Self-Assembly of Nano-Machines: No Intelligence Required?

In my research, I have recently come across the self-assembling proteins and molecular machines called nano-machines one of them being the bacterial flagellum…

Have you ever wondered what mechanism is involved in the self-assembly process?

I’m not even going to ask the question how the self-assembly process has supposedly evolved, because it would be offensive to engineers who struggle to design assembly lines that require the assembly, operation and supervision of intelligence… So far engineers can’t even dream of designing self-assembling machines…But when they do accomplish that one day, it will be used as proof that random, natural processes could have done too…in life systems.. lol

If you don’t know what I’m talking about, just watch this video:

The first thing that came to my mind when I debating the self-assembly process was one of Michael Behe’s books The Edge of Evolution. I wanted to see whether he mentioned any known, or unknown, mechanism driving the self-assembly process of nano-machines, like the flagellum…

In the Edge of Evolution Behe uses an illustration of a self-assembling flashlight, which parts possess the many different types of magnets that only fit the right type of part into it; each part having the affinity for the corresponding magnet…something like that…

It’s not clear to me whether Behe questions that the magnetic attraction is sufficient for the self-assembly of the flagellum (I might have to read the parts of the book on the theme again). Behe seems to question the ability of Darwinian processes to be able to evolve the sequence and the fitting process of each part of the flagellum, by random processes of random mutation and natural selection…

This is what BIOLOGOS have to say on the theme of self-assembly of the flagelum:

“Natural forces work “like magic”

Nothing we know from every day life quite prepares us for the beauty and power of self-assembly processes in nature. We’ve all put together toys, furniture, or appliances; even the simplest designs require conscious coordination of materials, tools, and assembly instructions (and even then there’s no guarantee that we get it right!). It is tempting to think the spontaneous formation of so complex a machine is “guided,” whether by a Mind or some “life force,” but we know that the bacterial flagellum, like countless other machines in the cell, assembles and functions automatically according to known natural laws. No intelligence required.1

Video animations like this one (video no longer available) by Garland Science beautifully illustrate the elegance of the self-assembly process (see especially the segment from 2:30-5:15). Isn’t it extraordinary? When I consider this process, feelings of awe and wonder well up inside me, and I want to praise our great God.

Several ID advocates, most notably Michael Behe, have written engagingly about the details of flagellar assembly. For that I am grateful—it is wonderful when the lay public gets excited about science! But I worry that in their haste to take down the theory of evolution, they create a lot of confusion about how God’s world actually operates.

When reading their work, I’m left with the sense that the formation of complex structures like the bacterial flagellum is miraculous, rather than the completely normal behavior of biological molecules. For example, Behe writes, “Protein parts in cellular machines not only have to match their partners, they have to go much further and assemble themselves—a very tricky business indeed” (Edge of Evolution, 125-126). This isn’t tricky at all. If the gene that encodes the MS-ring component protein is artificially introduced into bacteria that don’t normally have any flagellum genes, MS-rings spontaneously pop up all over the cell membrane. It’s the very nature of proteins to interact in specific ways to form more complex structures, but Behe makes it sound like each interaction is the product of special design. Next time I’ll review some other examples from the ID literature where assembly is discussed in confusing or misleading ways.”

To me personally, the self-assembly process, especially that of the molecular nano-machines like the bacterial flagellum, involves much, much more than random motion of molecules and the affinity of their binding sites for one another…

There has to be not only some kind of energy directing force but also some hidden information source to direct that energy…I have a hunch what that could be and there is only one way of finding it out…

Does anybody know what I have in mind? No, I don’t think it’s Jesus …

 

471 Replies to “Self-Assembly of Nano-Machines: No Intelligence Required?”

  1. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: Chemical substances do not need to change to be part of living beings because due to their attributes they are ideally suited to combine in ways that allow life to form. Why would they need to change? The nature of the chemicals do not change between life and non-life. It is the combination and organisation which changes.

    Coming around to our side? Ach no, I’ll bet that proteins are not chemical substances in your view, right?

    My views have not changed. And of course proteins are chemical substances. Their chemical makeup can be precisely determined. Of course there is more to them than just chemical makeup, for example chirality.

    CharlieM: You do know that urea is a waste product? It is formed by the action of living substances. There are several enzymes at work in the urea cycle and urea is the product of work, it does not carry out any work.

    You do know that urea is used in fertilizer? It is consumed again by living organisms as a nitrogen source for the production of proteins.

    Not sure why that would qualify it as a living substance. We consume salt, does that qualify it as a living substance?

    Your argument is getting pretty hard to follow, but “inner activity” seems to equate being able to “carry out work”. When can a molecule said to be doing that exactly? Are you talking about having catalytic function? Are you sure you want to argue that only living substance can act as a catalyst?

    Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth.

  2. CharlieM CharlieM
    Ignored
    says:

    Corneel: Lots of things are confusing the others here. Charlie’s arguments have been slowly morphing from “dynein motor proteins are little nano-beings” to arguing about some mysterious inner activity in some unspecified subset of organic molecules. I suspect clarity will not be forthcoming soon.

    I asked for opinions on the comparison of dynein complexes with worker ants carrying cargoes along a track. What is your opinion?

    I linked to videos showing the activities of specific protein complexes. What is mysterious about this? Maybe you do not believe that animals move, or bacteria move, of dynein complexes move through inner activity.

  3. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    I have nothing against the idea of “inner activity” but I think of it as non-linear or circular causality. That means we need to think in terms of organization or structure rather than in terms of stuff. I don’t see how appealing to machine metaphors will help us do that, though there are some important insights from cybernetics that are relevant.

  4. Mung Mung
    Ignored
    says:

    Kantian Naturalist: 1. “living organisms contain the same elements as non-living things but those elements are organized in a different way” …

    It’s not just that they are organized differently, it’s why they are organized the way they are.

    What is the reason that an atom is organized the way it is?

  5. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock: Tautomerism.

    Does urea tautomerize in order to perform some function?

    Also
    Urea can act as a catalyst.

    The human use of urea as a catalyst is more of a passive affair on the part of urea.

    Urea is food, in particular for the ureolytic bactiera that are being testing in the repair of damaged concrete (See, I can do irrelevant asides too).

    In what way is urea an active participant here? It is being acted upon.

    Crystals are halfway alive, you say?
    This is getting increasingly incoherent.

    Crystals have growth in common with life. Below is an image of frost growth patterns on my wife’s car.

  6. DNA_Jock
    Ignored
    says:

    CharlieM,
    Yes.
    I’m visualizing goal-posts cantering across a soccer field.
    It’s a fun visual.

  7. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    Mung: It’s not just that they are organized differently, it’s why they are organized the way they are.

    What is the reason that an atom is organized the way it is?

    At this point we’re touching on two closely related and delicate topics: the concept of a law of nature and the principle of sufficient reason.

    The instinctive response to “why are atoms organized as they are?” is to say “because of the laws of quantum mechanics” or something like that. That is, atoms are as they are because protons, neutrons, and electrons are as they are. But I think the question that one might ask here is, “why are the atomic orbitals as they are?” since it is the shape of the probability distribution of the electron that determines the kinds of interactions atoms of that kind can have with other atoms.

    I don’t know the vast literature on laws of nature amongst philosophers of science, though I do know that at least one philosopher, Nancy Cartwright, has argued in favor of anti-realism about laws but realism about causal powers.

    The trickier philosophical issue is the principle of sufficient reason, which says (depending on how you read it) that there’s an explanation for every fact. There are couple of different ways of interpreting this claim, and in my experience, when arguing with philosophically sophisticated theists it always comes down to this: is the PSR a claim about the structure of reality independent of us, or is it a claim about how we should go about conducting inquiry?

  8. CharlieM CharlieM
    Ignored
    says:

    Kantian Naturalist:

    Corneel: I suspect clarity will not be forthcoming soon.

    Probably not.

    And I suspect that there are many here who expect life to be simple.

    It’s not!

  9. CharlieM CharlieM
    Ignored
    says:

    Kantian Naturalist:
    I have nothing against the idea of “inner activity” but I think of it as non-linear or circular causality. That means we need to think in terms of organization or structure rather than in terms of stuff. I don’t see how appealing to machine metaphors will help us do that, though there are some important insights from cybernetics that are relevant.

    Again, we are in agreement. The systems of cause and effect of classical physics works perfectly well for the mechanics of human constructions and machines. But living systems are far too fluid, interdependent and convoluted to be governed by the laws of cause and effect.

    And the discoveries of quantum physics are also pointing to fact that the cause and effect laws of classical physics are not universal.

  10. phoodoo
    Ignored
    says:

    Kantian Naturalist: Mung: It’s not just that they are organized differently, it’s why they are organized the way they are.

    What is the reason that an atom is organized the way it is?

    At this point we’re touching on two closely related and delicate topics: the concept of a law of nature and the principle of sufficient reason.

    The instinctive response to “why are atoms organized as they are?” is to say “because of the laws of quantum mechanics” or something like that. That is, atoms are as they are because protons, neutrons, and electrons are as they are. But I think the question that one might ask here is, “why are the atomic orbitals as they are?” since it is the shape of the probability distribution of the electron that determines the kinds of interactions atoms of that kind can have with other atoms.

    I don’t know the vast literature on laws of nature amongst philosophers of science, though I do know that at least one philosopher, Nancy Cartwright, has argued in favor of anti-realism about laws but realism about causal powers.

    The trickier philosophical issue is the principle of sufficient reason, which says (depending on how you read it) that there’s an explanation for every fact.

    Gee, what a satisfying answer. But let me help you edit it down for clarity if I may.

    “Don’t ask. No idea.”

  11. Corneel Corneel
    Ignored
    says:

    CharlieM: In your opinion would the proteins in your body be classed as living substances?

    Do you consider a tree to be a living being? Is wood a living substance in your opinion?

    I don’t normally use the term “living substance”, so don’t ask me what I think it means. Use cell, cytoplasm, protein, tissue. More precise = more clear = better.

    CharlieM: Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth.

    How does a protein “ingest” energy? As for the rest of your definition: this is starting to edge close to standard chemistry, which does not posit distinct properties for molecules in living organisms. *

    CharlieM: I asked for opinions on the comparison of dynein complexes with worker ants carrying cargoes along a track. What is your opinion?

    I linked to videos showing the activities of specific protein complexes. What is mysterious about this? Maybe you do not believe that animals move, or bacteria move, of dynein complexes move through inner activity.

    I think there were two issues. The first was whether dynein motor proteins could be said to be living beings. I said they could not because they lacked certain characteristics, specifically reproduction.

    Then the discussion shifted to the question whether proteins like Taq polymerase could be said to be living tissue when they were outside the context of a living entity. I argued that this is not the case, because there is nothing in the chemistry of biomolecules that distinguishes them from inorganic molecules. You objected, alluding to some mysterious “inner activity”, but have been IMO unable to define it in a way that would truly distinguish proteins like Taq polymerase from other molecules. To confuse matters, you called table salt halfway alive, because of its ability to form crystals, which recruits a decent chunk of chemical substances (except ironically, many organic molecules) into the realm of living substance.

    That is where we are now. Unless you are able to flesh out this inner activity of living substance, I fail to see what we gain from calling individual proteins living beings or living substance.

    ETA: * I might make an exception for the “function” part, if you drop the idea that crystallization is a function. Polymerase function has clearly evolved by virtue of its adaptive value in organisms.

  12. BruceS
    Ignored
    says:

    Mung:
    KN: living organisms contain the same elements as non-living things but those elements are organized in a different way” …
    Mung: It’s not just that they are organized differently, it’s why they are organized the way they are.

    Because otherwise they would be dead?

    That’s not just easy humor, it’s also a one sentence summary of a scientific theory that gets discussed from time to time at TSZ (eg if one interprets ‘living organisms” are species or populations with a specific trait).

    ETA: To make that last bit clearer, “dead” in my first sentence should be generalized to include “never born at all. “

  13. BruceS
    Ignored
    says:

    Kantian Naturalist:and in my experience, when arguing with philosophically sophisticated theists it always comes down to this: is the PSR a claim about the structure of reality independent of us, or is it a claim about how we should go about conducting inquiry?

    If the theists know some cosmology, they are also likely to take a detour into Fine Tuning.

  14. CharlieM CharlieM
    Ignored
    says:

    DNA_Jock:
    CharlieM,
    Yes.
    I’m visualizing goal-posts cantering across a soccer field.
    It’s a fun visual.

    It isn’t me who is moving any goalposts, it is you who is beginning to have an inkling of understanding my position. You imagine the goalposts moving when all the time it is you who is moving. Your viewpoint has shifted, it’s all relative.

  15. DNA_Jock
    Ignored
    says:

    Nice summary, Corneel.
    I’ve had a pretty good ‘inkling’ of Charlie’s position since 1979; even biologists have been known to ascribe some sort of magical vitalism to enzymes. For instance, the lecturer who introduced us to the Haldane relationship (between Km and kcat for the forward and reverse reactions) described it as something that enzymes somehow ‘achieved’. Likewise, biologists often describe enzymes as magically “using” ATP hydrolysis to achieve otherwise unfavorable reactions.
    This is, of course, rubbish, and it is up to biochemists [pauses, polishes tiara] to set them straight.
    [General Tip for IDists: scientists sometimes step outside of their areas of expertise; when they do, they sometimes spout rubbish. Tornado in a junkyard…]

  16. phoodoo
    Ignored
    says:

    DNA_Jock: General Tip for IDists: scientists sometimes step outside of their areas of expertise;

    See “List of Steves” for example.

  17. CharlieM CharlieM
    Ignored
    says:

    Corneel: December 11, 2018 at 9:48 am

    CharlieM: In your opinion would the proteins in your body be classed as living substances?

    Do you consider a tree to be a living being? Is wood a living substance in your opinion?

    I don’t normally use the term “living substance”, so don’t ask me what I think it means. Use cell, cytoplasm, protein, tissue. More precise = more clear = better.

    So do you think it is possible to tell the difference between living cells, cytoplasm, proteins or tissues and dead cells, cytoplasm, proteins or tissues?

    CharlieM: Having inner activity means that it is able to ingest, convert and reuse energy in order to carry out a function such as movement or growth.

    How does a protein “ingest” energy? As for the rest of your definition: this is starting to edge close to standard chemistry, which does not posit distinct properties for molecules in living organisms. *

    Proteins “ingest” energy by taking in molecules such as ATP. to hydrolyse, just as we take in and break down food.

    CharlieM: I asked for opinions on the comparison of dynein complexes with worker ants carrying cargoes along a track. What is your opinion?

    I linked to videos showing the activities of specific protein complexes. What is mysterious about this? Maybe you do not believe that animals move, or bacteria move, of dynein complexes move through inner activity.

    I think there were two issues. The first was whether dynein motor proteins could be said to be living beings. I said they could not because they lacked certain characteristics, specifically reproduction.

    Does it matter whether we call dynein complexes machines or living beings? Precise definitions are less important than the concept that people attach to the words, especially young students. Most would associate machines with human constructed devices, whereas they would associate living beings with natural creatures that live and grow and die.

    I think that “living being” is a term which gives them a better idea that these structures have the properties of living substance. If we can use the “machine” metaphor why can’t we also use the “living being” metaphor if we wish? There seems to be an illogical (IMO) antagonism towards this way of thinking.

    I have to go as I’m off to watch my granddaughter being a star in a nativity play, so I’ll continue this later.

  18. Rumraket Rumraket
    Ignored
    says:

    Kantian Naturalist: There are couple of different ways of interpreting this claim, and in my experience, when arguing with philosophically sophisticated theists it always comes down to this: is the PSR a claim about the structure of reality independent of us, or is it a claim about how we should go about conducting inquiry?

    My issue with the way theists use the PSR is that if they had been using it consistently, then science would have stopped long before where we are today. There is no concievable observation we could not imagine came out like it did because of “the will of God”. Why does it rain? God wills it. Why did my dog get sick and die? God willed it. Why are the laws of nature like they are? God willed it.

    If the PSR means that we stop investigating when we merely have, conceptually, a “sufficient reason” capable of accounting for that to be explained, then the PSR would stop any investigation right out the gate.

  19. DNA_Jock
    Ignored
    says:

    Good point phoodoo,

    Steven Gollmer has a Ph.D. in Atmospheric Science
    Steve Overell has a Ph.D. in Solid State Physics
    Stephen Lloyd has a Ph.D. in Materials Science
    Stephen C. Tentarelli and Stephen A. Batzer have Ph.D.’s in Mechanical Engineering
    Stephen J. Cheesman has a Ph.D. in Geophysics
    Stephen Crouse is a Professor of Kinesiology
    Stephen C. Knowles has a Ph.D. in Marine Science
    Stephen C. Meyer has a Ph.D. in Philosophy of Science

    Or were you thinking of a different List of Steves? The one with over 700 biologists on it, perhaps?
    🙂

  20. Corneel Corneel
    Ignored
    says:

    CharlieM: So do you think it is possible to tell the difference between living cells, cytoplasm, proteins or tissues and dead cells, cytoplasm, proteins or tissues?

    Cells and tissue (by virtue of being composed of cells): yes
    Cytoplasm and proteins: no

    CharlieM: Proteins “ingest” energy by taking in molecules such as ATP. to hydrolyse, just as we take in and break down food.

    No, they don’t. That’s just you anthropomorphizing again.

    CharlieM: I think that “living being” is a term which gives them a better idea that these structures have the properties of living substance. If we can use the “machine” metaphor why can’t we also use the “living being” metaphor if we wish? There seems to be an illogical (IMO) antagonism towards this way of thinking.

    As stated previously, I don’t mind either type of metaphor, as long as young students (and certain TSZ residents) realize that proteins are neither machines nor living beings.

    CharlieM: I have to go as I’m off to watch my granddaughter being a star in a nativity play, so I’ll continue this later.

    That sounds like fun. Off you go 🙂

  21. Mung Mung
    Ignored
    says:

    Kantian Naturalist: The instinctive response to “why are atoms organized as they are?” is to say “because of the laws of quantum mechanics” or something like that. That is, atoms are as they are because protons, neutrons, and electrons are as they are. But I think the question that one might ask here is, “why are the atomic orbitals as they are?” since it is the shape of the probability distribution of the electron that determines the kinds of interactions atoms of that kind can have with other atoms.

    ok, that atoms. Should we be asking how to account for the adaptations present in atoms?

    Why can’t we just say of organisms that they are what they are because their “parts” are what they are and because of how those “parts” interact because of what they (their parts) are.“because of the laws of quantum mechanics” or something like that.

    There is, presumably, something quite different about organisms that leads people to try to explain them quite differently.

    It’s not just that they are organized differently, it’s why they are organized the way they are.

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