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 …

 

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

  1. OMagain: The advantage of following the Law of Demeter is that the resulting software tends to be more maintainable and adaptable.

    Do organisms would be even more maintainable and adaptable than they already are if only they followed the D in SOLID? What about the other four letters?

    OMagain: As biology seems to be yet more complex then mere computer programs, why were similar guidelines not followed?

    You’re contradicting yourself.

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  2. For those who would like to continue this conversation:

    There is enough solid evidence that quantum processes control life systems, including self-assembly of the molecular machines, such as the bacterial flagellum. There are a lot of speculations that life itself could be quantum; that the right or specific quantum arrangement of particles constitutes life. Paul Davies has been speculating about that for a while now but in his new upcoming book he apparently makes some bold statements about it. I didn’t hear him say that yet, so I will wait until my pre-ordered book arrives. What I do know is that quantum processes and q. information can be disrupted… If quantum processes, or quantum information are disrupted in the bacterial cell and it doesn’t self-assemble the flagellum, what logical, an unbiased conclusion can or should be made?

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  3. Mung: Do organisms would be even more maintainable and adaptable than they already are if only they followed the D in SOLID? What about the other four letters?

    You’re contradicting yourself.

    Is it not what supporting ideologies rather than evidence is all about?

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  4. J-Mac: If quantum processes, or quantum information are disrupted in the bacterial cell and it doesn’t self-assemble the flagellum, what logical, an unbiased conclusion can or should be made?

    The critical thing here will be to design the experiment such that other, more mundane, explanations have been ruled out.
    Happy to help out…

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  5. DNA_Jock: The critical thing here will be to design the experiment such that other, more mundane, explanations have been ruled out.
    Happy to help out…

    I agree. It’s not easy because of the nature of QM but it can be done…What do you have in mind? How can you contribute?

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  6. J-Mac,
    The way scientists usually help each other: critiquing their experimental design. I’m a biochemist by training, you claim expertise in QM; if you put forward a protocol, I will review it.

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  7. DNA_Jock:
    J-Mac,
    The way scientists usually help each other: critiquing their experimental design. I’m a biochemist by training, you claim expertise in QM; if you put forward a protocol, I will review it.

    If I claimed to be a moron, would it help your case? I don’t mind…

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  8. Mung: Organisms are adaptable. And they are not adaptable. That’s a contradiction.

    Individuals do not adapt, in the evolutionary sense.

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  9. Mung: Organisms are adaptable. And they are not adaptable. That’s a contradiction.

    There is a word for it: evolution lol

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  10. Just watched this video by Elizabeth Blackburn.

    It just so happens that what takes place at the intra-cellular level is controlled by our bahaviour and attitude. This seems obvious to me. We now have the ability to examine protein complexes right down to the amino acid level as demonstrated in the image below which shows just one part of a single dynein motor, but in the end the control comes from the level of the individual organism.

    And while we look at this image we should not forget that this is but a snapshot of what is a dynamic, never static, living process which is happening countless times in the vast majority of our body cells. And it must be happening in a coordinated balanced way from the level of the individual atoms and molecules, through the cellular level and the level of the organs, up to the level of the individual. No matter where we look the balance of nature is evident at all levels of life.

    The image was taken from here

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  11. DNA_Jock:
    CharlieM,
    ‘Dead’ and ‘alive’ have meaning at the level of cells and above, agreed.
    But the distinction is not clear-cut: there’s alive, dying, freshly dead and completely dead. Your CFU quote illustrates the ‘dying’ category nicely: cells that still have some metabolic activity, but will die before they divide.
    Anyone in cardiac arrest can be considered freshly dead; that’s how they teach CPR students.
    Lyall Watson wrote (badly) about this grey “Romeo error” area in 1975, for a shorter and more compelling discussion, see this 1987 work.
    But it makes no sense to apply these labels to proteins.
    Proteins may be functioning, reversibly inhibited, irreversibly inhibited, or denatured.
    Yes, researchers may colloquially refer to a non-functioning enzyme as ‘dead’; it doesn’t mean that the enzyme was ever ‘alive’, any more than re-naturing RNAseA is an example of “resurrection”.

    We can be certain that a person is dead when there is no metabolic activity in any of their somatic cells which means, among other things, that there will be no dynein or kinesin complexes moving along microtubules. Until that happens there can be ambiguity because some parts of the person may be alive while other parts have died. But if there is no molecular activity within each individual cell then that cell is dead and the processes of decay will set in immediately.

    For something to be alive there must be balance maintained between growth and decay. Any imbalance leads to illness and ultimately death. Cancer is an imbalance towards growth. Death is not like a single switch that can be turned on or off, it is a process. So I would take your 4 categories even further and say it is more analogue than discrete. 🙂

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  12. Corneel: What is problematic is that you are NOT talking about including organic chemistry but about some molecules having “inner [purposeful, organised] activity” without being able to clarify what the hell that means. To me it sounds an awful lot like élan vital, and I am not keen on swallowing that.

    So once again: tell me what “inner activity” is. Is it selected biochemical function? That might properly describe both DNA polymerase and dynein function to the exclusion of e.g. urea function.

    It is simply what is observed. Within a living person, inner activity is seen in the blood flowing through the vascular system, the beat of the heart, the rhythm of the breathing, these are examples of inner activity, and all this ceases at death. In a cell examples are the cellular metabolism, the transcription and translation of the DNA into proteins and the maintenance of membranes. In the protein complexes it is the constant conformational changes such as in the universal joint of a bacterial flagellum, the transport of substances within the complex.

    All these examples are activities that can be observed to take place within each of the subjects being studied. There is no undisclosed mystery behind this, it is purely the activity that is observed.

    We can say the same thing about an internal combustion engine. It displays inner movement with a purpose. But we cannot say the same thing about a river flowing towards the ocean.

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  13. Corneel:

    CharlieM: Well from what I can gather from some people’s thinking, we should consider them to be alive. Why are they less alive than red blood cells?

    CharlieM: I would say that crystals are dead matter that has an inherent form which it retains during growth. Living forms grow but they also differentiate.

    Well, I guess we need to upgrade the biology curriculum with some solid state physics and car mechanic classes then.

    Why?

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  14. CharlieM,

    Thanks for video Charlie!
    When the telomeres were first connected to longevity the hope was that one day the immortality through genetics could be achieved…Today we know it isn’t so…
    The connection between telomeres and healthy lifestyle makes this quote come alive more than ever:

    “The best doctors are Dr Diet, Dr Quiet, and Dr Merryman.” Cf. a1449 Lydgate Minor Poems

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  15. Kantian Naturalist: It’s not anthropomorphizing per se, but it is a nice case of the metonymic fallacy: attributing to a part of a system a property that is correctly attributed to the whole.

    There is nothing wrong with seeing equivalences between parts and the the whole as long as it is recognised that there factors that distinguish one from the other as well as factors that link them. So can you be specific about the way in which you think I am committing the fallacy?

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  16. CharlieM: It is simply what is observed.

    Not by me.

    CharlieM: We can say the same thing about an internal combustion engine. It displays inner movement with a purpose. But we cannot say the same thing about a river flowing towards the ocean.

    Nope. Doesn’t work for me. To me, purpose is a thing of conscious minds. Seeing purpose in a combustion engine looks an awful lot like projection to me.

    You can keep piling on example after example, but I simply don’t see what you see. I do not extend my empathy to blood, or proteins, or engines, like you seem to be doing.

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  17. CharlieM: Well, I guess we need to upgrade the biology curriculum with some solid state physics and car mechanic classes then.

    Why?

    Sshhhh. Did you just hear a whooshing sound? 😀

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  18. J-Mac:
    CharlieM,

    Thanks for video Charlie!
    When the telomeres were first connected to longevity the hope was that one day the immortality through genetics could be achieved…Today we know it isn’t so…
    The connection between telomeres and healthy lifestyle makes this quote come alive more than ever:

    “The best doctors are Dr Diet, Dr Quiet, and Dr Merryman.” Cf. a1449 Lydgate Minor Poems

    I’m glad you enjoyed the video.

    I’m sure that most here would agree that lifestyle affects individual development, but if we start talking about lifestyle affecting evolution then we will probably be accused of advocating Lamarkism. But the fact is that lifestyles do affect species evolution as can be seen in the case of moles or blind cave fish. In the case of teleomeres the determining factor is the lifestyle of the individual, in the case of moles and blind cave fish it is the life style of the whole group.

    By the way you might be interested you might be interested in this piece entitled “Quantum Puzzles” by Stephen Talbott. It was written in 2004 but it’s still relevant. I like his analogy of today’s science being imagined as a logical-mathematical grid laid over the world. There is an interesting video on YouTube featuring discussions between scientists and the Dalai Lama here

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  19. Corneel: To me, purpose is a thing of conscious minds. Seeing purpose in a combustion engine looks an awful lot like projection to me

    Of course you are correct about projection. We can see the purpose of the designer projected into the design of the engine. We can see how the designer was thinking when s/he planned the construction. This is one of the major differences between life and machines. With machines such as the internal combustion engine the source of its purpose is external to it.

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  20. Alan Fox: Individuals do not adapt, in the evolutionary sense.

    You must believe then, that organisms are also not adapted to their environment (niche).

    Features of organisms, such as the flagellum, are not adaptations?

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  21. CharlieM: This is one of the major differences between life and machines. With machines such as the internal combustion engine the source of its purpose is external to it.

    Yet just a moment ago you likened it to the “inner activity” of cells and proteins. So now the internal purpose of an engine is a projection of the external purpose of its designer? You know what this is beginning to sound like? How do you feel about the inner activity of watches?

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  22. Mung: You must believe then, that organisms are also not adapted to their environment (niche).

    Features of organisms, such as the flagellum, are not adaptations?

    Genomes of individuals are fixed. Changes occur at reproduction. Offspring are not clones of parents (in sexually reproducing species).

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  23. Corneel: Yet just a moment ago you likened it to the “inner activity” of cells and proteins. So now the internal purpose of an engine is a projection of the external purpose of its designer? You know what this is beginning to sound like? How do you feel about the inner activity of watches?

    Yes there is inner activity in an engine. For example the pistons move in a linear direction and the crankshaft has a rotary motion. The purpose of the mechanical arrangement is to allow a linear force to be converted into a rotary torque. Chemical energy is actively converted into mechanical energy.

    What originated as a conception in human minds becomes an active physical reality. And it is the same with watches. In fact we can see the progression in human thinking in the development of watches over the years.

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  24. CharlieM: Just watched this video by Elizabeth Blackburn.

    It just so happens that what takes place at the intra-cellular level is controlled by our bahaviour and attitude.

    This is absolutely gibberish. How is it possible to die from inhaling nerve gas if you can just “decide” to have a “I refuse to die”-attitude?

    Stop spewing absolute gibberish, it’s moronic. The chemical reactions will happen regardless of how much you feel you want them to stop, or do something else.

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  25. CharlieM: And it is the same with watches. In fact we can see the progression in human thinking in the development of watches over the years.

    You appear to miss what I am getting at, so let me spell it out for you:

    Your argument about seeing the purpose and design in biological entities echoes the watchmaker analogy. In fact, you were drawing an explicit parallel between the “inner activity” of proteins and cells and the designer’s purpose projected into the design of a combustion engine. That is a spitting image of the discussion I just had with phoodoo. Also, you argue that machines are conscious life’s attempts to recreate itself, which to me is just a reversal of phoodoo’s claim that cells are machines.

    Why the hell do you guys have such problems with telling organisms and machines apart?

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  26. Alan Fox: Genomes of individuals are fixed.

    Are not.

    Changes occur at reproduction.

    But not during development, or is that reproduction too?

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  27. Mung: But not during development, or is that reproduction too?

    Yes, an individual’s genome stays unchanged during development.

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  28. CharlieM,

    Its worth noting that the takeaway from this video is that this thing materialists call the bag of chemicals can determine what happens to the bag of chemicals and change the bag of chemicals.

    And what is it that is determines what happens to the bag of chemicals? Well, the bag of chemicals of course.

    And evolutionist claim they have an explanation for this.

    I do not like green eggs and ham.

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  29. phoodoo,

    What is this dark and mysterious pact between you and Charlie? You told me cells are machines. Charlie thinks machines are an attempt to recreate life. To me these are almost diametrically opposed viewpoints, yet you are in some sort of agreement. Most puzzling.

    Wait! It’s this purpose-thingy again isn’t it?

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  30. Alan Fox: It seems to be an agreement against evolution. There doesn’t appear to be any “for”.

    As long as people don’t think life is due to physics, they can think what they like about what it is due to, seems to be the general thrust of all the enthusiastic mutual head-nodding. You never see an argument between the evolution-doubters on mechanism – or anything else much.

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  31. Corneel:
    phoodoo,

    What is this dark and mysterious pact between you and Charlie? You told me cells are machines. Charlie thinks machines are an attempt to recreate life. To me these are almost diametrically opposed viewpoints, yet you are in some sort of agreement. Most puzzling.

    Wait! It’s this purpose-thingy again isn’t it?

    Did you even watch the video? It has nothing whatsoever to do with defining machines. Its about how through conscious will, we change the length of the telomeres in your DNA.

    Which in a materialist world view, where humans are just sophisticated bags of chemicals, makes no sense that the chemicals can choose (or not choose) to change their chemical structure.

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  32. phoodoo: Which in a materialist world view, where humans are just sophisticated bags of chemicals, makes no sense that the chemicals can choose (or not choose) to change their chemical structure.

    In non-material world view, design does not preclude humans beings being sophisticated bags of chemicals either. Unless you know something about the designer , somehow.

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  33. newton: In non-material world view, design does not preclude humans beings being sophisticated bags of chemicals either. Unless you know something about the designer , somehow.

    Right. Unless one believes in things that are immaterial. In which case one has a case for human beings being more than a bag of chemicals.

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  34. Rumraket:

    CharlieM: Just watched this video by Elizabeth Blackburn.

    It just so happens that what takes place at the intra-cellular level is controlled by our bahaviour and attitude.

    This is absolutely gibberish. How is it possible to die from inhaling nerve gas if you can just “decide” to have a “I refuse to die”-attitude?

    Stop spewing absolute gibberish, it’s moronic. The chemical reactions will happen regardless of how much you feel you want them to stop, or do something else.

    To look at what I wrote in context, I said:

    (The video shows that) It just so happens that what takes place at the intra-cellular level (growth and decay of telomeres) is controlled by our bahaviour and attitude (demonstated by Blackburn’s research and, if she is to be believed, by the “10000 scientific papers and counting” that links a person’s lifestyle with telomere length.)

    No one is saying that we consciously control our molecular processes. Have you watched the video?

    Nerve gas is an external influence which causes a loss of control of the cellular processes. Would you argue that because a pilot or computer is in control of an aircraft it becomes immune from being blown out of the sky? We may have conscious or unconscious control of our breathing but that does not prevent us from being strangled, suffocated or drowned. External influences can overcome internal control.

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  35. newton,

    I think the only other option that leaves is if we are all part of a computer simulation without any free will.

    That seems a pointless thing to believe in, and if it were true, you wouldn’t have the choice to believe or not believe in it.

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  36. Corneel:

    CharlieM: And it is the same with watches. In fact we can see the progression in human thinking in the development of watches over the years.

    You appear to miss what I am getting at, so let me spell it out for you:

    Your argument about seeing the purpose and design in biological entities echoes the watchmaker analogy. In fact, you were drawing an explicit parallel between the “inner activity” of proteins and cells and the designer’s purpose projected into the design of a combustion engine.

    I was also pointing out the differences. Any purposeful activity seen within a living entity has its source within that entity. The source of the purposeful activity of machines lies outside of them. Can you not see that this is a major difference?

    That is a spitting image of the discussion I just had with phoodoo. Also, you argue that machines are conscious life’s attempts to recreate itself, which to me is just a reversal of phoodoo’s claim that cells are machines.

    Why the hell do you guys have such problems with telling organisms and machines apart?

    It is you who doesn’t seem to comprehend the difference I have pointed out.

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  37. phoodoo:
    CharlieM,

    Its worth noting that the takeaway from this video is that this thing materialists call the bag of chemicals can determine what happens to the bag of chemicals and change the bag of chemicals.

    And what is it that is determines what happens to the bag of chemicals?Well, the bag of chemicals of course.

    And evolutionist claim they have an explanation for this.

    I do not like green eggs and ham.

    I’m saying nothing, we aren’t supposed to agree on anything 🙂

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  38. Alan Fox: It seems to be an agreement against evolution. There doesn’t appear to be any “for”.

    It all depends on how you define evolution.

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  39. CharlieM: It all depends on how you define evolution.

    If you mean a one-sentence summary, the change in allele frequency due to differential reproductive success of individuals within a population.

    So which bits are you for?

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  40. newton: Without an ordained goal or purpose.

    How about, to quote from “The Life of Brian”, “We are all individuals”. There is no, us and them, we are just a group of people with our own personal opinions and beliefs. Because of their differing beliefs, C.S. Lewis and Owen Barfield had what they referred to as the Great War:

    The ‘Great War’ is C.S. Lewis’s and Owen Barfield’s most significant philosophical debate, defining their life-long views on the roles of reason and the imagination in finding truth. It spanned several years of conversations, letters and treatises in the 1920’s

    But throughout this time they remained the best of friends. Nothing here quite compares to this extreme example, but I’m sure you get the drift.

    Some things we will agree on others we will disagree on and that is the way it should be. We learn more from our disagreements than we do from any common ground we may share. So I am happy to carry on disagreeing 🙂 I have learned a great deal from all of the contributors here.

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