Metaphors

These days researchers are obsessed with making models as an aid to understanding reality. But there is a danger here in that in concentrating on the models the actual living world around us is lost sight of. And the same can be said regarding the metaphors that are in frequent use. How true to reality is the mind picture evoked by the metaphor.

Kantian naturalist linked to a paper by Daniel J. Nicholson, titled “Is the cell really a machine?” here

This paper “argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.”


This increasingly accurate view demonstrates how misleading the machine metaphor is. Inventors and engineers are trying to build machines that are more like living systems but we are still a long way off from achieving this goal. Machines fall very far short of living systems.

A metaphor, as well as for its poetic use, can be used when an entity that is hard to describe is better understood in terms of an entity that can be much more clearly defined. But as our knowledge of these living systems becomes more detailed then the machine metaphor loses its usefulness and constrains our thinking.


Why call these dynamic complexes within cells “nano machines” when a more realistic term would be “nano beings”. They do not behave and function like dead machines with their levers, struts, braces, containers and clamping devices. They are living tissues and living beings, going through their own life cycles and functioning in ways reminiscent of higher animals such as insect colonies, or of growing vegetation. Their nature and activity is more like that of the animals and plants of our everyday sense world than that of human made machines.


We are at a stage of our evolution where we have become detached from the natural world. As Owen Barfield puts it, we have moved from the ancient position of being within nature, participating in the natural world along with the creatures around us, to the detached position of onlookers. In “Saving the Appearances” he relates the way we are after this transition:

For the generality of men, participation was dead; the only link with the phenomena was through the senses; and they could no longer conceive of any manner in which either growth itself or the metamorphoses of individual and special growth, could be determined from within. The appearances were idols. They had no “within.” Therefore the evolution which had produced them could only be conceived mechanomorphically as a series of impacts of idols on other idols.

The machine metaphor became dominant and it turned into a form of idolitry when it was taken literally and it still is being taken literally. It’s time to move beyond this way of thinking.

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76 thoughts on “Metaphors

  1. In my opinion, one of the problems with the machine metaphor is that our machines tend to be very digital while life is analog. A switch in a CPU is either on or off, but proteins, cells, and organs really don’t have this feature. For example, almost any two proteins will bind to one another at some concentration, so it isn’t correct to say that a protein did or didn’t bind. Rather, you give the concentration at which a certain percentage will bind, or some other measurement such as rate and equilibrium. While machines can be a helpful metaphor at some levels of resolution, it really breaks down when you get into the specifics.

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  2. I can see how metaphors might suggest fruitful lines of research. But they can also lead people in misguided directions. By their nature they aren’t entirely accurate depictions of the reality, and I have seen them used to defend inaccurate descriptions of reality by relying on those very shortcomings. We need to be a bit cautious about reasoning that goes: cells are machines, machines are designed by intelligent agents, etc.

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  3. Flint: We need to be a bit cautious about reasoning that goes: cells are machines, machines are designed by intelligent agents, etc.

    Why?

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  4. Why call these dynamic complexes within cells “nano machines” when a more realistic term would be “nano beings”.

    Regardless of metaphors, the basic idea is that life is captured completely by specifying how the dynamical processes of the biochemistry in a organism allow the organism to maintain a state far from thermodynamic equilibrium in its environment. Those processes include both internal ones and ones which maintain the boundary between the organism and its environment. They also include sensing and acting in the environment.

    Once those are specified, there is nothing more to say to explain the nature of life as it currently exists on earth.

    By referring to “beings”, your phrase seems to make life itself irreducible and fundamental. That is, it is an appeal to vitalism. That you hold that view would not surprise me nor would it be something I want to try to discuss further with you. But I thought it was important to make that vitalism explicit.

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  5. If someone could show us a process in the cell that does not occur mechanistically — that is, that cannot be explained by ordinary chemistry and physics — it would be a huge discovery. I’m not referring to arguments about how the particular cellular mechanism originated, I’m referring to how it works every time. If there were such a process, one which needed more than chemistry and physics to work, then vitalism would be validated and we could start confirming the presence of, say, leprechauns in the cell.

    Vitalism used to be given credit for biochemistry. When Wöhler showed in 1828 how to synthesize urea, that was a huge blow to vitalism — biochemistry turned out to be ordinary chemistry. Anyone wanting to revive vitalism has to show that we need leprechauns in the cell to make it function.

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  6. T_aquaticus:
    In my opinion, one of the problems with the machine metaphor is that our machines tend to be very digital while life is analog.A switch in a CPU is either on or off, but proteins, cells, and organs really don’t have this feature.For example, almost any two proteins will bind to one another at some concentration, so it isn’t correct to say that a protein did or didn’t bind.Rather, you give the concentration at which a certain percentage will bind, or some other measurement such as rate and equilibrium.While machines can be a helpful metaphor at some levels of resolution, it really breaks down when you get into the specifics.

    I can see what you mean but there are other aspects to machines besides digital code. All machines have hardware but not all machines rely on digital software. And those that do use software it is only within the switching of the logic circuits that we can speak of anything being digital. Hardware and software are designed and built up from parts by external designers to form machines. The formative and sustaining principles of life come from within and comprise a unity. The formative principle comes from the whole to serve the whole, unlike machines where the whole is built up from the parts and prior to this the function, the machine as a whole is present only as an idea in the mind of an external designer. Living systems are the opposite of machines in this respect..

    The metaphors we use reflects our beliefs and the way we think about a topic but it also influences the way the upcoming generations view any subject. It is very hard to overcome the thought of subatomic “particles” as minute solid balls, especially for those of us who were educated in this way. And it is hard to overcome the illusion of living systems as nothing more than mechanical devices.

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  7. Joe Felsenstein: If someone could show us a process in the cell that does not occur mechanistically — that is, that cannot be explained by ordinary chemistry and physics — it would be a huge discovery.

    Thoughts. Memory. Experiences.

    So is vitalism confirmed then?

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  8. Flint:
    I can see how metaphors might suggest fruitful lines of research. But they can also lead people in misguided directions. By their nature they aren’t entirely accurate depictions of the reality, and I have seen them used to defend inaccurate descriptions of reality by relying on those very shortcomings. We need to be a bit cautious about reasoning that goes: cells are machines, machines are designed by intelligent agents, etc.

    I agree. To call a cell a machine comes nowhere near to doing it justice. The intelligence of nature needs no agent because it lies within nature herself, it’s intrinsic. We may take inspiration from nature in building our machines, but the intelligence does not lie within the machine, it lies in an external mind or minds.

    But none of this prevents us from admiring the mechanical activity and processes in nature in the same way that we can admire the skills of a sculptor or crafts person and the movements of a dancer or athlete.

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  9. phoodoo:

    Flint: We need to be a bit cautious about reasoning that goes: cells are machines, machines are designed by intelligent agents, etc.

    Why?

    IMO it’s because there is so much more to cells than their mechanical aspects.

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  10. I have never liked “machine” as applied to biological things.

    To me, the term “machine” suggests rigid rule following without regard to anything else. And biological systems, by contrast, seem to be very adaptive to their surroundings.

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  11. BruceS: Regardless of metaphors, the basic idea is that life is captured completely by specifying how the dynamical processes of the biochemistry in an organism allow the organism to maintain a state far from thermodynamic equilibrium in its environment.Those processes include both internal ones and ones which maintain the boundary between the organism and its environment.They also include sensing and acting in the environment.

    Once those are specified, there is nothing more to say to explain the nature of life as it currently exists on earth.

    For analytical purposes, without making any presuppositions, we can separate all carbon based earthly life into two components. physical substance and living processes. Physical substances retain the same chemical and physical properties whether or not they are within living bodies.

    Living processes cannot be easily explained in relation to the properties of physical substances alone. It has already been suggested that proteins are not very specific in their binding affinities. Can you explain the physical properties that specify how microtubules are built up and broken apart in forming pathways in certain directions and how dynein and kinesin complexes use these pathways to transport various substances throughout the cell in the correct quantities and timing to maintain the function and viability of the cell? (sorry for posing such a long and detailed question, but think it’s important to think about these things.) Researchers are uncovering coordinated activity nobody knew existed a few decades ago. Directed activity like this is not something that is attributed to physical forces alone.

    By referring to “beings”, your phrase seems to make life itself irreducible and fundamental.That is, it is an appeal to vitalism.That you hold that view would not surprise me nor would it be something I want to try to discuss further with you.But I thought it was important to make that vitalism explicit.

    Yes I believe that inanimate matter is the product of life and not the other way round. But I’m happy to stick to discussing observations of the here and now.

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  12. CharlieM: Can you explain the physical properties that specify how microtubules are built up and broken apart in forming pathways in certain directions and how dynein and kinesin complexes use these pathways to transport various substances throughout the cell in the correct quantities and timing to maintain the function and viability of the cell?

    Yup, pretty much..

    Researchers are uncovering coordinated activity nobody knew existed a few decades ago.

    Co-ordinated physical and chemical activity.

    Directed activity like this is not something that is attributed to physical forces alone.

    Well, the researchers uncovering the activity do attribute it to physical forces.
    It’s funny: long ago, when I was an undergrad, the vitalism-of-the-gaps was still laying claim to “how do muscles generate force”. Now it’s reduced to “Thoughts. Memory.Experiences.”, apparently. That’s quite the come-down since 1828, when living things were thought to have their own chemistry, completely distinct from the chemistry of non-living things.

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  13. phoodoo: Thoughts. Memory. Experiences.

    Are those happening “in the cell”, or are they the product of interactions between lots of them?

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  14. I take issue with two implicit claims here.

    First, scientific models are not metaphors; they are analogies, and the difference is crucial. Analogical thinking is indispensable in model building but the thoughtful modeler is always aware of the limits of analogies, and where the analogy breaks down. Models are useful precisely because they are simplifications; a map of the world on a 1:1 scale would be useless (and where would you keep it?). By contrast, poetry and art do exploit metaphors, so neglecting this distinction between metaphors and analogies is tantamount to collapsing the distinction between art and science.

    Second, I am not at all sure of the governing assumption that thoughtful scientists and philosophers of science are blissfully ignorant of the limitations of their models. If anything, they simply take it for granted that their models are useful simplifications, to the point where pointing this out to them is like insisting that the sky is blue.

    If it should be the case that this epistemic humility is not communicated to non-scientists, we can blame the abysmal quality of science education and truly embarrassing quality of science “journalism”, but let’s not lay blame on practicing scientists themselves.

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  15. Joe Felsenstein:
    If someone could show us a process in the cell that does not occur mechanistically — that is, that cannot be explained by ordinary chemistry and physics — it would be a huge discovery.I’m not referring to arguments about how the particular cellular mechanism originated, I’m referring to how it works every time.If there were such a process, one which needed more than chemistry and physics to work, then vitalism would be validated and we could start confirming the presence of, say, leprechauns in the cell.

    Vitalism used to be given credit for biochemistry.When Wöhler showed in 1828 how to synthesize urea, that was a huge blow to vitalism — biochemistry turned out to be ordinary chemistry. Anyone wanting to revive vitalism has to show that we need leprechauns in the cell to make it function.

    If someone accidentally elbows you in the eye or someone deliberately elbows you in the eye the physics might be indistinguishable in both cases. But there is a difference over and above the physical event. Intentional actions require more than just physical forces to explain them.

    If it is unclear how kinesin and dynein complexes achieve their aims, how do we know that there are solely physical and chemical forces involved?
    Kinesin and dynein use distinct mechanisms to bypass obstacles

    Kinesin-1 and cytoplasmic dynein are microtubule (MT) motors that transport intracellular cargoes. It remains unclear how these motors move along MTs densely coated with obstacles of various sizes in the cytoplasm…

    Despite the complexity of the cytoplasm, kinesin and dynein drive intracellular transport with remarkable efficiency towards MT ends.

    In true Roy Rogers style, the mail must go through 🙂

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  16. Charlie is quoting from Ferro et al 2019, whilst omitting all mention of the experiments they describe which elucidate the physical and chemical interactions that drive kinesin and dynein behavior.
    This vitalism-of-the-gaps approach is guaranteed success if one insists on remaining as ignorant and incurious as possible.
    I think, however, that you may have missed the import of this quote from Ferro:

    Dynein has a large diffusional component in its stepping behavior, resulting in frequent sideways and backward steps (DeWitt et al., 2012).

    That’s a funny thing for a ‘machine’ to do.

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  17. Rumraket: Are those happening “in the cell”, or are they the product of interactions between lots of them?

    Ok, if the thoughts aren’t happening in the cell, where are they happening? In the vitalism space between them?

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  18. phoodoo: Ok, if the thoughts aren’t happening in the cell, where are they happening? In the vitalism space between them?

    It’s supernatural. It can’t be investigated or known.

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  19. Kantian Naturalist: First, scientific models are not metaphors; they are analogies,

    I found Gelfert’s overview paper on the ontologies of scientific models to be a helpful.
    https://www.academia.edu/26570119/The_Ontology_of_Models
    I like aspects of structuralism but also of the pragmatic (cognitive) view of models; unfortunately for me, they don’t seem to work together that well. Plus adding my bias for scientific realism means there is another tension there, at least with the pragmatic approaches.

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  20. CharlieM: For analytical purposes, without making any presuppositions, we can separate all carbon based earthly life into two components. physical substance and living processes.

    emphasis added

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  21. Neil Rickert:
    I have never liked “machine” as applied to biological things.

    That’s good to hear:)

    To me, the term “machine” suggests rigid rule following without regard to anything else.And biological systems, by contrast, seem to be very adaptive to their surroundings.

    And I would add they are very adaptive to their surroundings while their form is forever changing.

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  22. DNA_Jock

    CharlieM: Can you explain the physical properties that specify how microtubules are built up and broken apart in forming pathways in certain directions and how dynein and kinesin complexes use these pathways to transport various substances throughout the cell in the correct quantities and timing to maintain the function and viability of the cell?

    Yup, pretty much..

    Good, thoughtful, well researched answer. I thought you might have taken the chance to teach us about intracellular transport.

    Researchers are uncovering coordinated activity nobody knew existed a few decades ago.

    Co-ordinated physical and chemical activity.

    Co-ordinated activity with physical and chemical aspects to it.

    Directed activity like this is not something that is attributed to physical forces alone.

    Well, the researchers uncovering the activity do attribute it to physical forces.

    Did you notice my previous link, “It remains unclear how these motors move along MTs densely coated with obstacles of various sizes in the cytoplasm.”
    Nobody disputes that these complexes use physical and chemical forces to carry out their actions. In the same way nobody disputes that boxers use physical force in order to try to beat their opponents, or a nautilus uses physical force in order to propel itself through the water. But saying no more than that still leaves the question unanswered as to where all the purposeful activity comes from.

    It’s funny: long ago, when I was an undergrad, the vitalism-of-the-gaps was still laying claim to “how do muscles generate force”. Now it’s reduced to “Thoughts. Memory.Experiences.”, apparently. That’s quite the come-down since 1828, when living things were thought to have their own chemistry, completely distinct from the chemistry of non-living things.

    Yes Goethe was one of those who argued against there being any special physical or chemical forces within life which differed from those found outside of life.

    The physical and chemical properties of matter are exactly what life needs to be able to develop into the vast array of living forms with the ability to produce living substances that they need. Substances that are rigid or elastic, permeable or impermeably, have the strength or weakness required to function; and all the states in between to suit the particular situation.

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  23. Kantian Naturalist:
    I take issue with two implicit claims here.

    First, scientific models are not metaphors; they are analogies, and the difference is crucial. Analogical thinking is indispensable in model building but the thoughtful modeler is always aware of the limits of analogies, and where the analogy breaks down. Models are useful precisely because they are simplifications; a map of the world on a 1:1 scale would be useless (and where would you keep it?). By contrast, poetry and art do exploit metaphors, so neglecting this distinction between metaphors and analogies is tantamount to collapsing the distinction between art and science.

    Second, I am not at all sure of the governing assumption that thoughtful scientists and philosophers of science are blissfully ignorant of the limitations of their models. If anything, they simply take it for granted that their models are useful simplifications, to the point where pointing this out to them is like insisting that the sky is blue.

    If it should be the case that this epistemic humility is not communicated to non-scientists, we can blame the abysmal quality of science education and truly embarrassing quality of science “journalism”, but let’s not lay blame on practicing scientists themselves.

    The claims you are taking issue with are not my claims.

    Firstly, I did not say that metaphors and models are the same thing. I said that they can both be misunderstood in the same way.

    On your second issue. I am aware of the value of models. But as I know from experience when we are teaching our children about the world that we are discovering it is easy to forget that our explanatory models become reality in their minds. They cannot distinguish so easily and ideas tend to stick.

    What comes first into your mind when you think of “DNA”. Is it a substance buried deep within a complex of moving, dancing, substance? Or is it a solid line with the letter, A, T, G, and C, strung along it? I know that for me it tends to be the latter.

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  24. DNA_Jock: Charlie is quoting from Ferro et al 2019, whilst omitting all mention of the experiments they describe which elucidate the physical and chemical interactions that drive kinesin and dynein behavior.
    This vitalism-of-the-gaps approach is guaranteed success if one insists on remaining as ignorant and incurious as possible.
    I think, however, that you may have missed the import of this quote from Ferro:

    Dynein has a large diffusional component in its stepping behavior, resulting in frequent sideways and backward steps (DeWitt et al., 2012).

    That’s a funny thing for a ‘machine’ to do.

    Yes, it’s more like the behaviour of a foraging animal.

    I have noticed on looking through articles and papers on on the subject of these “nano-machines” how often there are phrases like, “how cells put together the molecules that make life work”, “Cells constantly build, destroy and rebuild these cylinders and reuse the molecular blocks like Legos” “how does the cell regulate…?”.

    And here is another instance of the creative power attributed to the cell:

    Tracking traffic in the divided world of a nerve cell:

    Nerve cells create an unknown number of axon- or dendrite-specific transmembrane proteins, which can be packaged in an unknown number of vesicles, and are ferried by up to 20 different motor proteins in a class called kinesins.

    And below more quotes from the same source demonstrating the variety of metaphors used, “factory”, “highway”, “personality”

    Axonal and dendritic proteins embedded in the membrane at either end — called transmembrane proteins — are built in the same cellular factory and travel on the same cellular highway. But for the cell to function property, they must be delivered to the correct domain. So how does the cell regulate that voyage?
    The split personality of a nerve cell illustrates a puzzle. Nerve cells are divided in two domains — the axon sends signals and the dendrites receive them. Axonal and dendritic proteins embedded in the membrane at either end — called transmembrane proteins — are built in the same cellular factory and travel on the same cellular highway. But for the cell to function property, they must be delivered to the correct domain. So how does the cell regulate that voyage?
    Nobody really knows, and that’s a problem in addressing diseases that affect the brain, says Marvin Bentley, an assistant professor of biological sciences at Rensselaer Polytechnic Institute and member of the Center for Biotechnology and Interdisciplinary Studies….
    Regulation of this journey takes many forms, and in one aspect of his current research, Bentley is examining the relationship between the vesicles and the motor proteins that carry them. This relationship is riddled with unknowns: Nerve cells create an unknown number of axon- or dendrite-specific transmembrane proteins, which can be packaged in an unknown number of vesicles, and are ferried by up to 20 different motor proteins in a class called kinesins.

    They agree that the cell regulates transport but they admit that “nobody really knows” how it achieves this impressive task.

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  25. CharlieM: Good, thoughtful, well researched answer. I thought you might have taken the chance to teach us about intracellular transport.

    LOL,Charlie, for anyone to teach you about intracellular transport, you would have to be willing to learn about intracellular transport. You are not, as this most recent exchange demonstrates.
    To recap:
    You quote from the first two sentences of the abstract of a paper (along with the first sentence of the discussion), wherein the authors lay out the problem, but you carefully omit the bits where they explain the experiments they performed to discover the answers to their questions. We call this “pulling a Dionisio”. In this particular case, you even failed to provide a link or any citation to the underlying article. I assumed that was an html failure on your part, so I replied — citing the paper in question, Ferro et al 2019, and providing a link.
    I also offered up a quotation from the paper’s Introduction which (if you had understood it) would have made you realize that you are imbuing dynein with agency that it lacks, I wrote

    I think, however, that you may have missed the import of this quote from Ferro:

    Your next comment to me:

    Did you notice my previous link,
    [now with a functioning link to Ferro]

    Say what? Yes, I noticed it. I cited it and linked to it (which you failed to do) and I quoted part of it back to you. How did you miss this?
    Evidently, you “looked through” the paper rather than reading it. You clearly did not comprehend it.
    So, go take a course in biochemistry from your local community college; you might learn about intracellular transport there.
    Or you could stick with your Panglossian woo. “Foraging animal” was cute.

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  26. phoodoo: Why?

    What an odd question. I carefully explained (at least, I tried to) that assuming an exact analogy could be dangerous because analogies are never exact. I tried to emphasize that those suffering either ignorance or mendacity could carefully extract aspects of the analogy which are least exact, in order to support a fallacious argument. I gave an example of a fallacious argument, one that carefully selects an aspect of a cell most different from an aspect of a machine, and treats that aspect as being the most exact!

    My error, I believe, was in taking it for granted that using a false analogy to support a misconception was a Bad Thing To Do. I understand now that for you, doing so is the whole point.

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  27. DNA_Jock:

    CharlieM: Good, thoughtful, well researched answer. I thought you might have taken the chance to teach us about intracellular transport.

    LOL,Charlie, for anyone to teach you about intracellular transport, you would have to be willing to learn about intracellular transport. You are not, as this most recent exchange demonstrates.
    To recap:
    You quote from the first two sentences of the abstract of a paper (along with the first sentence of the discussion), wherein the authors lay out the problem, but you carefully omit the bits where they explain the experiments they performed to discover the answers to their questions. We call this “pulling a Dionisio”. In this particular case, you even failed to provide a link or any citation to the underlying article. I assumed that was an html failure on your part, so I replied — citing the paper in question, Ferro et al 2019, and providing a link.
    I also offered up a quotation from the paper’s Introduction which (if you had understood it) would have made you realize that you are imbuing dynein with agency that it lacks, I wrote

    I think, however, that you may have missed the import of this quote from Ferro:

    Your next comment to me:

    Did you notice my previous link,

    [now with a functioning link to Ferro]

    Say what? Yes, I noticed it. I cited it and linked to it (which you failed to do) and I quoted part of it back to you. How did you miss this?
    Evidently, you “looked through” the paper rather than reading it. You clearly did not comprehend it.
    So, go take a course in biochemistry from your local community college; you might learn about intracellular transport there.
    Or you could stick with your Panglossian woo. “Foraging animal” was cute.

    I apologise for originally making a mess of the link.

    You may not like the term “agency” but the fact is that these nano-beings are agents of the cell, unconsciously carrying out their tasks for the benefit of the whole in a similar way to ants unconsciously carrying out their tasks for the benefit of the colony. Studying the mechanics of the leg movements of an ant is interesting in itself, but it tells us nothing about how it fits in to the workings of the colony as a whole. Studying the mechanics of these nano-beings is also very interesting, but does not tell us how, in their millions, they are put to work in such a coordinated way to maintain the viability of their parent organism.

    And taking it up a level, here is a white blood cell chasing a bacterium. Now I’m sure there is very little conscious awareness on the part of the cell, but it too is an agent. It is an agent of the organism, sensing and chasing, then eating the intruder.

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  28. I’ve linked to talks by Ron Vale in the past, but I can’t remember if I’ve referred to this one before, on the mechanism of dynein motility. At the end of the talk he says the following:

    So that gives an update of what we’ve learned about dynein in the last few years. But I must say we are still very much at the beginning and there are a tremendous number of unknown questions. So I illustrated some atomic structures and conformational changes that occur, but we don’t really know how those structural changes relate to the stepping of dynein on the microtubule. What would be particularly nice is instead of just getting static images of dynein,we can actually measure and monitor dynein structural changes while it’s in the act of motility. And there are ways of doing this, for example techniques such as single molecule FRET, which act as probes to measure certain conformational changes that occur in a protein, and perhaps those kind of techniques can be applied to dynein so we can actually see dynein stepping and simultaneously measure conformational changes. I also gave you structural information on the role of AAA3, showing that it can block a conformational change of dynein and thereby prevent its motility. But we don’t really understand how and why AAA3 does this. How does the cell use this control mechanism to regulate dynein motility? How does it actually control whether AAA3 has an ATP or ADP in the active site? So we have no idea on this issue right now, and this is obviously going to be important for understanding what the real purpose of AAA3 is in dynein cell biology.

    He is asking good, relevant questions. How does the cell use what it has at its disposal within its body?

    In another video he says that, “evolution also has learned to develop different kinds of mechanical elements, even within a superfamily, for different purposes.”

    Surely he means living systems have learned this. He is misusing the word. Evolution does not learn anything, things are learned during the course of evolution.

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  29. CharlieM: Surely he means living systems have learned this. He is misusing the word. Evolution does not learn anything, things are learned during the course of evolution.

    It’s a metaphor, obviously.

    Sheesh!

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  30. CharlieM: On your second issue. I am aware of the value of models. But as I know from experience when we are teaching our children about the world that we are discovering it is easy to forget that our explanatory models become reality in their minds. They cannot distinguish so easily and ideas tend to stick.

    I think that depends very much on how children are parented and educated. In any event I think that scientists are much less likely than non-scientists to confuse their models for reality because scientific practice is about constantly testing one’s models against reality as best as one can.

    In ideal science, we’re testing our theories against the data, not making our data conform to our theories. And that’s quite difficult to do, which is why we structure science as we do, with lots of collaboration and productive disagreement, including peer review — to function as iterated error filters against individual cognitive bias. It never works perfectly and sometimes fails rather badly, but it’s the best social practice we have yet invented for figuring out what the world is like.

    What comes first into your mind when you think of “DNA”. Is it a substance buried deep within a complex of moving, dancing, substance? Or is it a solid line with the letter, A, T, G, and C, strung along it? I know that for me it tends to be the latter.

    For me it’s quite definitely the former, but that’s a nice benefit of having had a pretty decent science education.

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  31. Corneel:

    CharlieM: Surely he means living systems have learned this. He is misusing the word. Evolution does not learn anything, things are learned during the course of evolution.

    It’s a metaphor, obviously.

    Sheesh!

    Exactly! Why did he use this metaphor? All eukaryote cells have these motile, load bearing complexes. As far as I know they have always had them. I’d like to hear from anyone that has any evidence to the contrary. Where is the evidence that there is any sort of learning process in the appearance of these complexes.

    After thinking a bit more about this, I’d like to know what this phrase “evolution learns” actually stands for.

    When I think of “learning”, it is a process that higher animals need to go through whereas lower animals and plants just perform their actions without this requirement. Attributes that are given to lower life forms as part of their nature are withheld from higher animals and individuals have to learn or be taught certain skills through their own efforts.

    Look at insects they emerge as adults that have mastered flight from the beginning. then look at a fledgling sparrow learning the skills of flight. They may be quick learners but the process is not without its mishaps.

    I’m trying to establish what we actually know from observation and what we tag on to align with our beliefs. I said “Surely he means living systems have learned this”. But is even this justified?

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  32. CharlieM: Look at insects they emerge as adults that have mastered flight from the beginning.

    And when I have pressed evolutionists on where this stored knowledge lies in the genes of animals, they just stammer and say, well, “Where do you think it is!? We are looking. We will find it some day…”

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  33. CharlieM: After thinking a bit more about this, I’d like to know what this phrase “evolution learns” actually stands for.

    It means a novel molecular function was acquired by a member of that protein family, most likely by the fixation of adaptive genetic mutations as a result of natural selection.

    CharlieM: I’m trying to establish what we actually know from observation and what we tag on to align with our beliefs. I said “Surely he means living systems have learned this”. But is even this justified?

    As a metaphor: sure. Note that Ron Vale also states right before that “evolution learns” remark that the “motor protein has learned to walk in a coordinated manner” (around the 27 minute mark). Nothing wrong with it, as long as we realize that he is just using figure of speech.

    In a literal sense: definitely not!

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  34. Corneel: most likely by the fixation of adaptive genetic mutations as a result of natural selection.

    What is this even supposed to mean? Adaptive mutations, not random ones? Which was brought on by natural selection? Huh?

    So do you believe natural selection drives adaptive mutations or adaptive mutations drives natural selection? Or do you mean both? Or neither? Or, whatever…

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  35. phoodoo: Adaptive mutations, not random ones?

    You spend all this time on this forum and you still grapple with the idea that natural selection fixes adaptive mutations?

    ETA: Ah, now I understand. Rephrase: beneficial mutations.

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  36. phoodoo: And when I have pressed evolutionists on where this stored knowledge lies in the genes of animals, they just stammer and say, well, “Where do you think it is!? We are looking.We will find it some day…”

    Where does the designer store it or does He teach each beetle to fly, fish to swim individually? Go ahead and don’t stammer.

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  37. Kantian Naturalist:

    CharlieM: On your second issue. I am aware of the value of models. But as I know from experience when we are teaching our children about the world that we are discovering it is easy to forget that our explanatory models become reality in their minds. They cannot distinguish so easily and ideas tend to stick.

    I think that depends very much on how children are parented and educated. In any event I think that scientists are much less likely than non-scientists to confuse their models for reality because scientific practice is about constantly testing one’s models against reality as best as one can.

    The problem comes when we have to deal with historical aspects of science such as trying to understand what is real over vast periods of evolutionary time. How do we get away from the fact that we are looking at these things from the perspective of modern human consciousness.

    In ideal science, we’re testing our theories against the data, not making our data conform to our theories. And that’s quite difficult to do, which is why we structure science as we do, with lots of collaboration and productive disagreement, including peer review — to function as iterated error filters against individual cognitive bias. It never works perfectly and sometimes fails rather badly, but it’s the best social practice we have yet invented for figuring out what the world is like.

    I agree that there is a lot to be said for the scientific method. I’m all for productive disagreement. That’s what I look to get from my participation here.

    What comes first into your mind when you think of “DNA”. Is it a substance buried deep within a complex of moving, dancing, substance? Or is it a solid line with the letter, A, T, G, and C, strung along it? I know that for me it tends to be the latter.

    For me it’s quite definitely the former, but that’s a nice benefit of having had a pretty decent science education.

    Good for you. Another image that quite often pops into my mind is the helical ladder.

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  38. phoodoo:

    CharlieM: Look at insects they emerge as adults that have mastered flight from the beginning.

    And when I have pressed evolutionists on where this stored knowledge lies in the genes of animals, they just stammer and say, well, “Where do you think it is!? We are looking.We will find it some day…”

    They have their beliefs and I have mine. I believe that there is such a thing as group minds.

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  39. phoodoo: Ok, if the thoughts aren’t happening in the cell, where are they happening?In the vitalism space between them?

    Don’t be stupid phoodoo, blood does not flow “in the cell” and that doesn’t make veins and arteries into “vitalism space.”

    There’s physics and chemistry out of “the cell” too.

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  40. newton: Where does the designer store it or does He teach each beetle to fly, fish to swim individually? Go ahead and don’t stammer.

    Maybe its in the morphic resonance.

    At least its an explanation, unlike what materialists offer for it.

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  41. Entropy: Don’t be stupid phoodoo, blood does not flow “in the cell” and that doesn’t make veins and arteries into “vitalism space.”

    There’s physics and chemistry out of “the cell” too.

    Ha.

    I thought I should save this post for posterity. Or at least for a posterior.

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  42. phoodoo: Maybe its in the morphic resonance.

    At least its an explanation, unlike what materialists offer for it.

    “Maybe” is no better then “We are looking for it”.

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  43. Corneel:

    CharlieM: After thinking a bit more about this, I’d like to know what this phrase “evolution learns” actually stands for.

    It means a novel molecular function was acquired by a member of that protein family, most likely by the fixation of adaptive genetic mutations as a result of natural selection.

    Could the first eukaryotes have functioned without a range of these nano-motile complexes? Protists still need to carry out all the functions of everyday life, cell division and/or conjugation which involves transporting substances, building structures where they are needed, breaking down and disposing of unwanted substances. And I don’t see how it would have been any different for the first eukaryotes. There is no evidence that the first cells weren’t just as capable of functioning in their habitat as any extant cell.

    CharlieM: I’m trying to establish what we actually know from observation and what we tag on to align with our beliefs. I said “Surely he means living systems have learned this”. But is even this justified?

    As a metaphor: sure. Note that Ron Vale also states right before that “evolution learns” remark that the “motor protein has learned to walk in a coordinated manner” (around the 27 minute mark). Nothing wrong with it, as long as we realize that he is just using figure of speech.

    In a literal sense: definitely not!

    Yes I had noticed what he said. And that’s what got me thinking. Do these motile complexes need to learn how to perform their tasks, or do they just jump right in and do what comes naturally right from the moment they become functional?

    Talking about natural selection, here is a video I found in which the narrator says regarding activities within a paramecium:

    Transport proteins shuttle the essential molecules across the vacuole membrane into an ocean of cytoplasm. Other teams greet the proteins with a thousand purposes, energy production, building projects. The machinery within paramecia operates at a feverish pace. Contractile vacuoles pump the paramecium away from certain doom. An explosive fate due to the invasion of water molecules Designed by natural selection its protein parts efficiently carry out all new chemical reactions. Out of countless random encounters throughout the cytoplasm, a paramecium’s life emerges into existence.

    What is the proposed pathway by which natural selection designed these motile complexes? And how did the cells function at the very early stage before the designs were put to use? IMO natural selection is a good term for the way that living systems, because they have a range of variation and are not all identical within a kind, can cope with a changing environment. Attributes that are already present in the group are “selected” to meet the needs of the time. I would say that any further power attributed to natural selection is just speculation.

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  44. CharlieM: Could the first eukaryotes have functioned without a range of these nano-motile complexes? Protists still need to carry out all the functions of everyday life, cell division and/or conjugation which involves transporting substances, building structures where they are needed, breaking down and disposing of unwanted substances. And I don’t see how it would have been any different for the first eukaryotes. There is no evidence that the first cells weren’t just as capable of functioning in their habitat as any extant cell.

    Looks like you are confusing several different critters. The last common ancestor of all extant eukaryotes is not the first eukaryote. The latter was most certainly lacking many of the defining features of modern eukaryotes, such as a complex cytoskeleton. Since bacteria and archaea can do without one, it probably wasn’t a big issue for the first eukaryotes either. The first living cells were even more primitive than that. There is roughly a billion years of evolution separating the first cells from the first eukaryotes. A lot can (and did) happen in that time.

    CharlieM: Do these motile complexes need to learn how to perform their tasks, or do they just jump right in and do what comes naturally right from the moment they become functional?

    I get the distinct impression that you are NOT using metaphors when you talk about “nano-beings”.

    CharlieM: Attributes that are already present in the group are “selected” to meet the needs of the time. I would say that any further power attributed to natural selection is just speculation.

    Sure you would, but that would be incorrect. one important point I always like to emphasize is that, because the frequencies of previously rare beneficial alleles rise, they get the opportunity to recombine to generate truly novel phenotypes that were never present in the ancestral population. Note that this happens in the absence of mutation. Hence, natural selection is a truly creative force (metaphor again).

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  45. phoodoo:
    Ha.
    I thought I should save this post for posterity. Or at least for a posterior.

    It’s up to you what you introduce into your ass.

    Consider to also “save” your assumption that if it’s not happening inside the cell it cannot be physics and chemistry, but vitalism.

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  46. Corneel:

    CharlieM: Could the first eukaryotes have functioned without a range of these nano-motile complexes? Protists still need to carry out all the functions of everyday life, cell division and/or conjugation which involves transporting substances, building structures where they are needed, breaking down and disposing of unwanted substances. And I don’t see how it would have been any different for the first eukaryotes. There is no evidence that the first cells weren’t just as capable of functioning in their habitat as any extant cell.

    Looks like you are confusing several different critters. The last common ancestor of all extant eukaryotes is not the first eukaryote. The latter was most certainly lacking many of the defining features of modern eukaryotes, such as a complex cytoskeleton. Since bacteria and archaea can do without one, it probably wasn’t a big issue for the first eukaryotes either. The first living cells were even more primitive than that. There is roughly a billion years of evolution separating the first cells from the first eukaryotes. A lot can (and did) happen in that time.

    I’m not confusing critters. The closest living creatures to the first recorded fossil eucaryotes would sit among the protists, such as red algae. And so the fossils and the protists are the things that are directly examined to get an idea of what the earliest eukaryotes were like. You may be able to imagine early eukaryotes that are more simple than protists but where is the direct evidence that they existed. Of course they are required to have existed to justify the theory of unguided evolution as they are too complex to have come into existence as fully functional protist-like cells.

    I’ll post separately some of the links and excerpts from websites where I’ve been reading about eukaryote origins, specifically in regard to cytoskeletons.

    CharlieM: Do these motile complexes need to learn how to perform their tasks, or do they just jump right in and do what comes naturally right from the moment they become functional?

    I get the distinct impression that you are NOT using metaphors when you talk about “nano-beings”.

    Talking about “Nano-beings” is less of a mouthful than talking about “intracellular motile living forms”.

    CharlieM: Attributes that are already present in the group are “selected” to meet the needs of the time. I would say that any further power attributed to natural selection is just speculation.

    Sure you would, but that would be incorrect. one important point I always like to emphasize is that, because the frequencies of previously rare beneficial alleles rise, they get the opportunity to recombine to generate truly novel phenotypes that were never present in the ancestral population. Note that this happens in the absence of mutation. Hence, natural selection is a truly creative force (metaphor again).

    Can you give us some examples where these truly novel phenotypes have been demonstrated to have been the result of natural selection?

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  47. Here are the links and quotes:

    Cytoskeletons in prokaryotes.

    It was speculated that constituents of today’s eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today’s bacterial proteins FtsZ and MreB/Mbl. Prior to the description of proteins MreB/Mbl, evidence had been obtained for the existence of a shape-preserving cytoskeleton ubiquitously present in all bacteria. In the meantime, structural studies allow to speculate on a possible role of bacterial elongation factor Tu (EF-Tu) as a structural element in such a “cytoskeletal web”. EF-Tu was long known to form fibrillar structures in vitro; now experimental data accumulate, pointing towards formation of intracellular protofilaments containing EF-Tu, and networks thereof as well. In addition, results of these structural studies suggest a so far unknown mode of complex formation of EF-Tu with active ribosomes: ribosomes/polysomes were seen to be attached to intracellular protofilaments. Implications for the understanding of EF-Tu-ribosome interaction, and a role of such a kind of putative protofilaments as a general site of attachment for cellular functional macromolecules are discussed. The notion is discussed that an EF-Tu-containing cytoskeletal web might have been the “primary” or “basic” kind of prokaryotic cytoskeleton, already in existence prior to the “invention” of precursors of today’s MreB.

    Origin and Evolution of the Self-Organizing Cytoskeleton in the Network of Eukaryotic Organelles

    Organization depends on the mechanochemical properties of the cytoskeleton that dynamically maintain cell shape, position organelles, and macromolecules by trafficking, and drive locomotion via actin-rich cellular protrusions, ciliary beating, or ciliary gliding. The eukaryotic cytoskeleton is best described as an “active gel,” a cross-linked network of polymers (gel) in which many of the links are active motors that can move the polymers relative to each other. Because prokaryotes have only cytoskeletal polymers but lack motor proteins, this “active gel” property clearly sets the eukaryotic cytoskeleton apart from prokaryotic filament systems…
    Prokaryotic cytoskeletal filaments may trace back to the first cells and may have originated as higher-order assemblies of enzymes…
    Advances in genome sequencing and comparative genomics now allow a detailed reconstruction of the cytoskeletal components present in the last common ancestor of eukaryotes. These studies all point to an ancestrally complex cytoskeleton, with several families of motors and filament-associated proteins and other regulators in place. Genomic reconstructions and comparative cell biology of single-celled eukaryotes allow us to infer the cellular features of the ancestral eukaryote. These analyses indicate that amoeboid motility, cilia, centrioles, phagocytosis, a midbody during cell division, mitosis, and meiosis were all ancestral eukaryotic cellular features. The availability of functional information from organisms other than animals and yeasts (e.g., Chlamydomonas, Tetrahymena, Trypanosoma) also allow more reliable inferences about the ancestral functions of cytoskeletal components (i.e., not only their ancestral presence or absence) and their regulation.

    The ancestral complexity of the cytoskeleton in eukaryotes leaves a huge gap between prokaryotes and the earliest eukaryote we can reconstruct (provided that our rooting of the tree is correct. Nevertheless, we can attempt to infer the series of events that happened along the stem lineage, leading to the last common ancestor of eukaryotes. Meaningful answers will require the use of a combination of gene family history reconstructions, transition analyses, and computer simulations relevant to cell evolution.

    The eukaryotic cytoskeleton evolved from prokaryotic cytomotive filaments. Prokaryotic filament systems show bewildering structural and dynamic complexity and, in many aspects, prefigure the self-organizing properties of the eukaryotic cytoskeleton.

    Patterns of kinesin evolution reveal a complex ancestral eukaryote with a multifunctional cytoskeleton.

    The genesis of the eukaryotes was a pivotal event in evolution and was accompanied by the acquisition of numerous new cellular features including compartmentalization by cytoplasmic organelles, mitosis and meiosis, and ciliary motility. Essential for the development of these features was the tubulin cytoskeleton and associated motors. It is therefore possible to map ancient cell evolution by reconstructing the evolutionary history of motor proteins. Here, we have used the kinesin motor repertoire of 45 extant eukaryotes to infer the ancestral state of this superfamily in the last common eukaryotic ancestor (LCEA).
    We show that a minimum of 11 kinesin families and 3 protein domain architectures were present in the LCEA. This demonstrates that the microtubule-based cytoskeleton of the LCEA was surprisingly highly developed in terms of kinesin motor types, but that domain architectures have been extensively modified during the diversification of the eukaryotes. Our analysis provides molecular evidence for the existence of several key cellular functions in the LCEA, and shows that a large proportion of motor family diversity and cellular complexity had already arisen in this ancient cell.

    I’d like to see the available evidence of how the cytoskeleton evolved between the first eularyotes and the last common ancestor of eukaryotes, if the two did not appear simultaneously.

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  48. CharlieM: You may be able to imagine early eukaryotes that are more simple than protists but where is the direct evidence that they existed. Of course they are required to have existed to justify the theory of unguided evolution as they are too complex to have come into existence as fully functional protist-like cells.

    That’s interesting. I didn’t realize you rejected UCD. First some remarks: “unguided evolution” has nothing to do with the question whether eukaryotes evolved from more primitive ancestors. Secondly, I have no clue what you mean by “direct” evidence so you’ll have to clear up what you mean by that, and why indirect evidence is not good enough for you.

    Now, the most straightforward indication that eukaryotes gradually acquired many of their distinguishing features during evolution is the evidence that they arose from an endosymbiotic event between a bacterial and an archaean cell, both groups lacking these features.

    A second argument would be that evolutionary change in eukaryotes is readily observable from the moment they enter the fossil record, so it is peculiar to assume that they were immutable before that time.

    CharlieM: Talking about “Nano-beings” is less of a mouthful than talking about “intracellular motile living forms”.

    Not metaphors then. But proteins are not life forms, since they do not reproduce. We discussed this previously.

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  49. CharlieM: Can you give us some examples where these truly novel phenotypes have been demonstrated to have been the result of natural selection?

    If you accept examples from artificial selection, that makes it rather easy (the concept is the same in natural selection). The idea is that you can create phenotypes that did not exist previously by selectively breeding individuals with an association of desired alleles, e.g. the ears of modern maize as compared to teosinthe. Part of that will have been fueled by new mutations, but quantitative genetics shows that you can get a long way using standing genetic variation as well.

    Picture from this site, where, in a completely coincidence, the same point is being made. 😀

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  50. Corneel:

    CharlieM: You may be able to imagine early eukaryotes that are more simple than protists but where is the direct evidence that they existed. Of course they are required to have existed to justify the theory of unguided evolution as they are too complex to have come into existence as fully functional protist-like cells.

    That’s interesting. I didn’t realize you rejected UCD. First some remarks: “unguided evolution” has nothing to do with the question whether eukaryotes evolved from more primitive ancestors.

    If you understood my constant reference to the example of buttercup leaves you would know where I stand on UCD. All the cells of the buttercup plant can be traced to a common ancestor but the form of the leaves are not descended one from the other in a sequential manner. Their sequential similarity can be accounted for in the fact that they all express an archetypal (in the Goethean sense) form in an individual way. And the individual plant can be seen as a metaphor for life as a whole. As above so below.

    Secondly, I have no clue what you mean by “direct” evidence so you’ll have to clear up what you mean by that, and why indirect evidence is not good enough for you.

    Fossils (and extant life) can be studied directly. their position in the earth can be observed and recorded, their form and structure can be examined. The living pre-Cambrian world cannot be examined directly, only its dead remains can. I would have thought it obvious that direct evidence is superior to making inferences.

    Now, the most straightforward indication that eukaryotes gradually acquired many of their distinguishing features during evolution is the evidence that they arose from an endosymbiotic event between a bacterial and an archaean cell, both groups lacking these features.

    And that is an inference which does have problems that need to be dealt with. It can be surmised where all the eukaryotic signature proteins came from where spliceosomal introns came from, or where the nucleus came from, but it’s only conjecture.

    A second argument would be that evolutionary change in eukaryotes is readily observable from the moment they enter the fossil record, so it is peculiar to assume that they were immutable before that time.

    Nothing in life is immutable. Eukaryotes have always been subject to change the same as everything else.

    CharlieM: Talking about “Nano-beings” is less of a mouthful than talking about “intracellular motile living forms”.

    Not metaphors then. But proteins are not life forms, since they do not reproduce. We discussed this previously.

    Proteins are unique to living systems and so must be regarded as life forms. And if this is too much of a stretch for the reductionist mindset then IMO, for protein complexes such as dynein, using the metaphor Nano-being is more accurate than using the term nano-machine.

    If we think of the cell as equivalent to a bee hive, then we have a living system in which there are a variety of beings, not all of which reproduce, but all work together for the good of the whole.

    We need to look at an entity such as a dynein complex, not just as a static form, but as a form which is conceived within the chromosomes, travels out of the nucleus, converges into its working form, carries out its tasks, dies and is broken down so that its basic pars can be reused as appropriate. It has a life cycle just like any other living form. The relevant genes, the RNAs, and the proteins are all an integral part of the life of a dynein complex. This is no different to accepting that the husk of a beech nut, even though it has been discarded by the time the sapling grows, is an integral part of the life of a beech tree.

    We have to look at the whole picture, or should I say, process. “Picture” here being a pretty poor metaphor. “Picture” is more to do with seeing with the eyes whereas “process” is more to do with seeing with the mind.

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