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 …

 

669 thoughts on “Self-Assembly of Nano-Machines: No Intelligence Required?

  1. BruceS: I don’t find you offensive. I do find your psychology mysterious.Perhaps it is the same mystery as that at the heart of the non-locality of QM?

    Nah….!(Insert appropriate wry humour emoji; I’m on the spectrum with respect to them).

    ETA:by avoiding psychology, I meant avoiding analysing motive, which breaks the rules.

    Perhaps the fact that my kids use my account at times can explain some of the mystery…

    Non locality is not really a mystery in a sense if one has an imagination…
    Do you?
    Can you imagine a dimension (s) where distance and time don’t exist or they don’t matter? Where everything; all the rule we know as logical and real are broken?

  2. J-Mac: I definitely agree that entanglement could a big part of the mechanism of self-assembly since it is already well known that cell division, mutations etc. are the processes controlled by quantum entanglement…

    I’m not sure I understand how polarity can be involved… I don’t know enough about it to comment I’m afraid…

    That’s okay. I think there is plenty here to discuss on the nature and structure of the bacterial flagellum alone.

    I’ll just mention one thing. Due to the nature of entanglement, sub-atomic “particles” need not only be considered as entities that have a point of influence. They can also regarded as having fields of influence which is not constrained by any localized point. The particles are linked regardless of distance..

  3. CharlieM: The video brings up an interesting comparison between bacteria and eukaryotes. She explains that bacterial and eukayote rfs (termination/release factors) are structurally similar and both perform the same function but they differ in their sequences suggesting they evolved independently of one another and thus convergent evolution is put forward as an explanation.
    J-Mac will be amused by the terminology of the video where Rachel Green speaks of:

    Wow! That’s a really nice find! Thanks!
    I totally forgot about the chasm separating the release factors of bacteria and eukaryotic cells… Convergent evolution can explain anything and everything… In other words convergent evolution is magic lol.

    RF difference is one of the reasons Craig Venter rejects common descent…

    R. Green uses the word machines in reference to RNA and such 🙂

  4. J-Mac: You don’t remember your own OP at TSZ?

    Yes, I do; I was raising an eyebrow at your clumsy phrasing. “Your speculations on the sex evolution”. If you’re not a native English speaker, I apologise.

  5. J-Mac: Typical excuses when asked about the so-called scientific evidence…

    But it is a fact. Science is not solely done by people in lab coats. If you think ‘scientific evidence’ is synonymous with ‘experimental evidence’, you demonstrate little in the way of clue. But if it IS the way science is done, let us see the experimental evidence for the involvement of Design, QM, and/or ‘some as yet undiscovered thingy’ in the self assembly of flagella.

    You wouldn’t want to operate a double standard, would you?

  6. J-Mac:
    The interesting thing about the bacterial flagellum is that it can’t even be intelligently design by human designers…

    Comedy gold. The flagellum can’t even be designed, so it must have been designed.

  7. J-Mac: Perhaps the fact that my kids use my account at times can explain some of the mystery…

    So when you appear to talk crap, it’s actually your kids? Busy kids.

  8. J-Mac:

    RF difference is one of the reasons Craig Venter rejects common descent…

    Venter can think what he likes; nonetheless, I think you made that up.

  9. J-Mac: Wow! That’s a really nice find! Thanks!
    I totally forgot aboutthe chasm separating the release factors of bacteria and eukaryotic cells… Convergent evolution can explain anything and everything… In other words convergent evolution is magic lol.

    RF difference is one of the reasons Craig Venter rejects common descent…

    I didn’t know that.

    R. Green uses the word machines in reference to RNA and such

    Below is a still from an excellent video by Bruce Alberts in which he gives a short account of the road to discovering the workings of DNA replication.

    The process turned out to be “much more complicated than anyone had imagined.”

    He describes the system as “a complex of proteins that works like what we call a protein machine.” They are like machines because, “…they also need ordered movements, in this case ordered movements of proteins and RNA molecules.” and “you need ordered movements to make machines”

    He states further that: “Nearly all cell processes will be based upon elegant mechanisms, too hard to predict.” He commentated that the view of life in the old days was, “basically everything was a random collision.”

    I would like to add that to compare living systems to machines is a vast simplification. Possibly in the future, scientists will be saying that life has turned out to be much more complicated than when we modelled it as the ordered interaction of nano-machines.

  10. Allan Miller:

    J-Mac:
    The interesting thing about the bacterial flagellum is that it can’t even be intelligently design by human designers…

    Comedy gold. The flagellum can’t even be designed, so it must have been designed.

    J-Mac wrote, “can’t even be intelligently design by human designers” which you interpret as, “can’t even be designed”. Why do you seem to think that humans are the only beings that are capable of producing designed objects?

    When it comes to design, we humans are always playing catch up to the natural world.

  11. CharlieM: J-Mac wrote, “can’t even be intelligently design by human designers” which you interpret as, “can’t even be designed”.

    Pretty sure you’re missing Allan’s point there. He’s mocking the classic creationist argument that organisms must be designed because they are so complex that we can’t design them.

  12. BruceS: BTW, that von Neumann work is a Pavlov’s bell for the Pattee groupies.

    I began to immediately salivate. It was cruel of you to post it, 500 dollars!?

    ETA: You found a book I don’t have!

    Yet. 🙁

    BruceS: You never called my bluff made in another thread on their research program.

    I apologize. 🙂

  13. J-Mac: What is the better metaphor to describe the living systems that perform the same or very similar functions man-made machines do?

    Our good friend Rumraket seems to favor the wind blowing the leaves.

  14. BruceS: On the other hand, all biological explanations must be constrained by physics, and in some isolated cases we may find mechanisms which directly involve quantum physics.

    But if the laws of physics are descriptive they don’t constrain anything. Constraints are determined by what a thing is, iow, by internal factors.

  15. Here is another video by Bruce Alberts. At about five and a half minutes in it shows a white blood cell chasing a bacterium. What’s the difference between this and a large fish chasing smaller fish or a cat chasing a mouse? As above, so below 🙂

  16. dazz: He’s mocking the classic creationist argument that organisms must be designed because they are so complex that we can’t design them.

    He would be right to mock that, but that’s not the argument. Critics of ID remind me so much of critics of evolution.

  17. Mung: But if the laws of physics are descriptive they don’t constrain anything. Constraints are determined by what a thing is, iow, by internal factors.

    And what determines those internal factors’ constraints?

  18. Mung: dazz: He’s mocking the classic creationist argument that organisms must be designed because they are so complex that we can’t design them.

    Mung: He would be right to mock that, but that’s not the argument.

    Sure it is. J-Mac must have made the taunt a hundred times that we are incapable of creating life in the lab. I recall once seeing Stephen Meyer making a similar statement. Yet they both claim that it is obvious that organisms bear similarities to man-made devices. So how can they be sure that humans are incapable of recreating life?

  19. Mung: But if the laws of physics are descriptive they don’t constrain anything.

    This seems obviously false.

    Personally, I don’t take the laws of physics to be descriptions. I take them to be conventions (human social conventions, if you want more detail).

    The laws of physics do constrain scientists, and that’s all that BruceS was claiming. Descriptions are also supposed to constrain behavior of the people who use those descriptions. If descriptions did not constrain anything, then there would be no point in having descriptions.

  20. Neil Rickert: This seems obviously false.

    Are you saying it is not true? Because I’d like to know which definition of truth you are working with today, especially if it’s the one where you don’t know what truth is.

  21. Allan Miller: Venter can think what he likes; nonetheless, I think you made that up.

    Now it is what you think is untrue… First it was untrue…
    Pretty consistent with your set of beliefs… lol

  22. CharlieM,

    Thanks for the video Charlie! I’ll try to watch it tonight…

    BTW: What was it that you were referring to that was going to amuse me?
    I thought you were referring to Green calling RNA “machines”, no?

  23. Mung: Our good friend Rumraket seems to favor the wind blowing the leaves.

    I think Rumraket prefers the hydro-vents’ creative and animate powers that first led to abiogenesis, then to the making the inanimate matter animate, then to the immortality of the first living organism until it could selfreplicate and evolve death…
    Don’t tell this story to your children though! They may think you made this fairytale up! That is… if you have any children… 😉

  24. CharlieM:
    Why do you seem to think that humans are the only beings that are capable of producing designed objects?

    Because we are the only such beings I am aware of.

    This is the dumb syllogism behind ID. “We design stuff, therefore other stuff must have been designed … oh no, we can’t design *that*.”.

    You don’t even agree on what does the designing. You go for waffly crystallization out of the fabric of the universe, most of ’em go for a personal God.

  25. Mung: Emulate Darwin and read Paley.

    Emulate Darwin, read Paley, then explain why Paley’s suppositions are rendered moot by the aforementioned, one should say. Things have moved on a tad.

  26. J-Mac: I didn’t know that… If you this is untrue you show us proof… and I will be more than happy to correct my view…Let’s see…

    Well, if Venter actually said that, it would be a simple matter to say where. Expecting me to prove the negative would be a bit dumb, I feel, if a simple positive existed.

    So, where does Venter say this?

  27. Bruce Alberts from the video I linked to earlier:

    I just want to emphasize the new feature in our textbook that was added. For students to really make sure that they don’t assume that there’s nothing left to discover because I think we would claim that maybe 5% of what we need to understand about cells is known. We know a lot of facts but we don’t understand the great complexity. And so we added a new feature at the end of each chapter called what we don’t know. These are important things that we don’t know and just what we don’t know. These are challenges for the future students and scientists to thus discover so there’s a huge amount left to do in this field of cell biology.

    Bruce Alberts is an expert who has done years of research and yet he shows a great deal of humility in being aware of our ignorance.

    John Horgan, on the other hand, wrote in the Afterword of “The End of Science” about the possiblity of him having self-doubt:

    …since my book’s publication last June, I have become even more convinced that I am right and almost everyone else is wrong…

  28. J-Mac: Now it is what you think is untrue… First it was untrue…
    Pretty consistent with your set of beliefs… lol

    All you have to do to make a monkey of me is to show it to be true. You’ve let two posts slip by without taking the opportunity to evidence your claim. I think I hear a cock crow.

  29. CharlieM:
    Bruce Alberts is an expert who has done years of research and yet he shows a great deal of humility in being aware of our ignorance.

    Which is, I have to say, more than one can say for the average Creationist.

  30. J-Mac:
    CharlieM,

    Thanks for the video Charlie! I’ll try to watch it tonight…

    BTW: What was it that you were referring to that was going to amuse me?
    I thought you were referring to Green calling RNA “machines”, no?

    I was just connecting what you had written:

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

    “Natural forces work “like magic”

    with Green’s use of the word “magic” 🙂

  31. CharlieM: CharlieMxIgnored says:

    November 25, 2018 at 3:15 pm

    Allan Miller:
    J-Mac:
    The interesting thing about the bacterial flagellum is that it can’t even be intelligently design by human designers…
    Comedy gold. The flagellum can’t even be designed, so it must have been designed.
    J-Mac wrote, “can’t even be intelligently design by human designers” which you interpret as, “can’t even be designed”. Why do you seem to think that humans are the only beings that are capable of producing designed objects?
    When it comes to design, we humans are always playing catch up to the natural world.

    Everyone in the right frame of mind knows what I meant… Just because Allan Miller is biased, because of his preconceived ideology, it doesn’t make my argument invalid… For the sake of my kids, and others who either think like kids or choose to, I will use an illustration.

    When my kids were small, they decided to build a doghouse or a birdhouse. I can’t remember now. When they realized the project was beyond them; they couldn’t design and assemble d/b house they came to me…Just to test their perceptions and a sense of reality I asked them whether it was possible for the d/b house to design and assemble itself…

    I don’t have to say how they responded… I think…

    When my kids realized the project was beyond what they could recreate (because they must have seen d/b houses somewhere) they didn’t turn to nature to do the job for them. They turn to a source of higher knowledge and ability to design and assemble their d/b house.
    Why didn’t they turn to nature for the random processes to do it instead of them?

    Because everyone, even small kids, knows that energy has to be precisely directed, carefully controlled in its application to the tools, nails, screws, wood etc. in order to assemble as simple design as d/b house… Darwinists are different though… Whenever they can’t recreate even the “simples” form of life, they automatically assume that random process must have done… rather than following the logic of everyone else, like my kids, and turn to the superior source of design…

    That’s why Darwinism doesn’t follow logic and can’t fit any scientific and consistent reasoning…

  32. Allan Miller: Which is, I have to say, more than one can say for the average Creationist.

    If people are going to be judged, I would prefer that they are judged as individuals and not because of any group to which they may thought of as belonging to.

  33. CharlieM: I was just connecting what you had written:

    with Green’s use of the word “magic”

    Thanks Charlie! I missed that… 🙂 I will have to watch the video again…unless you know when she said it…

  34. There’s also the perennial confusion between design and assembly. I can design a cell on a scrap of paper. Now build it.

  35. Allan Miller: All you have to do to make a monkey of me is to show it to be true. You’ve let two posts slip by without taking the opportunity to evidence your claim. I think I hear a cock crow.

    Don’t you think the same applies to you?

  36. CharlieM: If people are going to be judged, I would prefer that they are judged as individuals and not because of any group to which they may thought of as belonging to.

    Yes, very sententious. I’m sure you’ll direct the same at J-mac next time he takes a swipe at ‘Darwinists’. (Yes, I know that’s a tu quoque).

    But I stand by my sweeping generalisation. Y’all profess humility (especially the Bible-thumping ‘miserable sinner’ types), yet the collective you know that phylogenetics is based on a fiction, that geology (if of the 6000 year persuasion) is painstaking hogwash, that evolution of the mutation-selection kind does not occur … subjects about which you know nothing are summarily dismissed because you have a better idea. Am I wrong?

  37. J-Mac: I think Rumraket prefers the hydro-vents’ creative and animate powers that first led to abiogenesis,

    So true, the preferable explanation of how the designer obtained his powers and used them to animate is much more convincing and verifiable.

  38. J-Mac: Don’t you think the same applies to you?

    Strike three!

    No, I don’t. How on earth can I provide evidence that Venter did not say something the only evidence of which is that you say he did?

  39. J-Mac: Don’t you think the same applies to you?

    You claimed it was true, if you can’t support it, his claim you made it up, does have support.

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