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

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

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

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

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

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

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

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

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

“Natural forces work “like magic”

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

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

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

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

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

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

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

 

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

  1. phoodoo: If you can’t get that, much like Omagain can’t, that’s not my fault.

    If evolution were true, what would we expect to see?

    Given that we do not see that, what instead is the actual explanation?

  2. phoodoo: There needs to be a whole spectrum of progress, from the first mutation, to ones that are slowly
    spreading, to new uses of organs.

    The Evolution of Bacteria on a “Mega-Plate” Petri Dish
    https://www.youtube.com/watch?v=plVk4NVIUh8

    If you want to see evolution in near real time, which is what your complaint appears to be (why don’t we seeee it???) bacteria are what you have to accept as a demonstration. If you want to see noses grow in real time, go watch Pinocchio.

  3. DNA_Jock:
    Hey, phoodoo has learnt something. The last time we had this conversation, his opening gambit was

    Much hilarity ensued. With pictures!

    You understanding was woeful then and it is even more so now. You are approaching Omagain levels of incomprehension. Some members of the population carrying an attribute which other members don’t have, and which is being purposed for a new use. THAT is the issue Jock. You don’t get it.

    The point was never whther there can be a mutation which can cause an animal distortion. The point was when in that trajectory does it become an advantage which is being used by SOME of the population, slowly weeding out the ones without. THAT is the scenario we should expect to see if evolution were true, and we can’t find it. A cat with extra toes doesn’t do it. Forty percent of the cats in a population, which are using the extra digit as a compass, that the other cats in the same population don’t have with which to use, now that would qualify!

    You are just as bad as Rumraket saying, Well, some people have bigger arms that others. Yea, but they haven’t invented a NEW purpose for arms that will make other kinds of arms obsolete!! They haven’t turned their arms into snorkels.

    Your understanding of the issue is pathetic.

  4. DNA_Jock: Hey, phoodoo has learnt something.

    How many decades do you think it’ll be before phoodoo is actually disputing the sorts of things in our understanding of evolution that are actually worth disputing? 😛

    At what pixel do we shade from arguing against to arguing about?

  5. Rumraket: At what point does it cross over from not-nose, to nose? How different must the anatomical features be? How big must the structure be before it is a “nose” rather than a flat surface with an opening?

    Great great, then a flat surface with an opening. That would be just fine. And some members of the population have the flat surface with an opening an some don’t. And because some have it, they mate more, produce offspring more. It should be obvious which ones have it and which don’t right? After all, its enough to cause them to mate more, right?

    In the entire animal kingdom, the best example of ANY new function appearing, is bacteria resistance. That’s it!!?? What about all the rest, why don’t they evolve?

    Don’t give me the bullshit about it takes a long time. Fine, show me the ones that started thousand years ago then. And now half have it and half don’t. That should be simple as hell. You want to go with Jocks cats? Then you better show me the re-purposing of the new paws.

  6. phoodoo: You understanding was woeful then and it is even more so now.

    It’s “your” understanding.

    phoodoo: You are approaching Omagain levels of incomprehension.

    What is it that I don’t understand? You seem remarkably reluctant to explain.

    phoodoo: Some members of the population carrying an attribute which other members don’t have, and which is being purposed for a new use.

    What or who is doing the purposing? Can you give an example of when something is being purposed for a new use?

    phoodoo: THAT is the issue Jock. You don’t get it.

    Whatis the issue? That mutations originate in individuals? That purposing happens somehow?

    phoodoo: The point was never whther there can be a mutation which can cause an animal distortion.

    By “distortion” presumably you mean a change away from the perfection of the original biblical kind? There can be a concept of “distort” only if you have a reference you can measure distance from.

    phoodoo: The point was when in that trajectory does it become an advantage which is being used by SOME of the population, slowly weeding out the ones without.

    At the point it provides an advantage. That seems simple to me. Unless it’s visible to selection, it can’t be selected for.

    phoodoo: THAT is the scenario we should expect to see if evolution were true, and we can’t find it.

    Oh, you should have said!
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048992/
    Lactase persistence is one of the clearest examples of niche construction in humans. Lactase is the enzyme responsible for the digestion of the milk sugar lactose and its production decreases after the weaning phase in most mammals, including most humans. Some humans, however, continue to produce lactase throughout adulthood, a trait known as lactase persistence. In European populations, a single mutation (−13910*T) explains the distribution of the phenotype, whereas several mutations are associated with it in Africa and the Middle East.

    phoodoo: A cat with extra toes doesn’t do it. Forty percent of the cats in a population, which are using the extra digit as a compass, that the other cats in the same population don’t have with which to use, now that would qualify!

    Would it? Why? It might work in phoodoo-evolution but if you want to play the game with other people you have to accept things as they currently are defined.

    But congratulations! You have proposed an experement that potentially falsifies evolution. It’s shit, but it’s a start.

    phoodoo: You are just as bad as Rumraket saying, Well, some people have bigger arms that others. Yea, but they haven’t invented a NEW purpose for arms that will make other kinds of arms obsolete!! They haven’t turned their arms into snorkels.

    Again, in phoodoo-evolution, your mangled strawman, that might be the case. But look at the evidence – how many people have you successfully argued away from believing in evolution?

    phoodoo: Your understanding of the issue is pathetic.

    And yet given that understanding questions can be answered and references given. You can do no such thing. Therefore logic dictates your understanding is worse then pathetic.

  7. Rumraket: At what point does the usage of arms become new?

    When the arm causes some to be able to use it as a flashlight and some not. That would be new, got it? Same animal, still can breed with other animals without the new arm, but this one has a flashlight, and a lot of the other members of the pack don’t have the flashlight. Could be quite an advantage don’t you think?

    Now don’t say, oh a flashlight, that’s absurd, no animals have flashlights.

    Well, when no animals had eyes, and some got a light sensitive spot that let them see, that was just like getting a crude flashlight, right? And not all of them had it, only some right? And it made them better then the ones without it right?

    And that only happens before, not now?

  8. phoodoo: Great great, then a flat surface with an opening.

    Something I’m sure even your Intelligent Designer could manage.

    phoodoo: And some members of the population have the flat surface with an opening an some don’t. And because some have it, they mate more, produce offspring more.

    Or perhaps they just survive more, so there are more of them to mate with in the first place.

    phoodoo: After all, its enough to cause them to mate more, right?

    Or perhaps there are more of them to mate with?

    phoodoo: In the entire animal kingdom, the best example of ANY new function appearing, is bacteria resistance. That’s it!!?? What about all the rest, why don’t they evolve?

    No, but you seem to want to see it in real time. And that’s the best example of that. Evolution takes place over long periods of time. And, despite that, there is clear evidence of evolution. I won’t link you to anything however. Been there, done that.

    phoodoo: Don’t give me the bullshit about it takes a long time.

    Or, in other words, facts.

    phoodoo: Fine, show me the ones that started thousand years ago then.

    Even better, here is an example of rapid speciation: http://science.sciencemag.org/content/359/6372/224
    Oh, but where are the new organs? Well, if you want to play, you have to use definitions we share. This example shows that reproductive isolation, which typically develops over hundreds of generations, can be established in only three..

    phoodoo: You want to go with Jocks cats? Then you better show me the re-purposing of the new paws.

    Why? If evolution were true, what would you expect cat paws to look like? Given that they do not look like that, how do you explain them?

    See what I did there?

  9. OMagain,

    Lactase Man! The newest marvel superhero! Slay the cheese and gets all the chics! Who can stop him?

    Make Jock proud!

  10. phoodoo: And it made them better then the ones without it right?

    How many blind animals are there compared to sighted ones? Can you visualise how being able to see might be an advantage over not being able to see?

    phoodoo: And that only happens before, not now?

    It’s been a long time since the sighted have outcompeted the sightless. Why would you expect to see it happening now when it’s already happened? Biology has moved on.

    And in any case, there are plenty of blind cave fish whose ancestors started out sightless. So going blind made them better then the ones who spent energy building useless eyes. Odd that.

  11. phoodoo: Lactase Man! The newest marvel superhero! Slay the cheese and gets all the chics! Who can stop him?

    You are just like colewd. You ask for an example of something then when you get exactly what you asked for you ignore it’s significance. Do you think anyone is fooled?

    Next week you’ll be asking for the same example. Integrity much?

  12. phoodoo: Some members of the population carrying an attribute which other members don’t have, and which is being purposed for a new use.

    I gave you that example. Agree/Disagree?

  13. CharlieM: There is no vitalism required, if by vitalism you mean some external life-force hovering over the substance. The life-force belongs to the polymerase itself and is as much a feature of it as the physical matter of which it is composed. It only becomes dead substance when it loses the ability to have inner activity.

    Whether the life-force is “hovering over” or internal is not very relevant, is it? You are definitely advocating some form of vitalism.

    What exactly is this life force, this “inner activity”? Is it the polymerase activity? Then why are we able to describe the reaction mechanism in purely chemical terms, like we do for anorganic molecules? There is no ghost in the box, Charlie. We don’t need an extra ingredient to understand what happens in the test tube.

    CharlieM: The lack of self-replication does not preclude them from being living substance.

    Yes it does, because we have defined life that way. It’s not carved in stone so you are free to play the definition game, like phoodoo did, but then you may find some weird stuff qualifying as living things. Be warned!

    CharlieM: Anyone who just sees it all as physics and chemistry will deny this essential difference between living and dead substance and so will not even bother to undertake any further research into the difference. IMO this is a missed opportunity.

    What is that essential difference? Does ureum have life-force? Does ethanol (it’s already called spirits)? Sugars or lipids perhaps? I doubt that you will enjoy your futile search for life force.

  14. DNA_Jock:

    CharlieM: What happens in your PCR is a living process. They even talk of the polymerase used in PCR processes as having a half-life.

    Oh crap.
    Any process where the rate of reaction (e.g. decay) is proportional to the amount of substance unreacted will exhibit a so-called exponential decay. Radioactive decay is the most well-known example, but enzyme denaturation can also show this pattern. An intuitive way of describing the RATE of decay is to quote the “half-life”, that is the amount of time it takes for half of the substance to decay.
    After two “half-lifes” only a quarter remains, after three, an eighth, etc.
    It’s got NOTHING to do with having any vital essence.

    You talk about decay. Growth and decay are important features of life. What happens when an enzyme becomes denatured? It moves from a state of restless inner activity (life) to a static conformation (death). Whether it is in a test tube or in the organism to which it belongs it will demonstrate its living nature through its activity, and when it denatures or dissipates into the surrounding environment it can be considered dead.

    Life and death are the two necessities of the natural world.

    If you think about the “crap” that you like to talk about, you will see that it is the product of death and decay but it becomes a foundation for its opposite, growth and life. Each feeds of the other.

  15. OMagain,

    Lactase Man?

    Jock, do you pay Omagain to write stupid shit, over and over, to try to provide you cover for your abject misunderstandings?

  16. phoodoo: Jock, do you pay Omagain to write stupid shit, over and over, to try to provide you cover for your abject misunderstandings?

    Abject misunderstandings of what? Your position? What relevance does that have? Misunderstanding of evolution? According to who, you? How come, if you understand it all so well you never seem to answer any questions put to you? You give a great impression of someone criticizing something they don’t actually understand.

  17. How well has putting your fingers in your ears worked out for you phoodoo? How many people does that convince a year, I wonder?

  18. OMagain: Can you visualise how being able to see might be an advantage over not being able to see?

    Man, I sure love meta-jokes.

  19. phoodoo: In the entire animal kingdom, the best example of ANY new function appearing, is bacteria resistance. That’s it!!??

    Bacteria in the animal kingdom? Hahahahaa….

  20. Corneel,

    But here’s what I want to know Corneel. I doubt Omagain can figure it out, maybe you can. How come we can see Lactase Man? I mean, evolution takes a long time, right? Far too long for us to actually be able to see him appear right? So how can we see Lactase Man and not Lactase man?

    Doesn’t it take to long to be able to see them?

  21. BruceS: I do think that “Dynamics in Action” has an interesting take on purpose/teleology in organisms. I’m not saying it’s correct, only that it shows one way to build on ideas in dynamics and information without introducing anything like vitalism.

    Yes, that’s one of the reasons I like Juarrero’s approach. She’s also very good at explaining how modern thinking about causation and explanation led us awry.

    I also like Godfrey-Smith take on synthesizing these types of ideas into a unified approach to life, cognition, subjectivity, phenomenality.

    Oh, for sure. PGS is an excellent philosopher-scientist. His book on cephalopods is lovely. I use it in my philosophy of mind course. I’ll read the paper you linked to during my winter break.

  22. I see we have one person here thinking that bacteria are in the animal kingdom and another who thinks that radioactive decay is the same kind of thing as biological decay.

    Hmmmm.

  23. Kantian Naturalist,

    Yea, I guess Omagain does think that. Because I asked for examples of new organs forming, not organelles, and his example was bacteria resistance.

    Rumraket argues that every organ that comes into existence is by definition fully formed. So I guess all of our organs are both fully formed and undergoing trial and error. This is the absurdity of evolution.

    But to give him credit, he later did come up with Lactase Man.

  24. OMagain: That a single mutation has the power to generate a new organ in a single step?

    Why not? Is there a law against it? Do you just not understand the theory?

    ‘Untamed chance’, pure, naked chance, means ordered design springing into existence from nothing in a single leap. It would be untamed chance if once there was no eye, and then, suddenly, in the twinkling of a generation, an eye appeared, fully fashioned, perfect and whole. This is possible, but the odds against it will keep us busy writing noughts till the end of time.

    – Dawkins, Richard. The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe without Design

  25. Mung: Why not? Is there a law against it? Do you just not understand the theory?

    Clearly it’s you who doesn’t understand. It’s possible in principle to have an organism with a lot of mutations and a new eye, but the probability of all those mutations happening to a single organism is vanishingly low. FFS, where in that quote do you think it supports the idea that a single mutation can generate a new organ?

  26. Mung: Why not? Is there a law against it? Do you just not understand the theory?

    I was going to take a look at that Dawkins book, but before I could, all the air molecules went momentarily to the other side of the room and I passed out.

    I figured Dawkins is bad luck and decided to let sleeping Maxwellian demons lie.

  27. Corneel:

    CharlieM: There is no vitalism required, if by vitalism you mean some external life-force hovering over the substance. The life-force belongs to the polymerase itself and is as much a feature of it as the physical matter of which it is composed. It only becomes dead substance when it loses the ability to have inner activity.

    Whether the life-force is “hovering over” or internal is not very relevant, is it? You are definitely advocating some form of vitalism.

    I’m not all that keen on labels, but to say that I’m advocating some sort of vitalism is fine with me.

    What exactly is this life force, this “inner activity”? Is it the polymerase activity? Then why are we able to describe the reaction mechanism in purely chemical terms, like we do for anorganic molecules? There is no ghost in the box, Charlie. We don’t need an extra ingredient to understand what happens in the test tube.

    Yes what we observe is the living activity by which DNA is copied. We can describe the process in purely chemical terms just as we could describe the process by which Shakespeare wrote his works purely in terms of the make-up of the ink and paper. The problem is that the whole of the story is left out by doing so.

    So regarding just the physics and chemistry, what do we miss by looking at polymerase chain reaction (PCR) generating DNA. We miss the fact that someone has to organise the chemicals, and the appropriate environment. Then the medium needs to be heated and cooled to the correct range of temperatures in the correct sequence. The physics and chemistry tells us nothing about the organisation of the procedure. And there has to be an organising principle for anything to happen.

  28. BruceS: I was going to take a look at that Dawkins book, but before I could, all the air molecules went momentarily to the other side of the room and I passed out.

    😀

  29. Corneel:

    CharlieM: The lack of self-replication does not preclude them from being living substance.

    Yes it does, because we have defined life that way. It’s not carved in stone so you are free to play the definition game, like phoodoo did, but then you may find some weird stuff qualifying as living things. Be warned!

    Well if you want my definition of living substance it is a substance which has been formed in a living organism and has inner activity.at the molecular level or above.

    Do you have a preferred definition of living substance?

    CharlieM: Anyone who just sees it all as physics and chemistry will deny this essential difference between living and dead substance and so will not even bother to undertake any further research into the difference. IMO this is a missed opportunity.

    What is that essential difference? Does ureum have life-force? Does ethanol (it’s already called spirits)? Sugars or lipids perhaps? I doubt that you will enjoy your futile search for life force.

    While these substances may be the product of life, I do not consider them to be living substances.

  30. DNA_Jock: Urea (in Dutch, ureum) being rather famous for its role in discrediting vitalism in 1828.

    Which is why I chose it. You know your classics, Jock.

    ETA: Urea was discovered by my compatriot Herman Boerhaave. Phoodoo would have really liked him, because he proposed that certain functions of the human body could be understood by principles of machinery .

  31. CharlieM: So regarding just the physics and chemistry, what do we miss by looking at polymerase chain reaction (PCR) generating DNA. We miss the fact that someone has to organise the chemicals, and the appropriate environment. Then the medium needs to be heated and cooled to the correct range of temperatures in the correct sequence. The physics and chemistry tells us nothing about the organisation of the procedure. And there has to be an organising principle for anything to happen.

    All this applies to anorganic chemistry as well. Did you never make crystals from table salt when you were young?

  32. CharlieM: Do you have a preferred definition of living substance?

    As I said, this is not set in stone. The page I linked to has a decent list of properties. Of the top of my head, I would include having order, metabolism, growth and development, reproduction, evolution and being (composed of) cell(s) as criteria. That definition is quite stringent, as it leaves out viruses, which are much better candidates to qualify as living beings than dynein molecules IMO.

    ETA: I noticed you asked about a definition of “living substance” rather than “living beings”. That’s a bit of a vague term and I won’t offer a definition for it. I guess it could be used to refer to the stuff that living beings are made of.

  33. DNA_Jock:
    CharlieM,
    Why not?
    The substances Corneel lists meet your proffered definition of ‘living substance’.
    Urea (in Dutch, ureum) being rather famous for its role in discrediting vitalism in 1828.

    What inner activity does urea have?

    The fact that urea could be synthesised in the lab quite rightly discredited the idea of a ghost in the machine. This was similar to Goethe’s demonstration that there was no physical difference between humans and animals when he discovered that humans possessed an intermaxilliary bone

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

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

  34. CharlieM,

    I think your use of “substance” is confusing the others here.

    There’s a difference between

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

    2. “living things contain the same elements as non-living things plus some additional substance that non-living things lack”

    Your use of the word “substance” suggests you mean (2) but your reasons for saying that point back to (1).

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

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

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

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

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

  36. Corneel: Which is why I chose it. You know your classics, Jock.

    ETA: Urea was discovered by my compatriot Herman Boerhaave. Phoodoo would have really liked him, because he proposed that certain functions of the human body could be understood by principles of machinery .

    We can describe a human arm in terms of a lever but this doesn’t come anywhere near to a full description of the arm. We can describe the oar of a rowing boat as a lever and by doing so we have given a great deal of information about the oar. The difference between the two is immense because the arm is so very much more than a lever.

    Please take a look at this video by Ken Dill at TED. He says the following:

    If you scale up the protein molecule to the size of a penny, the number of protein molecules you have in your body is the same as the number of pennies that would fill the pacific ocean…

    He is a strong advocate of the machine metaphor and he uses the word very frequently throughout the video. Here is an example.

    There is a half a trillion big world machines out there right now. You have more machines in the tip of your little finger than there are big world machines out there

    Whether we like the machine metaphor or not, this is a remarkable figure. The organisation that must be required here is beyond my comprehension and well beyond present human abilities.

  37. Corneel: All this applies to anorganic chemistry as well. Did you never make crystals from table salt when you were young?

    Yes crystals show some of the features of life. And their ability to readily form and grow into three dimensional structures shows how suited minerals are to being integrated into living forms. Crystals are a stage between static mixtures of matter and growing, differentiating life.

  38. Kantian Naturalist: I think your use of “substance” is confusing the others here.

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

  39. CharlieM: What inner activity does urea have?

    Tautomerism.
    Also
    Urea can act as a catalyst.
    Urea is food, in particular for the ureolytic bactiera that are being testing in the repair of damaged concrete (See, I can do irrelevant asides too).
    Crystals are halfway alive, you say?
    This is getting increasingly incoherent.

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

    Probably not.

  41. Corneel: As I said, this is not set in stone. The page I linked to has a decent list of properties. Of the top of my head, I would include having order, metabolism, growth and development, reproduction, evolution and being (composed of) cell(s) as criteria. That definition is quite stringent, as it leaves out viruses, which are much better candidates to qualify as living beings than dynein molecules IMO.

    ETA: I noticed you asked about a definition of “living substance” rather than “living beings”. That’s a bit of a vague term and I won’t offer a definitionfor it. I guess it could be used to refer to the stuff that living beings are made of.

    Yes, you have given of living beings when I specifically asked for a definition of living substance. In your opinion would the proteins in your body be classed as living substances?

    Do you consider a tree to be a living being? Is wood a living substance in your opinion? I prefer examples to definitions and I think it is fairly easy to distinguish living cells from dead cells. Like you say, when it comes to life and the natural world definitions can be vague.

  42. Kantian Naturalist:
    CharlieM,

    I think your use of “substance” is confusing the others here.

    There’s a difference between

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

    2. “living things contain the same elements as non-living things plus some additional substance that non-living things lack”

    Your use of the word “substance” suggests you mean (2) but your reasons for saying that point back to (1).

    Definitions are confusing and that is why I prefer to compare examples instead of getting bogged down in definitions. Corneel’s confusion mainly came from her/his misreading of my question.

    As for your (2), I do not believe that living things contain additional substance that non-living things lack.

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