–40 genes?

    [I’d like to know how they can come up with even one gene!]

    09. What is the list of prebiotic molecules present in primodal cells?
    The “free ticket” of thermodynamic control is however not sufficient: if a chemist is given all these compounds in any amount he wishes, he would be unable to make life. For making life, one needs a series of additional reactions and products under kinetic control – enzymes and nucleic acids are not with us because they are the most stable chains. Thus, the origin of life can be traced back to the origin of kinetic control. Do you agree with this statement; and how would you envisage the prebiotic evolutionary bridge between thermodynamic and kinetic control?
    10. On Contingency vs. Determinism
    The proteins (or nucleic acids) existing on our Earth correspond to an infinitesimal part of the theoretically possible sequences – the ratio between possible and existing structures corresponds more or less to the ratio between the space of the universe and the space occupied by one hydrogen atom. The above ratio can be interpreted as an indication that our “few” proteins have not been selected primarily because of distinctive properties (such as thermodynamic or thermal stability, solubility, particular kinetic processes of formation etc…) – but rather due to a most significant contribution of the vagaries of contingency.
    Do you agree with this statement, and with its corollary, that then life on our Earth, which is based on these “few” proteins, is not an obligatory pathway, but is largely based on contingency?

    11. How to Make Prebiotically Long Hetero-Peptides or Hetero-Nucleotides?
    There are no or rather scanty reports in the literature on how to make under prebiotic conditions long – say 30 residues – specific sequences of co-oligopolypeptides (or polynucleotides) in many identical copies containing say five to six different amino acid residues or three to four bases (the Merrifield method cannot be considered a prebiotic method)… Do you agree then that we do not know – neither conceptually nor experimentally – how to make macromolecular sequences in many identical copies under prebiotic conditions? And if it so, would you not conclude that the bottom-up (sentence ends abruptly)

    12. On the origin of catalytic cycles
    The question. How do you envisage the origin of sequentially catalytized reactions in a prebiotic scenario? And can you provide facts or scientific arguments, not simply beliefs, about this critical point?

    13. Life as unity or confederacy

    14. Universality – What properties of life are universal?

    15. What is the physical mechanisms underlying the assembly of primitive cell-like structures?

    http://www.lifephys.dis.titech.ac.jp/oq … age_id=180

  15. An alternate link to the 2014 OOL conference:

    http://www.takinoue-lab.jp/oqol2014/proposed-open-questions-in-oqol2014/

    Note these words:

    13. Life as unity or confederacy

    ….For instance, one could take separately the appearance of self-reproducing systems and the formation of vesicles, biogenesis of proteins different from setting up metabolic cycles, origin of reductive power different from prebiotic chemistry, etc The degree of both contingency and of what some have called “irreducible complexity” in life will depend strongly on how tightly or loosely its subsystems are coupled.

    I like “irreducible complexity” being mentioned at an OOL conference. I salute their consideration of this issue.

  16. stcordova:

    I like “irreducible complexity”being mentioned at an OOL conference.I salute their consideration of this issue.

    Psst…hey Sal…science has worked out how “irreducibly complex” features can evolve through completely natural processes. Of course as an ID-Creationists you’ll never be honest enough to admit it.

  17. stcordova,

    What does

    …animals and single-celled creatures share some similar DNA

    imply about how many times multicellularity has evolved? What does it say about land plants, ulvophyte green algae, volvocine green algae, red algae, brown algae, fungi, cellular slime molds, cyanobacteria, Myxobacteria, Sorogena, Zoothamnium, or any of the other dozen or so known multicellular groups? Most of these were thought to be independent transitions to multicellular life long before DNA sequence data were available.
    The argument that animals and unicells sharing some DNA implies that the evolution of multicellularity is easy is daft. It sounds like it was intentionally constructed to sound ridiculous. That’s why I asked if any evolutionary biologist had ever actually said it. You’ve given no example of anyone actually making that argument, so for the time being I’m going to (provisionally) conclude that it is a strawman.

  18. stcordova,

    It does not take yet another massive copy-paste dump to support the contention that there are numerous unsolved problems in OoL research. We know.

  19. stcordova,

    So the irony is that your claim that you can do PCR amplification without all that machinery sort of illegitimately compartmentalizes and hides the fact you were relying on living creatures for the key ingredient in your PCR amplification, namely, the polymerase enzyme. That polymerase enzyme wouldn’t be in your lab if all those other enzymes I talked about in DNA replication weren’t doing their job.

    This is a rather feeble dodge. You gave a long list of enzymes that you claim are essential for DNA replication, and many a pretty picture to show how complicated they all are in modern cells.

    In fact there is only one: polymerase. The fact that this is manufactured in cells that have all the others is really not an effective defence of your initial contention.

  20. stcordova: So we have extant life. How did that originate?

    Will you ever get bored of saying how life did not originate and finally get onto how it did?

  21. Kantian Naturalist: I don’t expect any of the creationists who come here will understand the very simple point I’m making.

    More to the point would be to get them to understand your probability calculations.

    Post your numbers.

  22. Richardthughes: Bonus content

    Isn’t it miraculous how we can describe the order in which something is constructed? Before you know it people will be building entire houses!

  23. FierceRoller: I am an evolutionary biologist who studies the evolution of multicellularity.

    I study the evolution of sort-of-multicellular / sort-of-not-multicellular. I believe that the original forms of life we in this category of sort-of-multicellular / sort-of-not-multicellular and from them evolved our not-multicellular life forms and our multicellular life forms.

    The group I am in have made great progress in coming up with imaginary genomes for these ancestral sort-of-multicellular / sort-of-not-multicellular organisms and hope our model of evolution from them will be acceptable to both evolutionists and de-evolutionists.

    sort-of-multicellular -> sort-of-not-multicellular -> not multicellular

    sort-of-not-multicellular -> sort-of-multicellular -> multicellular

  24. Allan Miller: On a world teeming with bacteria, it is far less likely that a poor replicator will get very far before being consumed or out-competed, when compared to a sterile world.

    I can’t be the only one here who would love to see your calculations. Have they been published? Peer reviewed?

  25. Richardthughes,

    More quick thoughts.

    Create a population of numbers 1,2,3…99,100.
    Randomly select a pair and pick a winner – odds of wing = your number : opponents number.
    Discard loser
    Return winner to the pile
    Repeat until only 1 number is left.

    Let me know your observations on 1000 runs of this (min, max, mean, stdev, etc)

  26. Rumraket: The living context you are providing is how life is today, now. Not how it was when life first originated. You don’t know how life was when it first originated, or even how life was when DNA first evolved, which could be signficantly later.

    You don’t know how life was when it first originated either, or even how life was when [if] DNA first evolved, which could [or could not] be signficantly later. You just don’t know.

    The living context you are providing is how life is today, now. Not how it was when life first originated.

    So? Do you have an argument that doesn’t boil down to an argument from ignorance?

  27. stcordova: Kind of not very meticulous on your part.

    You see Rumraket, even if humans could engineer an artificial enzyme that would copy DNA it would mean you need humans to copy DNA!

    Oh, and DNA. Some DNA would be good too.

    😉

  28. Richardthughes: Randomly select a pair and pick a winner – odds of wing = your number : opponents number.

    In English or pseudocode please. How do you decide which number is the winner and which is the loser?

  29. So to answer the original question, naturalism is perfectly fine with miracles as long as they are natural miracles.

  30. Mung,

    The living context you are providing is how life is today, now. Not how it was when life first originated.

    So? Do you have an argument that doesn’t boil down to an argument from ignorance?

    This is a good point. I think Venter’s experiments are confirming that life may never have been much simpler than what we see today in prokaryotic cells.

  31. Mung:
    So to answer the original question, naturalism is perfectly fine with miracles as long as they are natural miracles.

    How do you know that?

    And…while you’re at it, define “miracle.”

  32. colewd:
    Mung,

    This is a good point.I think Venter’s experiments are confirming that life may never have been much simpler than what we see today in prokaryotic cells.

    Why do you think that?

  33. colewd:
    Pedant,

    When Craig reduces genes much below 500 the bacteria dies.

    Why do you think the first life 3.8 billion years ago was as complex as now and needed the same extant genes (and proteins) organisms today use? That almost certainly is not the case.

  34. Pedant: What???

    You’ll have to do better than that, or you’re off my radar.

    He’s talking about Craig Venter and the minimal genome experiments he did, seeing what the smallest number of genes required by an extant organism could be.

  35. Mung: In English or pseudocode please. How do you decide which number is the winner and which is the loser?

    Cool!

    Let’s say 34 gets drawn vs 90

    There are 34+90 ‘outcome points’ (124)

    34 wins 34/124 of the time and 90 wins 90/124 of the time. This resolves to two percentage chances that add to 100%, which can be tested vs a RND call (if one passes the other fails, obviously).

  36. Mung,

    I can’t be the only one here who would love to see your calculations. Have they been published? Peer reviewed?

    You think I actually need to calculate that? Isn’t it obvious?

  37. colewd,

    I think Venter’s experiments are confirming that life may never have been much simpler than what we see today in prokaryotic cells.

    Creationist bingo! I’ve got the flagellum, 20^500 chances of a protein in the ‘Hoyle-o-matic’, and you can’t dismember it so it could never have been put together. I’ll take the enormous stuffed bear, ta.

  38. colewd: When Craig reduces genes much below 500 the bacteria dies.

    It no longer has the capacity to keep functioning, due to it’s constituents not having the requisite properties to allow continued growth and division.

    To pick out an example, if you leave it with a phospholipid cell-membrane and remove the genes for membrane-embedded transport proteins, it can no longer transport essential nutrients across the membrane and will quickly run out of fuel and die. That’s because phospholipid membranes are almost completely sealed off.

    But if the membrane was not made of phospholipids, but instead of simpler fatty acids, it would be semipermeable to small molecules, and so the sophisticated transport apperatus would not be strictly required.

    And there’s an intermediate stage between the two extremes of a 100% fatty acid membrane and a 100% phospholipid membrane. A mix of fatty acids and phospholipids will produce a less permeable membrane than one of 100% fatty acids. Which basically means there’s a selective pressure along the way to generate membrane transporter proteins, as the membrane permeability decreases the selection coefficient for transport capacity of membrane-soluble proteins increases.

    All Craig Venter is showing is that the components of life today are adapted to each other. Not that simpler forms of life aren’t possible.

    You keep making the mistake of thinking that simpler life means life made of exactly the same components as today, but just fewer of them. Them components themselves have changed over the history of life too and the nature of the membrane lipids is an example of this. As you go back and start removing components of cells, you also need to understand that there were ancestral versions of the remaining ones that functioned in different ways.
    The amino acid compositions of proteins were different, many of the enzymes catalyzed different reactions, the environments where the organism lived were different (had less or no oxygen, for example, or the temperature was much higher and so on and so forth).

    You can’t just remove parts and think what remains will work, without altering the remaining parts to compensate for the changes and consider what kinds of environments those altered components functioned in.

    We have concrete examples where we know the ancestral functions of extant systems and that they functioned differently. Particularly for enzymes, many of the ancestors are less efficient, but promiscous catalysts. They got duplicated and the individual copies were free to adapt towards more specific tasks. Today, if you remove one or both of the copies and it turns out to be an essential metabolic enzyme, your cell will die and you will conclude cellular can’t exist without that particular enzyme. But actually, in the past, there was a single enzyme that could do the job of both. It was not as efficient, but it worked. This is an example of ancestral simplicity you’d mistakenly think the modern form of could not be reduced to.

  39. An adult human can’t live without at least a trillion cells remaining alive.

    Therefore, I am assured that humans don’t exist with less than a trillion live cells. Humans composed of just a few cells, let alone just one, are clearly a materialist myth.

    Glen Davidson

  40. colewd:

    I think Venter’s experiments are confirming that life may never have been much simpler than what we see today in prokaryotic cells.

    And there are also conceptual mathematical considerations. The difficulty is not building a replicator, but a self-replicator that reads from a template or blueprint — that is known as the von-neuman self-replicating automaton.

    None of them are simple, and even what little ones we’ve built are not really 3D replication machines that can work with chemical environments. This is like building a 3D-printer that can print itself. Not so trivial!

    https://en.wikipedia.org/wiki/Von_Neumann_universal_constructor

Leave a Reply