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 …

 

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

  1. J-Mac
    Ignored
    says:

    I know that self-assembling machines are a part of everyone’s regular life…
    But, let’s get real…

    Just imagine you get an IKEA delivery and your desk self-assembles when you open the box…
    You may have ordered IKEA furniture in the past and had to assemble it yourself, but self-assembly is a treat… Can anybody relate to that?
    Self assembly of molecular nano-machines is deep…

  2. Mung Mung
    Ignored
    says:

    No, I don’t think it’s Jesus…

    The baby Jesus?

    Nice find from over at BioLogos, could you post the link?

    I don’t think the flagellum assembles itself. That’s just more poor writing over there. I wonder if they think atoms self-assemble.

  3. CharlieM CharlieM
    Ignored
    says:

    Hi J-Mac, I was thinking of starting a post on discussing the ever-more detailed images that are being produced of these “nano-machines” in action, so I am pleased to see this post appearing. The video you provided is very interesting and adds a few new findings since I last looked at flagellar growth. I have been watching a few videos on this general subject, one video in an excellent series can be seen here. Its about chromosomal DNA replication.

    I would quite like it if instead of nano-machines we used terms like nano-beings and nano-life, as these things have much more to them than any human designed objects. To me, dynein and kinesin “motors” are far more suggestive of marching ants than rail wagons or highway trucks. They are living entities.

    Does what you have in mind have anything to do with quantum physics?

  4. J-Mac
    Ignored
    says:

    Mung: The baby Jesus?

    Nice find from over at BioLogos, could you post the link?

    I don’t think the flagellum assembles itself. That’s just more poor writing over there. I wonder if they think atoms self-assemble.

    The link was in the OP and then… I don’t know anymore.. Can’t blame the kids…They had notin to do with it…
    https://biologos.org/blogs/kathryn-applegate-endless-forms-most-beautiful/self-assembly-of-the-bacterial-flagellum-no-intelligence-required
    Nothing self-does it unless it is intelligent or it is guided by intelligence… Third option would be the quantum world, because it usually defeats logic…
    How about you? Any ideas?

  5. J-Mac
    Ignored
    says:

    CharlieM:
    Hi J-Mac, I was thinking of starting a post on discussing the ever-more detailed images that are being produced of these “nano-machines” in action, so I am pleased to see this post appearing. The video you provided is very interesting and adds a few new findings since I last looked at flagellar growth. I have been watching a few videos on this general subject, one video in an excellent series can be seen here. Its about chromosomal DNA replication.

    I would quite like it if instead of nano-machines we used terms like nano-beings and nano-life, as these things have much more to them than any human designed objects. To me, dynein and kinesin “motors” are far more suggestive of marching ants than rail wagons or highway trucks. They are living entities.

    Does what you have in mind have anything to do with quantum physics?

    I’m glad we are on the same page… I like your analogy…If nano-machines are not alive, what makes them behave as if they were intelligent machines?
    Is Quantum Physics going to explain self-assembly? If it doesn’t, God’s guidance would have to…I think…There is a way of testing quantum guidance… If it is true, it could be significant…

  6. newton
    Ignored
    says:

    J-Mac: If nano-machines are not alive, what makes them behave as if they were intelligent machines?

    Are atoms nano-machines?

  7. Allan Miller
    Ignored
    says:

    J-Mac,

    Is Quantum Physics going to explain self-assembly? If it doesn’t, God’s guidance would have to.

    That is what is known as a false dichotomy.

    The problem here is exporting macro level intuitions to molecular scales. Physics isn’t the same ‘down there’. While one might imagine that bolting together cells is much the same as bolting together a fridge, it just ain’t. You can’t just shove atoms around and not have them react while you manoeuvre them into place. So, you invoke magic: the temporary suspension of physics.

  8. Alan Fox Alan Fox
    Ignored
    says:

    newton: Are atoms nano-machines?

    Lipid rafts are a classic example of how molecules self-assemble according to their inherent properties.

  9. CharlieM CharlieM
    Ignored
    says:

    J-Mac: I’m glad we are on the same page… I like your analogy…If nano-machines are not alive, what makes them behave as if they were intelligent machines?
    Is Quantum Physics going to explain self-assembly? If it doesn’t, God’s guidance would have to…I think…There is a way of testing quantum guidance… If it is true, it could be significant…

    I think we both agree that quantum effects can’t be ignored, especially when dealing with matter at the molecular and atomic level. I’ve previously put forward some of my thinking on this. IMO there is a polarity between the infinitely small (point) and the infinitely large (plane), neither being more fundamental than the other. The formation and “self-assembly” of matter comes about by the interplay from both directions, and the reason that quantum entanglement is a known phenomenon is because both particles are separate from a point-wise perspective but from the other direction they both share the one plane at infinity. This is what unites them. Quantum entanglement makes no sense from a point-wise perspective, but it does make sense from a plane-wise perspective.

    Playing around with Plato’s five regular solids, in pairs, in relation to a sphere as they shrink and expand, is a good way of imagining the polar effects. We are used to imagining fundamental particles while we ignore the fundamental plane which unites them.

  10. CharlieM CharlieM
    Ignored
    says:

    J-Mac:
    From your link
    Kathryn Applegate writes:

    Scientists are pretty clever at teasing out the workings of microscopic machines like the flagellum. The general order of assembly was meticulously worked out by removing individual protein components one at a time and observing what occurred. If you remove the flagellin protein, for instance, you get the base and the hook, but not the tail. This tells us that the tail forms late in the assembly process. If you remove one of the proteins that make up the MS-ring, on the other hand, the motor elements do not assemble and neither does the rest of the flagellum. That’s how we know the MS-ring isn’t just tacked on at the end.

    Well removing flagellin tells me that the tail is made up of this protein and so would be hard to assemble without it. It is “tacked on” at the end which is precisely where it should be, that is why it is called the tail.

    I think that she is trying to hint that the tail is just an afterthought, so to speak.

  11. CharlieM CharlieM
    Ignored
    says:

    Alan Fox: Lipid rafts are a classic example of how molecules self-assemble according to their inherent properties.

    Yes, the properties of matter are ideal for producing living substances. Where would we be without the ability of matter to form a staggering variety of polypeptides and such like?

  12. BruceS
    Ignored
    says:

    Four intermixed issues in the OP: three scientific, one psychological (“Does anyone know what I [J-Mac] have in mind?]. Addressing the last would likely violate Lizzie’s Laws, so I will stick to others.

    The three science issues are: origin of life requires self-assembly; living cell replication; evolutionary reproduction, ie how can evolutionary mechanisms produce complex machines. OOL is partly addressed in preceding posts, and evolution of the flagellum and other “irreducible” complexity is well-addressed in other posts on TSZ.

    On self-replicating machines: Von Neumann started modern research into self-replicating machines. He said there were four theorectical requirements:
    (1) constructor to build given explicit blueprints
    (2) blueprint copier
    (3) controller causing (1) and (2) processes to alternate
    (4) set of blueprints

    For modern living cells, according to linked book, there four are fulfilled by:
    (1) ribosomes
    (2) DNA polymerase enzymes
    (3) expression-control molecules in the cell (eg repressor, depressor molecules)
    (4) DNA

  13. BruceS
    Ignored
    says:

    FWIW, there is also a philosophical issue alluded to in the post and subsequent comments: will we ever be able to be able to completely express explanations of the biological processes of OOL, replication, reproduction and evolution using only the language of quantum physics?

    Few believe the extreme reductionism that says we will have such explanations. 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.

  14. J-Mac
    Ignored
    says:

    newton: Are atoms nano-machines?

    Do they self-assemble???

  15. J-Mac
    Ignored
    says:

    Allan Miller:
    J-Mac,

    That is what is known as a false dichotomy.

    The problem here is exporting macro level intuitions to molecular scales. Physics isn’t the same ‘down there’. While one might imagine that bolting together cells is much the same as bolting together a fridge, it just ain’t. You can’t just shove atoms around and not have them react while you manoeuvre them into place. So, you invoke magic: the temporary suspension of physics.

    Of course it is false dichotomy… I didn’t mean it… I meant to tease the theistic evolutionists, like Dr. Swamidass, who use exactly the same analogy, which is obviously false…

    Am I invoking magic? I think you got be confused with the biologos boys… lol

    I’m trying to explain it from a scientific point of view which could invoke quantum physics and possibly some kind of an unknown energy and a mechanism for directing that energy…
    But this kind of an assumption is not unknown to the world of physics, don’t you know?

  16. J-Mac
    Ignored
    says:

    Alan Fox: Lipid rafts are a classic example of how molecules self-assemble according to their inherent properties.

    Of course…I’ve mentioned similar properties in the OP and did Behe in his books…
    Do these properties explain the reversed production and the assembly of the rod? Can they explain the self-assembly process outside of the cell-membrane?

  17. J-Mac
    Ignored
    says:

    CharlieM: I think we both agree that quantum effects can’t be ignored, especially when dealing with matter at the molecular and atomic level. I’ve previously put forward some of my thinking on this. IMO there is a polarity between the infinitely small (point) and the infinitely large (plane), neither being more fundamental than the other. The formation and “self-assembly” of matter comes about by the interplay from both directions, and the reason that quantum entanglement is a known phenomenon is because both particles are separate from a point-wise perspective but from the other direction they both share the one plane at infinity. This is what unites them. Quantum entanglement makes no sense from a point-wise perspective, but it does make sense from a plane-wise perspective.

    Playing around with Plato’s five regular solids, in pairs, in relation to a sphere as they shrink and expand, is a good way of imagining the polar effects. We are used to imagining fundamental particles while we ignore the fundamental plane which unites them.

    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…

  18. Neil Rickert
    Ignored
    says:

    BruceS: FWIW, there is also a philosophical issue alluded to in the post and subsequent comments: will we ever be able to be able to completely express explanations of the biological processes of OOL, replication, reproduction and evolution using only the language of quantum physics?

    That’s backwards.

    We describe quantum physics in a language that derives from biology (from our biology).

  19. J-Mac
    Ignored
    says:

    BruceS: Four intermixed issues in the OP: three scientific, one psychological (“Does anyone know what I [J-Mac] have in mind?]. Addressing the last would likely violate Lizzie’s Laws, so I will stick to others.

    If you were trying to offend me you have not succeeded… All radical ideas initially meet this kind of criticism… Many years ago I was severely criticised for one of my ideas… Today, it provides me with a comfortable living and respect… Unfortunately, the critics spoke too soon and it didn’t go over well for them… 😉

    BTW: When have I offended or tried to offend you?

  20. BruceS
    Ignored
    says:

    Neil Rickert: That’s backwards.

    We describe quantum physics in a language that derives from biology (from our biology).

    Hilbert spaces etc are derived from biology?

    The language and concepts of quantum physics to me means appropriate mathematics as used by physicists. It does not mean whatever is used by various commentators on TSZ or popularizers of QM.

    And I was not referring to epistemology of concepts.

    ETA: reworded for clarity and/or greater pedantry

  21. OMagain
    Ignored
    says:

    J-Mac: I’m trying to explain it from a scientific point of view which could invoke quantum physics and possibly some kind of an unknown energy and a mechanism for directing that energy…

    “could”, “possibly”, “unknown”.

    Some “explanation”.

  22. OMagain
    Ignored
    says:

    J-Mac: All radical ideas initially meet this kind of criticism

    But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.

  23. BruceS
    Ignored
    says:

    J-Mac

    BTW: When have I offended or tried to offend you?

    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.

  24. Allan Miller
    Ignored
    says:

    J-Mac:I’m trying to explain it from a scientific point of view which could invoke [waffly waffly handwave vague allusion sciency-sounding stuff]

  25. Neil Rickert
    Ignored
    says:

    BruceS: Hilbert spaces etc are derived from biology?

    No. But Hilbert spaces don’t describe QM.

    Yes, we can use Hilbert space in our descriptions of QM. But we have to go beyond the mathematics to make that connection.

    You can have a pure language — one that is not dependent on our biology. And mathematics can reasonably be said to be such a language. But, by itself, mathematics can only talk about abstract entities. You need the biology if you want intentionality, as in the ability to talk about things in the actual world.

  26. J-Mac
    Ignored
    says:

    Allan Miller: J-Mac:I’m trying to explain it from a scientific point of view which could invoke [waffly waffly handwave vague allusion sciency-sounding stuff]

    Really? How does this compare to your vague allusion science-sounding stuff on the sex evolution? Can you experimentally prove it? Until then, your speculations are just as good mine… Well, maybe with the exception that my assumptions can be experimentally tested…

  27. Allan Miller
    Ignored
    says:

    J-Mac: Really? How does this compare to your vague allusion science-sounding stuffon the sex evolution? Can you experimentally prove it? Until then, your speculations are just as good mine… Well, maybe with the exception that my assumptions can be experimentally tested…

    ‘The sex evolution’? 😃

    Experimental proof is certainly not the only way to do science. If it were, perhaps you could demonstrate assembly of a functional flagellum using Design.

  28. DNA_Jock
    Ignored
    says:

    Moved a post to guano.

  29. Mung Mung
    Ignored
    says:

    Allan Miller: That is what is known as a false dichotomy.

    🙂

    So, you invoke magic: the temporary suspension of physics.

    To me, physics is magic. So when you invoke physics, you invoke magic.

  30. Gregory Gregory
    Ignored
    says:

    “the self-assembly process has supposedly evolved”

    What does ‘the self-assembly process’ extend from? What are its origins? Stop talking enough already about ‘supposedly evolved’ and chose instead alternative grammar that is applied in a coherent way.

    In this case, the definition of ‘self’ (with assembly/assembling or other action verbs) appears quite limited & slanted in a particular way. It’s folk IDism at the end of the day, which relies on unknown better thinking even to maintain it, yet without gratefulness.

  31. Allan Miller
    Ignored
    says:

    Mung:

    To me, physics is magic. So when you invoke physics, you invoke magic.

    So when your basic physics operates, it’s magic, and when that physics is suspended by some mysterious means, that is also magic. Sucking the meaning out of language, one word at a time!

    “The Monk currently believed that the valley and everything in the valley and around it, including the Monk itself and the Monk’s horse, was a uniform shade of pale pink. This made for a certain difficulty in distinguishing any one thing from any other thing … “

  32. J-Mac
    Ignored
    says:

    Gregory: What does ‘the self-assembly process’ extend from? What are its origins? Stop talking enough already about ‘supposedly evolved’ and chose instead alternative grammar that is applied in a coherent way.

    In this case, the definition of ‘self’ (with assembly/assembling or other action verbs) appears quite limited & slanted in a particular way. It’s folk IDism at the end of the day, which relies on unknown better thinking even to maintain it, yet without gratefulness.

    Are you telling me there is empirical, experimental evidence that proves the flagellum can evolve?
    Are you referring to the experiments where a bacteria without a flagellum evolved a flagellum?
    Or are you referring to the experiment where a gene for the flagellum was deleted and the bacteria has evolved a flagellum?
    Or are you referring to the experiment where a point mutation was inserted into the flagellum gene and natural selection eliminated this mutation over many generations?
    Or is there another experimental evidence I have not thought about?

  33. Mung Mung
    Ignored
    says:

    Allan Miller: Sucking the meaning out of language, one word at a time!

    I even have my own Wikipedia page!

    https://en.wikipedia.org/wiki/Mung_(computer_term)

  34. Mung Mung
    Ignored
    says:

    BruceS: On self-replicating machines: Von Neumann started modern research into self-replicating machines.

    Are you buying into the machine metaphor for living organisms? We’ll make an IDist of you yet. 😉

  35. Alan Fox Alan Fox
    Ignored
    says:

    J-Mac: Or is there another experimental evidence I have not thought about?

    I imagine there’s quite a lot you haven’t thought about. If you dissolve sugar in water and leave the solution in a dish where the water can evaporate, the sugar comes out of solution and forms crystals of a specific shape and structure. How does that happen? The scientific explanation is emerging properties.

  36. Alan Fox Alan Fox
    Ignored
    says:

    In idle moments I wonder if there is some law of the universe holding back development of intelligent beings. Say we could design and build intelligent machines that were just a bit more intelligent than us. Could they not then design and build new intelligent machines that were a bit more intelligent than them. Those new more intelligent machines could then… That it hasn’t yet happened, does that mean it can’t?

  37. BruceS
    Ignored
    says:

    Mung: Are you buying into the machine metaphor for living organisms? We’ll make an IDist of you yet.

    No, I’m only buying into the theoretical possibility of self-replicating machines. And to the fact that von Neumann was smarter than anyone posting at TSZ, even possibly in the aggregate.

    I am not sure what the machine metaphor for living cells means or entails, so I’ll plead the 5th on that. Although I do not know if a Canadian can plead the 5th, especially one posting on a blog hosted in the UK (soon to be only England).

    Perhaps your post was meant as a pre-emptive retort to something Gregory might say. If so, well-played.

    BTW, that von Neumann work is a Pavlov’s bell for the Pattee groupies. You never called my bluff made in another thread on their research program.

  38. BruceS
    Ignored
    says:

    Alan Fox:
    Say we could design and build intelligent machines that were just a bit more intelligent than us. Could they not then design and build new intelligent machines that were a bit more intelligent than them. Those new more intelligent machines could then… That it hasn’t yet happened, does that mean it can’t?

    Whole philosophical careers are based that idea.

    It is also important to the various philosophers and AI true believers who think we must research immediately how to give machines morality.

  39. Alan Fox Alan Fox
    Ignored
    says:

    BruceS,

    One day, I’ll have an original thought! 🙂

  40. Kantian Naturalist Kantian Naturalist
    Ignored
    says:

    BruceS:
    FWIW, there is alsoa philosophical issue alluded to in the post and subsequent comments:will we ever be able to be able to completely express explanations of the biological processes of OOL, replication, reproduction and evolution using only the language of quantum physics?

    Few believe the extreme reductionism that says we will have such explanations.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.

    I think that any putative reduction of biological phenomena to fundamental physics is — I shall be blunt — conceptually impossible, because there is no possible translation from a tensed logic to a tenseless logic. The equations of fundamental physics are time-reversible.

    But biology requires not only time (which enters the scene with thermodynamics) but also history: what has come before constrains what can happen now. And that can only be expressed in a tensed logic — a logic with temporal operators.

    So even though we can get some nice mileage out of extending quantum mechanics to certain biological mechanisms, I’m severely skeptical of any whole-scale reduction from biology to physics.

  41. Alan Fox Alan Fox
    Ignored
    says:

    Kantian Naturalist: But biology requires not only time (which enters the scene with thermodynamics) but also history: what has come before constrains what can happen now. And that can only be expressed in a tensed logic — a logic with temporal operators.

    Is the universe strictly determined. Know enough about the present and you are informed about past and future. IDists seem to think (IDists please correct me if I err) that they can tell something about the history of a system by some kind of numerical transformation of numbers derived from its present state.

  42. Allan Miller
    Ignored
    says:

    I don’t see – and doubt I will be made to see by any unexpected outbreak of clarity – what saying “QM” gives us here. Even granting that the electromagnetic force, the basis of atomic and molecular interaction, is basically a quantum phenomenon (mediated by photons; we’re held together by light!).

  43. J-Mac
    Ignored
    says:

    Alan Fox: I imagine there’s quite a lot you haven’t thought about. If you dissolve sugar in waterand leave the solution in a dish where the water can evaporate, the sugar comes out of solution and forms crystals of a specific shape and structure. How does that happen? The scientific explanation is emerging properties.

    Allan,
    How does your comment relate to my comment and the OP?
    Please give me one reason why I should even read your comments further…

  44. J-Mac
    Ignored
    says:

    Mung: Are you buying into the machine metaphor for living organisms? We’ll make an IDist of you yet.

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

  45. Alan Fox Alan Fox
    Ignored
    says:

    J-Mac: Allan,

    It’s Alan, One ‘L’.

    How does your comment relate to my comment and the OP?

    An example of self-assembly. Under suitable conditions, in the case of crystal formation – saturation – results in crystals, molecules in a specific ordered formation. Do you not think it is such an example? What about bilipid layers in cell membranes. DNA spirals, protein alpha helices?

  46. Alan Fox Alan Fox
    Ignored
    says:

    J-Mac: Please give me one reason why I should even read your comments further…

    Nope.

  47. J-Mac
    Ignored
    says:

    Allan Miller: Experimental proof is certainly not the only way to do science. If it were, perhaps you could demonstrate assembly of a functional flagellum using Design.

    Typical excuses when asked about the so-called scientific evidence… Speculations and assumptions are another way of doing science, or I should rather say, the only way to support the Darwinian ideology…
    That’s why I’m on the opposite side because each time I demand experimental evidence I get excuses and speculations instead…

    The interesting thing about the bacterial flagellum is that it can’t even be intelligently design by human designers… There is just no way.. similarly to the MIT cheetah that doesn’t even come close to the superior design of the living cheetah…

    To biased Darwinists it means random process must have done what human intelligence can’t…

    http://theskepticalzone.com/wp/special-intelligence-required-to-detect-design/

    That’s way a very special kind of intelligence is required to detect design… lol

  48. J-Mac
    Ignored
    says:

    Alan Fox: Nope.

    Good bye!

  49. J-Mac
    Ignored
    says:

    Kantian Naturalist: So even though we can get some nice mileage out of extending quantum mechanics to certain biological mechanisms, I’m severely skeptical of any whole-scale reduction from biology to physics.

    What evidence is your scepticism based on?

  50. CharlieM CharlieM
    Ignored
    says:

    BruceS: On self-replicating machines: Von Neumann started modern research into self-replicating machines. He said there were four theorectical requirements:
    (1) constructor to build given explicit blueprints
    (2) blueprint copier
    (3) controller causing (1) and (2) processes to alternate
    (4) set of blueprints

    For modern living cells, according to linked book, there four are fulfilled by:
    (1) ribosomes
    (2) DNA polymerase enzymes
    (3) expression-control molecules in the cell (eg repressor, depressor molecules)
    (4) DNA

    Thanks for drawing our attention to this very interesting book which can be read in full here.

    They quote von Neumann making a distinction between self-reproduction and self-replication. And this is the distinction between life and non-living crystals.

    …von Neumann: “One of the difficulties in defining what one means by self-reproduction is that certain organizations, such as growing crystals, are self-reproductive by any naive definition of self-reproduction, yet nobody is willing to award them the distinction of being self-reproductive. A way around this difficulty is to say that self-reproduction includes the ability to undergo inheritable mutations as well as the ability to make another organism like the original [i.e., make a copy].” The mere ability to make a viable copy, but not to undergo heritable mutation, is therefore not self-reproduction but only self-replication.

    And so there is a big difference between making self-replicating machines and making self-reproducing machines.

    Living cells easily fulfil these four requirements listed above but they are so much more than self-replicating machines.

    Ribosomes are worth looking at in detail.

    Freitas and Merkle give a brief description of the ribosome:

    The core of the bacterial ribosome consists of 4565 “molecular parts” (nucleotide bases) of only four different “parts types” (the nucleotide bases A, C, G, and U), and the supporting protein structural framework of total mass ~0.85 MDa is constructed of 52 distinct proteins composed of ~6025 amino acid residue “parts” (assuming ~0.1411 kD/residue) of 20 different “parts types.” Thus we may say that the bacterial ribosome assembler is a partially self-replicating machine that is built of ~10,590 “molecular parts” and 24 different “parts types.” (Using the same counting method, the mammalian ribosome has ~18,780 parts.) These totals do not count the external supporting environment which includes tRNA “parts holders” and aminoacyl-tRNA synthetase “parts holder reloaders” of 20 different types each, various elongation factors that cyclically associate and dissociate with the ribosome, rRNA polymerase enzymes that construct both mRNA “instruction tapes” and rRNA feedstock molecules via transcription, various chaperone molecules to assist in proper protein folding, and the mRNA instruction tape itself. Note that because the ribosome cannot produce its own most important component, rRNA, the ribosome is not a fully self-contained self-replicating machine, but may most precisely be regarded as the key component of a self-replicating system.

    A video which gives more details on the ribosome can be found here. Of course the ribosome does not function in isolation. For a start it requires exogenous protein factors for its operation.

    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:

    …the magic of how the robosomes identify the appropriate AUGs” (start codons)

    and:

    …we also know that there is a very magical event that takes place, which is that when the ribosome identifies the correct tRNA, conformational changes take place within the ribosome that accelerate some of the forward rate constants in this scheme making these events go more quickly when the right tRNA is bound.

    Physics, biology, it’s all magic!

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