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

  1. Allan Miller
    Ignored
    says:

    CharlieM,

    The entire thrust of living beings may be centred on procreation, but this is not the case when it comes to humans

    Really. That would explain why they’ve all died out, I suppose.

  2. Corneel Corneel
    Ignored
    says:

    CharlieM: I was talking about finch beaks or peppered moth melanism, and in these cases the variations already exist in the populations, it is just the frequency that changes.

    Isn’t it interesting how stuff can change and change, without ever resulting in something new?

    CharlieM: The entire thrust of living beings may be centred on procreation, but this is not the case when it comes to humans.

    Which explains why there are only 7.5 billion of us.

    CharlieM: Do you believe that animals have personality on a par with humans, that they should be considered people? Have you ever kept slow worms, stick insects, or the like as pets?

    One of my boys keeps a praying mantis (Hymenopus coronatus) as a pet. They are easy to identify individually because they have extensive colour polymorphism, but I doubt that he can identify us as individual beings. The point I am trying to make here is that humans are geared towards perceiving individual differences, because we are social animals. Of course, we excel in particular at identifying individual humans.

    Now consider this: Every day you visit this site, you glance at the penguins at the top. Would you be able to tell them apart from other chinstrap penguins? Of course not. Yet fishing penguins need to find their family back in huge colonies, like the one shown below. How do they manage that if all penguins lack distinguishing features? They couldn’t, so probably they do have them. It’s just that you are incapable of picking up on those features (the secret is that they recognise each other’s calls).

    And that’s your anthropocentrism at work. You mistake our ability to recognise other humans but not other animals for actual high levels of individuality in humans

    picture from here

  3. CharlieM CharlieM
    Ignored
    says:

    Rumraket:

    CharlieM: When we say “I am conscious” we have already divided reality into entities, myself and that which I am conscious of. What justifies us in making this distinction?

    Well I think the justification for that is the very experience in question. I have the experience of being myself, of being present in a particular location, of having some sort of spatial boundary, and an experience that there are other things that are not part of me but I only interact with. I don’t have an experience of being the chair I sit in, or the the coffee I drink.

    I can see out my window and the trees are moving in the wind. I cannot feel that wind, I don’t think I’m the tree standing in the wind, and it isn’t part of me. I’m pretty sure I’m “just” this semi-hairy primate sitting in my chair.

    Of course you are justified because of the separation you experience between yourself and the world around you. This is a necessary stage of evolution. We are cast out into the void so to speak. So much so that some people even doubt their own existence. Owen Barfield spoke about this in 1970:

    In my opinion a great deal of what is going on around us today can be traced to the presence in very many minds of an unspoken question and an unspoken answer to it. For the most part both question and answer remain not merely unspoken; they are not even consciously formulated. The answer, if it were formulated, would be either ‘No’ or ‘I don’t know’. As to the question, in the ordinary life of society perhaps the nearest it usually comes to formulation occurs in early adult life in the shape of what is sometimes called ‘the identity crisis’. In circles interested in philosophy or metaphysics however it is sometimes explicitly formulated and as explicitly answered in the negative. The question is ‘Do I exist?’

    IMO humans have descended from a unity with nature to our present dualistic position through which we experience of division between us and nature. This is the lowest point of human descent. Further evolution brings an ascent back to unity, only this time in full awareness.

    Here you are practicing what Barfield described as “onlooker consciousness”. But you are not alone, we all do it. According to Barfield, human consciousness has evolved from a condition of original participation, a time when we felt ourselves to be a part of nature and did not think of it as a separate world “out there”. Our feeling of separation came with the rise in self-consciousness just as our individual self-consciousness arises slowly as we develop from birth. Then came the “onlooker consciousness” which is our usual mode of thinking and by which you see yourself in your room separate from the wind blowing outside, after all this is what your senses are telling you. This is the same thinking which has been practiced by scientists and has brought us the great discoveries about our universe. Observation of nature required us to stand back and look on it as separate entities. To observe something you need to stand outside it. But we are moving towards a time of enhanced consciousness which Barfield calls “final participation”. The difference between this and “original participation” is that we participate in a more self-conscious way. It is up to us as individuals whether we remain at the stage of “onlooker consciousness” or whether we participate. The discoveries of quantum physics have hinted at this, showing that whether or not we are conscious of it, we are participating in reality, we are not just standing outside looking in. The very process of observation does not leave nature untouched.

    There is no physical substance you can point to and say, “this is me”. The physical substance is forever changing, never remaining constant. And so if you believe that physical substance is all there is then the logical conclusion to draw from this is that the “I” is not real.

    Here is an extract from ‘Immortal Diamond’ by Richard Rohr, 2013 who is a Franciscan priest:

    Consciousness emerged worldwide with the Eastern sages, the Jewish prophets, and the Greek philosophers, all around 500 B.C. It was the birth of systematic and conceptual thought. In the East, it often took the form of the holistic thinking that is found in Hinduism, Taoism, and Buddhism, which allowed people to experience forms of participation with reality, themselves, and the divine. In the West, the Greek genius gave us a kind of meditated participation through thought, reason, and philosophy…

    Barfield, foresaw the coming of a new Consciousness, when the best of each era will combine and work together: the prerational, the rational, and the transrational. We live in such a time! In this consciousness, we can now enjoy intuitive and body knowledge, along with rational critique and deeper synthesis, thus encouraging both intelligent and heartfelt participation “with our whole heart, soul, mind and strength,” as Jesus puts it (Mark 12:30).

    There is a path towards wholeness and it is up to us to take it or to remain separate and isolated. And that is my opinion.

  4. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:

    The entire thrust of living beings may be centred on procreation, but this is not the case when it comes to humans

    Really. That would explain why they’ve all died out, I suppose.

    The point I am making here is that at the present time there is a difference between humans and animals. For instance rabbits follow their urges without any thought about what they are doing. If they get the urge to mate they go ahead and do it at every opportunity. On the other hand humans, unless they blindly follow their animal nature for personal pleasure, make conscious decisions about these things. So procreation cannot be considered to be the entire reason for their being, it must be viewed on an individual basis.

    I would hope that we have moved past the stage of evolution where procreation is the main thrust (insert nudge, nudge joke here) of our existence.

  5. Allan Miller
    Ignored
    says:

    CharlieM,

    Procreation is the reason for any organism’s being. Meaning that if its parents hadn’t procreated, it wouldn’t be here. That doesn’t mean that all we must do is procreate, nor equally that, as a set of lineages, we have somehow transcended the basics of inheritance.

    Whatever nobility you perceive in non-procreational pursuits – and of course there is much more to life – it remains a biological fact that lineages that don’t procreate die out. That’s what matters for evolution – a DNA sequence has a limited shelf life, and must be copied or lost. But it does not need to be what matters for individuals.

    I think life is fundamentally defined by reproduction; that does not mean I want as many kids as I can generate. I think you are confusing description and prescription.

  6. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: I was talking about finch beaks or peppered moth melanism, and in these cases the variations already exist in the populations, it is just the frequency that changes.

    Isn’t it interesting how stuff can change and change, without ever resulting in something new?

    Here is a translation of an extract from Goethe’s poem “Nature”:

    Eternally she creates new forms. What now is, never was in time past; what has been, cometh not again – all is new, and yet always it is the old.

    We live in the midst of her, and yet to her we are alien. She parleys incessantly with us, and to us she does not disclose her secret. We influence her perpetually, and yet we have no power over her.

    It is as if she founded all things upon individuality, and she recks nothing of individuals. She builds forever, and destroys forever, and her atelier is inaccessible.

    She lives in her children alone, and the mother, where is she? – She is the sole artist, from the simplest material she passes to the extremest diversity; with no hint of strain she arrives at the fullest consummation – at the exactest precision, always veiled in a certain obscurity. Each thing she makes has its own being, each of her manifestations is an isolated idea, and yet they are all one.

    His poem sums up the situation nicely.

    CharlieM: The entire thrust of living beings may be centred on procreation, but this is not the case when it comes to humans.

    Which explains why there are only 7.5 billion of us.

    Okay, so populations grow. But they also decline. So here we observe the universal law of growth and decay which is happening at every level of life from the level of molecules to the level of organism populations. A molecuar example I gave was telomeres. Both of these process are vital in maintaining life as I’ve mentioned previously here.

    CharlieM: Do you believe that animals have personality on a par with humans, that they should be considered people? Have you ever kept slow worms, stick insects, or the like as pets?

    One of my boys keeps a praying mantis (Hymenopus coronatus) as a pet. They are easy to identify individually because they have extensive colour polymorphism, but I doubt that he can identify us as individual beings. The point I am trying to make here is that humans are geared towards perceiving individual differences, because we are social animals. Of course, we excel in particular at identifying individual humans.

    I am not talking about individual differences, I am talking about personality. My wife has a collection of teddy bears. She can tell them apart because each one different from another. This does not mean that they have individual personalities.

    Now consider this: Every day you visit this site, you glance at the penguins at the top. Would you be able to tell them apart from other chinstrap penguins? Of course not. Yet fishing penguins need to find their family back in huge colonies, like the one shown below. How do they manage that if all penguins lack distinguishing features? They couldn’t, so probably they do have them. It’s just that you are incapable of picking up on those features (the secret is that they recognise each other’s calls).

    I have asked others if they would like to compose a list of attributes that demonstrate individuality. You too are welcome to compose a list of all the attributes that demonstrate individuality in chinstrap penguins. You can put down as first on your list the fact that they can recognise individual calls. What other attributes do they possess?

    And that’s your anthropocentrism at work. You mistake our ability to recognise other humans but not other animals for actual high levels of individuality in humans

    picture from here

    It is not just a case of picking other humans out of a crowd. It is a case of studying their life, their habits, their preferences, their talents, their creativity and much else besides.

  7. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    CharlieM,

    Procreation is the reason for any organism’s being. Meaning that if its parents hadn’t procreated, it wouldn’t be here. That doesn’t mean that all we must do is procreate, nor equally that, as a set of lineages, we have somehow transcended the basics of inheritance.

    Whatever nobility you perceive in non-procreational pursuits – and of course there is much more to life – it remains a biological fact that lineages that don’t procreate die out. That’s what matters for evolution – a DNA sequence has a limited shelf life, and must be copied or lost. But it does not need to be what matters for individuals.

    I think life is fundamentally defined by reproduction; that does not mean I want as many kids as I can generate. I think you are confusing description and prescription.

    Okay, I’m happy to agree that procreation is the main thrust of life. So we have procreation which is growth, and to balance this we have death which is decay. So we have two opposing forces, thrust and drag, growth and decay, which on a higher level are not in opposition but are complimentary, both necessary to maintain the balance of nature. What seems like death and destruction from a narrow point of view can be seen from a higher point of view as wisdom.

  8. Corneel Corneel
    Ignored
    says:

    CharlieM: Here is a translation of an extract from Goethe’s poem “Nature”:
    […]
    His poem sums up the situation nicely.

    Love it. You have a romantic soul 🙂

    However, I have no idea whether you are agreeing or disagreeing with me.

    CharlieM: Okay, so populations grow. But they also decline. So here we observe the universal law of growth and decay which is happening at every level of life from the level of molecules to the level of organism populations.

    No, we are talking about reproduction (procreation), not growth. I don’t think I can improve upon Allan’s comment re. this matter.

  9. Corneel Corneel
    Ignored
    says:

    CharlieM: I am not talking about individual differences, I am talking about personality. My wife has a collection of teddy bears. She can tell them apart because each one different from another. This does not mean that they have individual personalities.

    The way I understand it, You are using distinct personalities as an expression of individuality. You are switching between “being different” and “having distinct personality” to support your original claim that there is some ascending scale of individuality going from “prokaryotes” to humans. This is what earned you the allegation of being anthropocentric, because you picked a trait that humans highly value, but gives us no useful intuition about evolutionary trends in general.

    CharlieM: I have asked others if they would like to compose a list of attributes that demonstrate individuality. You too are welcome to compose a list of all the attributes that demonstrate individuality in chinstrap penguins.

    I would say that any feature that enables us to distinguish individual beings from each other contributes to their individuality. I am going retreat to my comfy zone and put genetic differences on the table as an appropriate objective measure. Humans score pretty badly on this scale BTW.

    CharlieM: It is not just a case of picking other humans out of a crowd. It is a case of studying their life, their habits, their preferences, their talents, their creativity and much else besides.

    I’d say these are all valuable attributes, speaking as a human being. Speaking as a biologist, mmmmm not so much.

  10. CharlieM CharlieM
    Ignored
    says:

    Corneel: Love it. You have a romantic soul

    However, I have no idea whether you are agreeing or disagreeing with me.

    No, we are talking about reproduction (procreation), not growth. I don’t think I can improve upon Allan’s comment re. this matter.

    Are you saying that reproduction does not contribute to the growth of the population??

  11. Corneel Corneel
    Ignored
    says:

    CharlieM: Are you saying that reproduction does not contribute to the growth of the population??

    No.

    I am making the point that a lot of useful insights can be gained by distinguishing between replication of distinct entities and a generic increase in size.

  12. Allan Miller
    Ignored
    says:

    CharlieM,

    I think you err in trying to equate reproduction and growth. They are linked, because growth depends on cellular reproduction. But critically, that collection of cells relies upon each other and, equally critically, they are close relatives with a common ‘interest’: nurturing gene copies in gametes. Any given somatic cell foregoes its direct reproduction for that of its gene copies in gametes – a zero-sum trade for any given gene: 100% for direct reproduction vs two 50% chances in the gamete pair generated for average replacement.

    This doesn’t happen in distributed, non-cohered lineages. Without the incentive provided by a soma-gamete relationship, you lose what is essential about growth, in multicellular organisms. With dispersal, the effect of relationship on cohesion diminishes rapidly, apart from some kin selection effects, most notable in the social insects.

  13. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: I am not talking about individual differences, I am talking about personality. My wife has a collection of teddy bears. She can tell them apart because each one different from another. This does not mean that they have individual personalities.

    The way I understand it, You are using distinct personalities as an expression of individuality. You are switching between “being different” and “having distinct personality” to support your original claim that there is some ascending scale of individuality going from “prokaryotes” to humans. This is what earned you the allegation of being anthropocentric, because you picked a trait that humans highly value, but gives us no useful intuition about evolutionary trends in general.

    I am definitely talking about individuality. Being physically different is just one minor aspect of individuality. But even in this humans demonstrate their individuality by the use of tattoos, body piercings, jewellery, clothing, hair styles and other such things. Writing, painting, sculpture, music and all forms of art and creativity are all individual activities which each of us create in our own individual style.

    Are you saying that any visiting extra-terrestrial alien (if there were such things) would not recognise these as objective indications of human individuality which sets us apart from the rest of nature?

    Of course one more thing that sets us apart: Humans can be accused of being anthropocentric. What other organism can be accused of being [insert species name]centric 🙂

    And if categorising things by their individual differences was not an objective, scientific enterprise why is the system of Linnaeus still the mainstay of biological classification?

  14. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: I have asked others if they would like to compose a list of attributes that demonstrate individuality. You too are welcome to compose a list of all the attributes that demonstrate individuality in chinstrap penguins.

    I would say that any feature that enables us to distinguish individual beings from each other contributes to their individuality. I am going retreat to my comfy zone and put genetic differences on the table as an appropriate objective measure. Humans score pretty badly on this scale BTW.

    Yes these features contribute, but only in a small way.

    Retreating to genetics is equivalent to saying that the creative output of a language is dependent on the number of letters in its alphabet. It’s not the human genome size you should be looking at, it’s the number and variety of the molecular products of transcription and translation. Alternative splicing makes counting numbers of nucleotides in the genome pretty pointless. The amount of protein and cell variety would be a more realistic objective measure. And don’t forget that some of the products of transcription and translation are the substances and cells that make up the human central nervous system.

  15. CharlieM CharlieM
    Ignored
    says:

    Corneel:

    CharlieM: It is not just a case of picking other humans out of a crowd. It is a case of studying their life, their habits, their preferences, their talents, their creativity and much else besides.

    I’d say these are all valuable attributes, speaking as a human being. Speaking as a biologist, mmmmm not so much.

    On your path through life you as an individual have chosen to become a biologist. Can you name an individual of any other species that has chosen their path in a similar way?

  16. CharlieM CharlieM
    Ignored
    says:

    Corneel: No.

    I am making the point that a lot of useful insights can be gained by distinguishing between replication of distinct entities and a generic increase in size.

    And a lot of useful insights can be gained by comparing as well as distinguishing. Increase in the size of what? Is it not true that the increase in size of an individual generally comes about by the increase in the number of cells populating that body? So our growth has everything to do with population growth.

  17. DNA_Jock
    Ignored
    says:

    CharlieM: Of course one more thing that sets us apart: Humans can be accused of being anthropocentric. What other organism can be accused of being [insert species name]centric

    This one’s a keeper.
    Every. Single. One.
    Charlie’s anthropocentrism is so strong that he is completely unaware of it.
    What if the aliens that landed here were blind and communicated via smell?
    “…tattoos, body piercings, jewellery, clothing, hair styles and other such… ” would leave them unmoved. We would be judged by our choice of soap and deodorant, and non-primates would be viewed as the smart mammals…

  18. CharlieM CharlieM
    Ignored
    says:

    Allan Miller:
    CharlieM,

    I think you err in trying to equate reproduction and growth. They are linked, because growth depends on cellular reproduction. But critically, that collection of cells relies upon each other and, equally critically, they are close relatives with a common ‘interest’: nurturing gene copies in gametes. Any given somatic cell foregoes its direct reproduction for that of its gene copies in gametes – a zero-sum trade for any given gene: 100% for direct reproduction vs two 50% chances in the gamete pair generated for average replacement.

    This doesn’t happen in distributed, non-cohered lineages. Without the incentive provided by a soma-gamete relationship, you lose what is essential about growth, in multicellular organisms. With dispersal, the effect of relationship on cohesion diminishes rapidly, apart from some kin selection effects, most notable in the social insects.

    I’m not equating growth with reproduction, I am comparing growth and differentiation of cell populations within an individual to growth and differentiation of populations of organisms. As above so below.

  19. Allan Miller
    Ignored
    says:

    CharlieM: I’m not equating growth with reproduction, I am comparing growth and differentiation of cell populations within an individual to growth and differentiation of populations oforganisms. As above so below.

    That sounds like the stance I was criticising, to me. The rephrasing makes no material difference to the points I made in relation to it.

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