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JAD on “Self-Replicating Machines and OoL”

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Here at UD, we often have commenters whose remarks are well worth headlining. Here, we have JAD in action, suggesting to GP: “Here is something you might consider as a seed for a future topic for a future OP.” Yup, and even as an embryonic thought, it is well worth posting — a first, rough draft on a big topic:

>>The origin of life is like the origin of the universe. It appears to be a singular, non-repeating, highly improbable event which occurred very early in earth’s history. Furthermore, all the clues of how and why it occurred have been lost. But then added to that problem are other problems: how does chemistry create code? What is required to create an autonomously self-replicating system which has the possibility of evolving into something more complex? The naturalist/ materialist then compounds the problem by demanding a priori that the origin of life must be completely natural– undirected without an intelligent plan or purpose.

That seems like it was a miracle… Well, maybe it was. But a completely “naturalistic miracle” seems to be an absurd self-defeating claim for the naturalist/materialist to make.

One of my pipe dreams as a real life (now retired) machine designer is to design a self-replicating machine or automata– the kind that was first envisioned by mathematician John von Neumann. My vision is not a machine that could replicate itself from already existing parts but a machine– well actually machines– which could replicate themselves from raw material they would find on a rocky planet in some distant star system. [–> this brings in the metabolising side, to join the self-replication facility]

One practical advantage of such machines is they could be sent out in advance some far-in-the-distant-future expedition to terraform a suitable planet in another star system preparing it for colonist who might arrive centuries or millennia later.

By analogy, that is what the first living cells which originated on the early earth had to do.

A view of the minimal requisites of biological self-replication

Even the simplest prokaryote cell is on the sub-cellular level a collection of machines networked together to replicate the whole system. To suggest that somehow the first cell emerged by some fortuitous accident is betray an ignorance how really complex primitive cells are.

Try thinking this through on a more macro level, as I have described above, and I think you will begin to appreciate how really daunting the problem is.>>

Several comments later, GP responds, and so we clip again:

>> . . . My personal view is that there is no difference between OOL and evolution, in essence. Both problems are about the origin of complex functional information in a non design system. Which is impossible. Therefore, both problems lead to a strong, unavoidable design inference.

The idea that self replication can help solve the problem of the origin of new complex functional information is simply wrong.

Self- replication just implies as assumption the existence of some complex functional information, the information which implements self-replication. In that scenario, the existing information may undergo simple modifications, and computation systems already present in the system (for example, NS) can derive some new information from what already exists. But that computation (which is nothing else than well known microevolution) is extremely limited, because it can only:

a) Generate very low levels of new functional information, because of the extreme limitations in the variation component

b) Compute that low information only as regards the already defined function (replication), and not for any other new function

I have discussed in detail these aspects in two specific OPs:

What are the limits of Natural Selection? An interesting open discussion with Gordon Davisson

https://uncommondescent.com/intelligent-design/what-are-the-limits-of-natural-selection-an-interesting-open-discussion-with-gordon-davisson/

and:

What are the limits of Random Variation? A simple evaluation of the probabilistic resources of our biological world

https://uncommondescent.com/intelligent-design/what-are-the-limits-of-random-variation-a-simple-evaluation-of-the-probabilistic-resources-of-our-biological-world/

That’s why I see no reall difference between OOL and evolution: the transition from prokaryotes to eukaryotes, for example, is as impossible as OOL in a non design setting.

The same could be said for the Cambriam explosion, of for the transition to vertebrates.

In the ultimate sense, each new complex and functional protein which arises in the course of natural history is as impossible as OOL, in a non design scenario.

Moreover, my firm conviction is that life originated on our planet with LUCA, and that LUCA was essentially a full fledged prokaryote.

So OK, I can agree that OOL presents some very special difficulties, but believe me, all that happens after that presents very special difficulties too! 🙂>>

JAD continues, responding to GP:

>>I don’t have time to respond to all the points you raised but let me key on a couple.

You wrote:

Self- replication just implies as assumption the existence of some complex functional information, the information which implements self-replication. In that scenario, the existing information may undergo simple modifications, and computation systems already present in the system (for example, NS) can derive some new information from what already exists. But that computation (which is nothing else than well known microevolution) is extremely limited, because it can only:

a) Generate very low levels of new functional information, because of the extreme limitations in the variation component

b) Compute that low information only as regards the already defined function (replication), and not for any other new function

The very fact of self-replication raises the question of what I call “evolvability.” Is self-replication alone sufficient for a simple cell to evolve into something more complex? For example, is the ability of a smallest known prokaryote, Mycoplasma genitalium, to replicate, sufficient for it to eventually evolve into a eukaryote? (A lot of Darwinists without proof or evidence would “argue” yes.) Do all eukaryotes have the potential of evolving into multicellular life forms? What is it that gives them that potential? And of course, from there follow the questions about higher life forms… specialization and diversification of not only organisms but the specialized cellular architecture and organs within distinct organisms. In other words, if they evolved what are the sufficient conditions for them to evolve? Can evolution, as the naturalist/ materialist believe, occur without evolution itself being designed?

Moreover, my firm conviction is that life originated on our planet with LUCA, and that LUCA was essentially a full fledged prokaryote.

Why? Even Darwin was open to the suggestion that the origin of life could be polyphyletic.

From a design perspective a polyphyletic explanation for OoL makes a lot of sense. Let me give you a couple of examples:

First, suppose a super advanced race of ETI beings visited the earth some 3.7 billion years ago and decided to seed it with life. Would they seed it with a single simple prokaryotic life form or would the seed it with a cocktail of microorganisms. Statistically one isolated organism wouldn’t have much chance of surviving.

Or second, does it necessarily follow that a transcendent creator (God), if that’s that’s the cause, would be required to start with a single simple microbe?>>

GP responded:

>>A couple of simple comments to your comments:

“Is self-replication alone sufficient for a simple cell to evolve into something more complex?”

My answer is: no. IMO, as I have already said, already existing self-replication can only:

a) Generate very low levels of new functional information, because of the extreme limitations in the variation component

b) Compute that low information only as regards the already defined function (replication), and not for any other new function

IOWs, the existing information which allows self-replication can undergo some tweaking in the limited measure that RV and NS can allow, and nothing more. No new functions, no new original complex functional information. Just limited adaptations of the complex functional information that alrwady exists.

“Why? Even Darwin was open to the suggestion that the origin of life could be polyphyletic.”

You are perfectly right. But even biologists admit that LUCA was not necesserily one orgnaism, but possibly a set of organisms.

I am a convinced believer in common descent, but I have always said that there is no real evidence that it needs be universal common descent.

However, what we know tends to favor, at present, the idea that prokaryotes appeared first, and eukaryotes much later. Not all agree with that, but in general I would accept that scenario, at least as the best explanation available at present.

However, even if OOL was polyphyletic, there is no doubt that a lot of basic information necessary for life is almost universally shared between all forms of life that we know.>>

This sets up a serious discussion on technically rich matters, but on recent track record, let’s see if we will get more of they won’t sing and they won’t mourn. END

30 Replies to “JAD on “Self-Replicating Machines and OoL”

  1. 1
    kairosfocus says:

    JAD (and GP) on “Self-Replicating Machines and OoL”

  2. 2
    gpuccio says:

    KF:

    Thank you. It’s a very interesting topic, indeed. I hope some good discussion may ensue. 🙂

  3. 3
    john_a_designer says:

    Thank you, kf!

    In making arguments I like to focus on a key premise, proposition or question. I think the key question here is:

    Is self-replication alone sufficient for a simple cell to evolve into something more complex?

    Many OoL researchers seem to imply in their writings that it is. Thus the hypothesis about simple replicators to fill the gap between the “primordial soup” and simple prokaryotes like Mycoplasma genitalium which they agree is too improbable to have originated by Monod’s chance + necessity. But their hypothesis commits a logical error by not distinguishing between necessary conditions and sufficient conditions. We all agree that replication is necessary for the evolution of life but it does not follow that it is sufficient.

    Here are some thoughts of the late NYU biochemist Robert Shapiro on the problem.

    Many scientific theories of the origin of life suggest that life began with the spontaneous formation of a replicator (a self-copying organic polymer) within an unorganized chemical mixture, or “soup.” A profound difficulty exists, however, with the idea of RNA, or any other replicator, at the start of life. Existing replicators can serve as templates for the synthesis of additional copies of themselves, but this device cannot be used for the preparation of the very first such molecule, which must arise spontaneously from an unorganized mixture. The formation of an information-bearing homopolymer through undirected chemical synthesis appears very improbable. The difficulties involved in such a synthesis are illustrated by considering the prospects for the assembly of a polypeptide of L-alpha-amino acids, based on the contents of the Murchison meteorite as an example of a mixture of abiotic origin. In that mixture, potential replicator components would be accompanied by a host of interfering substances, which include chain terminators (simple carboxylic acids and amines), branch-formers, D-amino acids, and many classes of substances for which incorporation would disrupt the necessary structural regularity of the replicator. Laboratory experiments dealing with the nonenzymatic synthesis of biopolymers have not addressed the specificity problem. The possibility that formation of the first replicator took place through a very improbable event cannot be excluded, but greater attention should be given to metabolism-first theories, which avoid this difficulty.

    https://www.ncbi.nlm.nih.gov/pubmed/10868906

    A pdf for the full article is available for free.

  4. 4
    gpuccio says:

    john_a_designer:

    My idea is simple: a self-replicating molecule is not life.

    The idea that a self-replicating molecule could have given origin to life is based on no evidence at all, for a couple of basic reasons:

    a) No information rich self-replicating molecule spontaneously exists in nature, nobody has ever seen such a thing. When somebody will be able to build one in the lab, and then seed it in some natural environment, and we see what it does, then we can start a discussion.

    b) Life, as we know it, always requires, at least: a genome, a transcriptome, a transcription system, metabolism, a membrane which actively generates a difference between what is out and what is in, proteins, and far from equilibrium states.

    By the way, I would like to remind here that M. genitalium is a parasitic microbe which cannot live independently, and therefore is not at all a good model for what is necessary at OOL. From Microbe Wiki:

    M. genitalium lack any genes for amino acid biosynthesis and contain few genes for nucleic acid, vitamins, and fatty acid biosynthesis. They must acquire these components from their host or through an artificial medium. This makes them difficult to study in the lab under in vitro conditions, due to their strict growth requirements. They also lack genes for oxidative metabolism (Kreb cycle, or Entner-Doudoroff pathway), gluconeogenesis, catalase and peroxidase, or other toxic oxygen protective enzymes.

  5. 5
    john_a_designer says:

    gpuccio,

    By the way, I would like to remind here that M. genitalium is a parasitic microbe which cannot live independently, and therefore is not at all a good model for what is necessary at OOL

    Yes indeed! You beat me to the punch. I was also going to suggest M. genitalium may be the result of de-evolution or “devolution” rather than evolution. That only underscores the difficulty of “rewinding the tape,” especially since there doesn’t appear to be a real tape to rewind. In other words, the bad news is that whatever “simple cell” kick started evolution may be a lot more complex.

  6. 6
    Eric Anderson says:

    “Is self-replication alone sufficient for a simple cell to evolve into something more complex?”

    Absolutely not.

    First, it is a trivial matter to conceive of a self-replicating entity, such as a single-celled organism, that self-replicates 100% faithfully each generation. If there is any deviation from the parent, the daughter cell is destroyed before being allowed to continue. In such a case there would be no “evolution”. The organism would remain exactly the same form forever, regardless of how many child cells were produced.

    Second, evolution as envisioned by Darwin and later adherents, is absolutely dependent on two key assumptions. Note that these are assumptions — not proofs, not observations, but assumptions.

    (a) A population of organisms over time will experience variations of scope and extent (i.e., the kind of variations and the number of variations) sufficient to produce everything in biology. Sufficient variation to turn an amoeba into an elephant, to turn a land animal into a whale, or, to put it bluntly, to turn a single-celled organism into a human being.

    (b) Organisms are flexible enough (Darwin used the word “plastic” in The Origin) to integrate all these variations into their constitution without missing a beat. To just go right on ticking, thank you very much, as all these vast changes are incorporated into the form. Sure, there have been some dead ends along the way, but every organism alive today just happens to have been a descendant in a line that happily incorporated all these vast variations without cracking the chain, without dying out, without breaking down.

    This latter assumption was more believable when people didn’t know anything about cellular mechanics, DNA, digital code, regulatory networks, protein complexes, molecular machines, and everything else required to keep an information-rich, complex, functionally-integrated system running. It is easy to mistakenly think of the organism as a flexible, malleable, plastic entity that can simply incorporate all manner of changes and be easily molded to the needs of the environment, when one’s naive view of the cell is a simple blob of “protoplasm.”

    Darwin might perhaps be forgiven for this oversight, given his lack of understanding of the cell. Yet even with a more sophisticated view of the cell today, evolutionary proponents maintain this central assumption of plasticity and malleability, in spite of evidence to the contrary.

    Both of these assumptions are central to evolutionary theory. Both go far beyond a simple observation of reproduction. Both go far beyond a simple observation of minor variations within populations.

    —–

    Finally, let me just add that despite the central role reproduction/self-replication plays in the rhetoric of evolutionary theory, reproduction is not really that central to evolution. I know, I know. A pretty controversial statement. I’ve been meaning to write up an OP on this point, but it probably isn’t going to happen any time soon, given other responsibilities. But hopefully some food for thought for anyone else who wants to tackle the issue in the meantime: What does reproduction actually bring to the table in terms of evolution?

  7. 7
    Allan Keith says:

    Eric A,

    I’ve been meaning to write up an OP on this point, but it probably isn’t going to happen any time soon, given other responsibilities.

    You little tease. 🙂

  8. 8
    Eric Anderson says:

    gpuccio @4:

    No information rich self-replicating molecule spontaneously exists in nature, nobody has ever seen such a thing. When somebody will be able to build one in the lab, and then seed it in some natural environment, and we see what it does, then we can start a discussion.

    You are too kind. 🙂

    I agree with you that we should require a self-replicating molecule that can exist in the natural world and contain information.

    I’m still looking for an example of any self-replicating molecule, of any level of complexity, in any environment. Haven’t found one yet.

    Certainly for OOL what we need, at a minimum is:

    – The molecule has to form under natural conditions, without help from a lab technician.

    – The molecule then has to be able to make copies of itself by locating and ordering specific atoms or small molecules, not by simply catalyzing a reaction between previously-prepared sections of itself (like the work of Kiedrowski, Lincoln and Joyce, and others).

    – The molecule has to be stable enough to exist in real-world conditions (the proverbial primordial soup) without breaking down too quickly and without getting bogged down with interfering cross reactions.

    – The molecule, at least to be a precursor for evolution, must have the capacity to mutate, while still retaining the ability to faithfully replicate its now-mutated self.

  9. 9
    Eric Anderson says:

    KF mentioned in passing John von Neumann, who did some excellent work on the requirements for self-replication back in the 1940’s. His analysis has proven to be well supported and has not been overturned in the intervening decades.

    He argued that replicators, at a minimum require:

    1- A coded representation of the replicator.

    2- A mechanism for effecting construction of the replicator within the relevant environment.

    3- A mechanism to copy the coded representation.

    Note the key role information plays in this whole process, including the need for a coded representation of whatever is being built (i.e., the next generation copy).

    We can’t get away from this requirement. Vague claims about kinetics or favorable reactions or reproductive success or special environments or lots of probabilistic resources or other things proposed to get over this hurdle don’t cut it.

    —–

    With my engineering hat on, I should also add that any successful self-replication process will require control processes. From an engineering standpoint, such controls are only possible if, at a minimum, we have (i) a sensory/feedback mechanism, and (ii) information processing.

    Without that you will never get self-replication.

    All the current abiogenesis models that focus on a self-replicating molecule as the first step in the process (with information, controls, coded representations, etc., coming afterwards) are irretrievably broken. (For those who are new to this area, please be aware that this means most of the abiogenesis proposals that are being worked on by key researchers in this area.)

    It’s not just that these proposals underestimate the odds. It’s not just that these proposals still have some details to be filled in. It’s not just that these proposals face various hurdles in terms of resources, energy, reaction rates, interfering cross reactions and so on. These are formidable hurdles, to be sure. But they aren’t even the key problem.

    The most widespread abiogenesis paradigm today, with a self-replicating molecule as the first step, is completely upside down and backwards. It is like claiming that up is down. It is like claiming that gravity is a repulsive force, rather than an attractive force. The paradigm is fundamentally and irretrievably flawed at the most basic level.

  10. 10
    Origenes says:

    Eric Anderson @

    EA: What does reproduction actually bring to the table in terms of evolution?

    A discussion about the fundamentals of evolutionary theory is IMHO very important.

    I have posted the following analogy a couple of times. So far no response from the other side.

    Suppose a DVD copy machine which produces a few random copy-errors every time it makes a copy. Suppose we use this machine to make 10 copies of a newly purchased DVD containing Windows 7. Now remove the original DVD and repeat the imperfect copy process starting with functional second generation “mutated” copies (dysfunctional copies are removed from the process). Next remove all second generation copies and repeat the copy process starting with functional third generation mutated copies. And so forth.

    Who would expect that this imperfect copy process is anything other than the degeneration of Windows 7 eventually leading to mutated copies which are, without exception, dysfunctional? Who of us expects versions of Windows 7 with improved functionality?

  11. 11
    Allan Keith says:

    JAD,

    Is self-replication alone sufficient for a simple cell to evolve into something more complex?

    No.

  12. 12
    es58 says:

    so, if GP/JAD are right, then, even if Hawking’s test for parallel universes ends up both valid and verified, for life to occur “naturally” the way we see it today, you’d still need to raise the gazillion universes to the gazillionth power for every disjoint/unique/otherwise unattainable life form on earth. ok

  13. 13
    Eric Anderson says:

    es58:

    There are so many problems with the multiverse, it is hard to know where to start.

    You are quite right that the requirements for building a living organism by purely natural processes are far beyond the probabilistic resources of our universe or, as you say, even a “gazillion” universes.

    But there is a more basic problem. Insofar as people attempt to use the multiverse as an “explanation” for life, it completely fails.

    It doesn’t matter if our universe was formed with just the right parameters of physics and chemistry to support life — in other words, if our universe was finely tuned for life as we know it.

    The question on the table for the origin of life is:

    Given our universe, with precisely the fine-tuned properties of physics and chemistry that we observe, what is the most rational explanation for the origin of life?

    And the answer to that question certainly isn’t, “Well but there are lots of other universes out there too!” Some other universe for which we don’t have any observable evidence and which has no causal connection with what happens in our universe, has precisely zero impact on the question of how life arose in our universe.

    Thus, at a very fundamental level, the multiverse/multi-worlds hypotheses, don’t even address the key question on the table.* They aren’t even relevant to the primary question on the table.

    —–

    * The only way to attempt to get around this is to propose an infinite number of universes, which proposal, unfortunately, collapses into internal absurdity and incoherency.

  14. 14
    Eric Anderson says:

    Origenes @10:

    Good example.

    It is remarkable what evolutionary theory actually claims if you boil it down to the basic details. Your example helps highlight the absurdity of the claim.

    Most people can readily sense that evolution’s evidentiary story is severely lacking, but there is an incredible hold the rhetorical part of the story has over the minds of many people. People who would otherwise recognize the nonsense in any other context seem almost mesmerized by the evolutionary tale, especially when it is couched in vague terms and when the timeframes seem so impressive. Something they would never believe could happen under normal circumstances somehow becomes believable if it took a long time . . . with reverent, hushed tones about the great power of time to turn the absurd into the believable.

    When we break through the hazy mists and start asking for hard details, the story breaks down. This is why it is so important for us to help people focus on where the rubber meets the road. As Phillip Johnson used to ask his debating opponents (after dispensing with irrelevancies, such as the age of the Earth and the like), “What is your evidence that random mutations and natural selection can do all this work of creating?” The response offered would usually be the peppered moth story, or insects and insecticide, or one of the other stock stories. But never any real details about how this grand, vague, creative power of evolution was actually supposed to work.

    —–

    The impression of evolutionary theory’s explanatory power is inversely proportional to the specificity of the discussion.

  15. 15
    ronvanwegen says:

    “One practical advantage of such machines is they could be sent out in advance [by] some far-in-the-distant-future expedition to terraform a suitable planet in another star system preparing it for colonist[s] who might arrive centuries or millennia later.”

    Millenia later the colonists arrive to find…
    Windows Message
    Terraform Planet?
    Yes No Cancel

    Doh!

  16. 16
    kairosfocus says:

    JAD, the life architecture we know pivots on a metabolic entity using a von Neumann kinematic self replicator with coded information that is specifically tied to the metabolising entity, including a complex reaction framework (easily dwarfing say a petroleum refinery) as is often charted by biochemists. Executed, using molecular nanotech. That is what needs to be accounted for. KF

  17. 17
    kairosfocus says:

    RVW, you are right, very likely. KF

  18. 18
    john_a_designer says:

    My point about terraforming is: if we tried to terraform another planet either close by (like Mars) or in some distant star system using self-replicating Von Neumann machines we would have to so intentionally. We would have to have a purpose and a well thought out plan. If we were discover these kind of machines designed by ETI’s on another planet, even if it was a failed attempt, we would rightly infer design and a plan and purpose.

    But what if we decided to try to terraform another planet using bioengineered microorganisms. Carl Sagan suggestion in 1973 in Icarus; and then later in his book and T.V. series Cosmos.

    In 1973, Sagan published an article in the journal Icarus titled “Planetary Engineering on Mars“, where he proposed two scenarios for darkening the surface of Mars. These included transporting low albedo material and/or planting dark plants on the polar ice caps to ensure they absorbed more heat, melted, and converted the planet to more “Earth-like conditions”.

    https://www.universetoday.com/113346/how-do-we-terraform-mars/

    Obviously we recognize this as a plan which also required intention and foresight– INTELLIGENCE!

    But what if the earth had been terraformed very early on? Is there any evidence of that? You could make that interpretation. There is evidence that early life actually made the planet more habitable. For example, life as we presently know it wouldn’t exist without photosynthesis appearing very early. Even some non-ID’ists think this is very significant. For example:

    The Gaia Theory posits that the organic and inorganic components of Planet Earth have evolved together as a single living, self-regulating system. It suggests that this living system has automatically controlled global temperature, atmospheric content, ocean salinity, and other factors, that maintains its own habitability. In a phrase, “life maintains conditions suitable for its own survival.” In this respect, the living system of Earth can be thought of analogous to the workings of any individual organism that regulates body temperature, blood salinity, etc. So, for instance, even though the luminosity of the sun – the Earth’s heat source – has increased by about 30 percent since life began almost four billion years ago, the living system has reacted as a whole to maintain temperatures at levels suitable for life.

    The Gaia theory was developed in the late 1960’s by Dr. James Lovelock, a British Scientist and inventor, shortly after his work with NASA in determining that there was probably no life on Mars. His research led to profound new insights about life on Earth. The theory gained an early supporter in Lynn Margulis, a microbiologist at the University of Massachusetts. In the past 15-20 years, many of the mechanisms by which Earth self-regulates have been identified. As one example, it has been shown that cloud formation over the open ocean is almost entirely a function of the metabolism of oceanic algae that emit a large sulfur molecule (as a waste gas) that becomes the condensation nuclei for raindrops. Previously, it was thought that cloud formation over the ocean was a purely chemical/physical phenomenon. The cloud formation not only helps regulate Earth’s temperature, it is an important mechanism by which sulfur is returned to terrestrial ecosystems.

    http://www.gaiatheory.org/overview/

    In other words, the accidental occurrence of a single prokaryote is not sufficient to explain life as we know it. From a naturalistic/materialistic perspective it requires not just one highly improbable accident but a string of highly improbable accidents. But if you’re a metaphysical naturalist in the of tradition Jacques Monod all you have as an explanation is chance + necessity– and in my opinion that doesn’t get you very far, even if you are very generous about the probabilities (or improbabilities.) An objective analysis of the evidence points to a purpose and a plan– intelligent design!

  19. 19

    I think calling the OOL and subsequent evolutionary milestones “a miracle” dangerously understates the nature of what is being discussed. Anyone can imagine a few miraculous convergences of chance over the course of billions of years.

    What cannot be imagined as remotely possible are the ongoing, second by second concurrent miracles that must work in perfect concert for the initial molecular construction of any biological mechanism. The correct chemical ingredients must be gathered, sorted and purified, kept in different environments and affected in diversely particular ways before coming together.

    Every step along the way must be protected in a very particular way to avoid degradation and contamination. There are an endless number of ways that such a process can fail and only a very, very narrow window of success – not just “once”, but every second throughout the ingredient gathering and the construction process for every element being used in the construction of the mechanism.

    Unless there is design for a purpose, every “chance” construction of a mechanism has virtually limitless opportunity to be either of no functional value, or of negative value to any other mechanism already in existence. There is far more potential for non-compatibility and mutual destruction than for any sort of compatibility whatsoever, much less mutual functional benevolence.

    How does a proto-mechanism remain in existence when all around, at every turn and in each sequential second of time, there are countless forces looking to degrade or contaminate?

    And then, when a coding and replication mechanism has been built, where does new functional information come from, both in the initial construction, then simultaneously in the blueprint library, and then in the perfectly concerted 3D expression thereof?

    We’re not looking at “a miracle” or a handful of miracles”, but billions of years of ongoing, simultaneous, second by second, event by event specifically organized “miracles” that converge on creating intelligent life.

    Naturalism/Materialism can only exist in the minds of the ignorant or the willfully blind.

  20. 20
    john_a_designer says:

    kf,

    I am using Von Neumann machines on the macro scale as an analogy for what is happening on the sub-cellular microscopic scale. I am convinced that most of our regular interlocutors haven’t a clue of the staggering complexity and improbability of the even the simplest cell. They should try somethings besides Wikipedia– anything besides Wikipedia.

    PS Of course if we did discover an artificially constructed “macroscopic” Von Neumann machine terraforming another planet everyone would recognize it as the result of intelligent design, even if we didn’t know who the designer/ designers were.

  21. 21
    gpuccio says:

    john_a_designer:

    “They should try somethings besides Wikipedia– anything besides Wikipedia.”

    Well, even Wikipedia would be more than enough, if they do the right searches! 🙂

  22. 22
    Origenes says:

    EA: Something they would never believe could happen under normal circumstances somehow becomes believable if it took a long time . . . with reverent, hushed tones about the great power of time to turn the absurd into the believable.

    WRT my ‘windows 7 example’ (see #10), it seems perfectly clear, that time does not help at all. Enough time simply guarantees that random copy errors accumulate to the point that every mutated copy is dysfunctional.
    So, the question is: what is it about time that makes the evolution story for many (more) believable?

  23. 23
    Eric Anderson says:

    Origenes @22:

    So, the question is: what is it about time that makes the evolution story for many (more) believable?

    I think a couple of things.

    First, evolutionists continue to harp on time as their friend in the rhetoric of evolutionary theory, so some people probably just go along.

    Second, and more substantively, there are many natural processes for which deep time is a factor. Whether we are talking about explanations for large-scale cosmological structures or things closer to home, like the movement of tectonic plates to create vast mountain ranges or the flow of a river to carve a great canyon.

    So it is quite true that some natural processes that we don’t readily observe in our lifetimes can take place over deep time and can produce real effects. We can see hints and clues that give us great confidence we are on the right track with the “current observable process + time = big result” formula.

    Darwin was impressed with the effect of deep time in geology and partly drew upon it in formulating his theory. And if one thinks, as Darwin did, that organisms are rather simple conglomerations of rather simple cells, then it isn’t so hard to make the mental leap from “simple rocks + upheaval + time = amazing mountain range” to something like “simple cell + more cells + time = amazing organism”.

    Darwin over and over asked his readers to make such a mental leap. “Is it so hard to believe . . .” he would ask, in effect, at critical junctures in The Origin.

    We now know that the attempt to analogize from, say, geology to biology is terribly flawed and stems from a gross misunderstanding of what is required for biological systems. But for those who don’t think very deeply about the biological systems, it is easy to be impressed with all those millions or billions of years the evolutionists keep talking about and to believe the evolutionary claim that what we see in biology is really not that different from what we see in something like geology.

    —–

    I should add, as a very important aside and with a hat tip to Phillip Johnson, that one of the things that is very definite in the Darwinist mind is precisely this: that what we see in biology is really no different than any other long, drawn-out, natural process.

    This is part of the reason why the proponents of evolution are so incredibly sloppy in their discussions about evolution and their attempts to define what it is. A star forming from interstellar dust? Yep, that’s evolution. The formation of the Solar System? Another example of evolution. Changes in the makeup of continents and oceans? Evolution. Changes in the percentage of light and dark moths in a population? Evolution. Turning a single-celled organism into an elephant? Evolution.

    Indeed, one of the great proponents of the neo-Darwinian synthesis (Sir Julian Huxley, if memory serves) was quoted as saying that “all reality is a single process of evolution.” This is an incredibly telling statement that gives us great insight into the Darwinist mindset.

    —-

    Back to time . . .

    I think the only way to help people to escape from this intellectual straight-jacket is to help them recognize that there is something very different going on in biology than in other natural processes. While no analogy is perfect, what goes on in biology is certainly much more analogous to human invention and design (including incredibly sophisticated machinery and functionally-integrated, information-rich systems) than to geology, or solar system formation, or any other natural process for that matter.

    There are so many examples and so many great points to press on. Your DVD example is a good one for underscoring the point about digital information and the degradation that occurs with time — well-known evidence that is directly contrary to the evolutionary tale.

  24. 24
    john_a_designer says:

    Eric Anderson,

    I think the only way to help people to escape from this intellectual straight-jacket is to help them recognize that there is something very different going on in biology than in other natural processes. While no analogy is perfect, what goes on in biology is certainly much more analogous to human invention and design (including incredibly sophisticated machinery and functionally-integrated, information-rich systems) than to geology, or solar system formation, or any other natural process for that matter.

    Let me play devil’s advocate (since the real “devil’s” advocates are staying away.) What about crystals… what about snowflakes and other kinds of chemical self-organization we observe in the natural world? Couldn’t have life have somehow begun that way? Isn’t life just another form of chemical self-organization?

  25. 25
    Eric Anderson says:

    john_a_designer @24:

    No.

    Not only could life not have begun that way, these aren’t even examples of self-replication, much less a precursor for life.

    Unfortunately I don’t have time this morning to do a detailed expose of the issue, but a couple of quick things off the top of my head:

    – Crystals form from an exothermic reaction that makes the molecules involved in the reaction become more “ordered”, in the sense of a repetitive pattern.

    – This is precisely the opposite of what we need for a non-repetitive, information-rich system, like DNA. In other words, the process that creates crystals not only is not helpful, it is anathema to what is required for life.

    – Using crystals as some kind of substrate for the chemical reactions (as opposed to crystals themselves leading to a living system) is also pointless, for the same reason.

    – From a standpoint of thermodynamics (which I realize most people hate to talk about, but it is an important issue) life is a far-from equilibrium state. This is recognized even by committed Darwinists who hope for some kind of naturalistic OOL. This is why we’ve had people like Prosser (h/t Nick Matzke in these very pages a few years ago) and England propose absurd claims about how living systems can tend toward those far-from equilibrium states (a non-sequitur, but they’re grasping at any straws they can).

    – Crystals, it should be readily noted, are precisely the opposite of this far-from-equilibrium state and tend aggressively toward equilibrium, as does essentially every other unmoderated natural chemical reaction of this type.

    – Crystals do not self-replicate and cannot, contrary to some silly OOL proposals, serve as initial self-replicators for OOL. Crystal formation is essentially a process whereby a precipitate falls out of solution at a certain level of saturation and temperature. Despite our use of the word “grow” to describe the sugar crystals we all made in our grade school science experiment, the crystal is not “growing” in any sense relevant to biology. We are simply witnessing more of the precipitate fall out of solution and adhere to the other precipitate in a lattice-like, thermodynamically-downhill, framework. A crystal “growing” in a solution is no more an example of self-replication than a puddle of water “growing” when it rains, or a sand dune “growing” as wind deposits more sand on the dune.

    – Finally, and most obviously, but I’ve left it for last because the point is sometimes lost on many people, crystals — even beautiful and intricate ones like snowflakes — don’t contain any information. Unlike what we see in biology, there is no representation of anything outside themselves, no code, no symbolic system.

    So, no, crystals don’t help. They are just completely irrelevant to the key issues involved in OOL.

    —–

    Well, that ended up being longer than I had planned, even though just a quick bullet-point list. Hopefully some food for thought.

  26. 26
    Eric Anderson says:

    BTW, you used a term that I should have discussed, as it was popularized by Kauffman and others and got a lot of hype for a while (a couple of decades ago): “self-organization.”

    As with crystals, any form of “self-organization” as a process to allegedly help with OOL is a complete dead end. That isn’t to say that a creative designer couldn’t take advantage of a very specific self-organizing process in a very specific aspect of a system’s design. But as an explanation for the origin of life — or any other information-rich, functionally-integrated system, for that matter — self-organization is utter nonsense.

    The primary value of self-organization has been to provide notoriety and funding and research opportunities for those pushing the idea.

    Real, concrete contributions to our understanding of anything in biology? Not so much.

  27. 27
    john_a_designer says:

    Eric Anderson,

    As with crystals, any form of “self-organization” as a process to allegedly help with OOL is a complete dead end.

    Let’s explore in a little more depth as to why.

    Charles B. Thaxton argued that information needs to be distinguished from just Order and Complexity. He comes up with three categories.

    Order: Periodic and Specified

    Complexity: Aperiodic and Unspecified

    Information: Aperiodic and Specified

    He then gives some examples:

    Order: Periodic and Specified

    Examples of ordered structures are a repeating wallpaper or floor tile pattern, the hexagonal pattern appearing on the surface of heated oil, the single structure repeated over and over in a crystal, and a sequence of alphabetical letters ABABABABAB…. The characteristic feature of an ordered structure is the PERIODIC AND SPECIFIED arrangement of its constituent parts. That means the parts are arranged in a highly repetitious and specific fashion. Such structures have a low information content and require only a few instructions to specify them.

    Complexity: Aperiodic and Unspecified

    On the other hand, aperiodic structures, i.e., structures that lack periodicity, are called “complex.” Complex structures are of two types. The simplest type of complexity is a random structure. A random structure has no order, but, like an ordered structure, it has little information because few instructions are needed to specify it. By definition random structures are APERIODIC AND UNSPECIFIED, such as a lump of granite, a pile of leaves, a random polymer, or a sequence of letters drawn at random.

    Information: Aperiodic and Specified

    It is the second type of complexity, however, that is most relevant for biology. Written messages, artifacts, DNA, and proteins are all examples of specified complexity. By definition structures characterized by specified complexity are those whose constituent parts are arranged in an APERIODIC AND SPECIFIED manner. Such structures have a high information content, which means that many instructions are needed to specify them.

    As an example, if you wanted to print out a copy of Lincoln’s Gettysburg Address that begins “Four score and seven years ago…,” you could not find any brief set of instructions to give your computer. Your instructions would be as long as the famous address itself. You must specify every letter, one at a time, in the correct sequence. There are no shortcuts.

    It would be quite impossible to give a chemist a set of a few instructions to synthesize the DNA of even the simplest bacterium. The instructions would have to include every chemical letter, one by one. That would be several million of them. Rather than a few sentences of instructions, there would be enough to fill a large book.

    [emphasis added]

    http://www.discovery.org/a/137

    So as to your point, yes indeed. Any kind of self-organization when it comes to explaining OoL is a dead end, because coded DNA and RNA cannot be created like a crystal or a snow flake with a short set of instructions. The key question that needs to be answered then by the naturalist/materialist is: what mindless natural process can create de novo complex, aperiodic specified order or information. Or, to state the question more succinctly: how can chemistry create code?

  28. 28
    Eric Anderson says:

    john_a_designer @27:

    Agreed, and thanks for sharing the quotes.

    I might quibble with a couple of minor details in Thaxton’s description, but his central point is still spot on and is absolutely central to design detection.

  29. 29
    john_a_designer says:

    Barry, has pointed out in another OP, A Materialist Gets It (Almost) that Richard Dawkins has conceded that life could have been intelligently designed. Here’s a You Tube clip from an interview he did with Ben Stein.

    https://www.youtube.com/watch?v=BoncJBrrdQ8

    However, while Dawkins shows some tentative willingness to accept the idea that the first life on earth could have been intelligently designed, it appears he is only willing to accept this idea if the intelligence was a super intelligent ET and not God. (So apparently for an atheist it’s okay to be super intelligent but not too super intelligent.)

    Of course other atheists have admitted the same thing. The following Scientific American article discusses similar views held by Nobel Laureate Francis Crick and British chemist Leslie Orgel.

    https://blogs.scientificamerican.com/guest-blog/the-origins-of-directed-panspermia/

    I believe it was Crick and Orgel who coined the term directed panspermia.

    To be fair I think Dawkins later tried to walk back his position. (However, we still have the tape!) Maybe Crick and Orgel did as well. But the point remains, until you prove how life first originated by natural causes alone intelligent design is a logical possibility.

    Ironically, in the Ben Stein interview Dawkins said that if life were intelligently designed (by space aliens) the scientific research may be able to discover their signature. Didn’t someone write a book about the origin of life with the word signature in the title? Who was that? I wonder if he picked up the idea from Dawkins. Does anyone know? Anyone?

    BONUS QUESTION: Ben Stein is famous for one word. Does anyone know what that one word is? Anyone?

  30. 30
    Eric Anderson says:

    john_a_designer @29:

    Yeah, the exchange about Dawkins and the aliens is interesting, but I’m not convinced we can make too much of it. It wasn’t clear to me that he felt strongly about the idea of life being designed by aliens. Rather, it seemed that he was just intent on arguing that life could not have been created by God — therefore, even if life was created by someone, it was probably aliens or something.

    Now this is a terrible line of reasoning, and Dawkins deserves to be hoisted on his petard over it. But it really stems, not from support from the design inference as a valid approach, but from a mistaken idea that intelligent design is a direct argument for God. So if he can find something — anything — that argues against God, then he thinks he wins the argument against intelligent design.

    Years ago in a debate with Stephen Meyer, University of Washington astrobiologist, Stephen Ward, made a similar logical faux pas. It was on a different point (discussing DNA), but it shows how an incorrect understanding of the design argument can lead an anti-ID debater to argue for design — as long as God isn’t the designer.

    I wrote up a very brief summary of the exchange at my long-defunct website. You can see it here — Rather short and well worth reading, I must say: 🙂

    https://web.archive.org/web/20070625070712/http://www.evolutiondebate.info:80/WhatWard.htm

    I’m not sure either Ward or Dawkins appreciated the significance of the road they were going down when they referred to other potential designers (other than God). Once the heat of the debate is over and they have a chance to think about what they said, I doubt they would openly admit to agreeing with the design inference.

    But as you point out, they have put themselves between a rock and a hard spot, and later attempts to weasel out of the inference show the debater’s true colors and, ironically, show the validity of the design inference.

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