Observations and Interpretations

I make observations and interpret what I see from my own personal perspective and world view. If I am, a creationist, a physicalist, a vitalist, a specialist, religious, atheist or whatever, my explanations will be fashioned accordingly to some extent. Some subjects are more contentious than others, and some people can take a more objective stance than others. The metaphors used in biology frequently demonstrate how life is thought of in mechanistic terms.

Many people may be surprised with the results of a survey discussed in the article, “First worldwide survey of religion and science: No, not all scientists are atheists”

Should the personal beliefs of scientists matter?

I watched the following video, “The Inner Life of the Cell” by Harvard and HHMI narrated by Carol Tydell, a lecturer in physiology. I noted how her descriptions of the cellular components and processes swung between anthropomorphism and a mechanistic viewpoint. (Incidentally, “component” originally used to mean one person within a group, now it more often than not refers to a part of a machine.) I would have preferred if some of the terminology used by Dr Tydell had been rephrased.

According to Tydell, the molecular components are depicted “entirely accurately”. I can assume that the depiction is as accurate as they can make it, but I would add that it’s relatively static and a very much simplified representation of the workings of a living cell.

When she talks about dynein complexes, mitochondria and ribosomes she likes to use terms such as, ‘these guys’ and ‘fellows’. While she may be anthropomorphizing at least she is referring to them as living beings. But she takes if further. Listening to Tydell it sounds like the cell is full of self-conscious, decision making entities with integral goals an desires. I don’t see any of these complexes showing sign of having consciousness on this level.

And at the other extreme, regarding those molecular complexes that are doing something, she says, “We don’t consider them to be alive. They are just proteins”. Would she also say, “Those things that build their mounds in Africa, Australia and South America, we don’t consider them to be alive. They are just termites.”?

She refers to proteins moving like some kind of dinosaur or some kind of machine. Which is it? Are they living or are they dead matter?

I consider protein that is active within organisms to be living substance, not dead matter.

Of all the pieces I’ve listened to or read on the subject of biology, quite a few of them are extremely mechanistic. Dr Tydell is much more even-handed here. Metaphysical naturalism is quite often the order of the day in areas where methodological naturalism is called for.

68 thoughts on “Observations and Interpretations

  1. CharlieM: Are we in agreement that that, at present on earth, urea is known to be created from two sources and both of them involve life?

    Well, you are still wrong about that, so agreement will not be forthcoming.

    Here we are discussing, what I consider to be a relatively simple compound, CO(NH2)2. (In the above quote they class urea as a “complex organic molecule” because it consists of eight molecules[sic].) Now picture all those other far more complex interacting compounds and chemical arrangements that are fundamental to life, and are only found to be produced by living systems. It’s no wonder that the origin of life from basic non-living substances is a theory that has never been demonstrated. And it’s not for the want of trying.

    I encourage you to go and learn about all the research that is being done into abiogenesis. Although, for starters, you might want to internalize the difference between a molecule and an atom.

  2. DNA_Jock: I encourage you to go and learn about all the research that is being done into abiogenesis.

    I’ve been dallying at Uncommon Descent lately (as much as their cranky software will allow). In the process, I’ve realized RNA world ideas have led to some interesting research. I might try an OP if I find time.

  3. CharlieM: Me: If not, then why on earth did you use the phrase “products of life”, which apparently literally includes the kitchen sink?

    Charlie: Because we are alive and we produce them. I don’t consider wood to be alive, even if it is the product of living trees.

    Your claim is that there is something that sets living beings apart from non-living objects. This claim extends to some of the molecules that make up living organisms, since you believe dynein motor proteins to be possessed by some “inner activity”. This is essentially a vitalist claim.

    This claim is challenged by the fact that we can artificially synthesize organic molecules such as urea, but also more complex ones like polynucleotides (DNA and RNA) and polypeptides. This demonstrates that there is no fundamental difference between organic and inorganic chemistry.

    Now, unless you believe that manufactured objects are somehow relevant to your claim, I would very much like you to drop the obfuscating language such as the totally irrelevant and wildly confusing “products of life”. Thanks!

    CharlieM: Getting down to basics. In the standard model all particles are excitation of fields and the vacuum excitation value, the total energy value of these fields averages out to zero. But physical existence relies on there being a break in this symmetry. This is where Higgs comes in. The vacuum expectation value, the lowest energy state, of the Higgs field isn’t zero, it’s 246GeV (giga electronvolts). For matter to exist as known by us it must have mass. And massive particles can only form because of the vacuum energy of the Higgs field. Precise measurements of the values associated with fundamental particles says nothing about why they have those values.

    ALSO, I would like you to stop spamming this discussion with random and completely irrelevant chunks of particle physics. If you don’t have any decent counterarguments, just say so.

    CharlieM: It is my belief that living matter condenses out of surrounding dynamic fields in like manner to the way crystals condense out of solution. In this way the complexity of life does not just suddenly poof by magic out of dead chemicals. The complexity is already prefigured in the dynamic life field.

    I believe this is a more parsimonious explanation than the reliance on so many serendipitous events coming into alignment which has allowed us to be here discussing this.

    If you like. But a belief is just a belief and I do not find your explanation with the completely unsupported “etheric life principle”, “formative fields”, “archetypes”, “point-wise radial forces” and “plane-wise peripheral forces” parsimonious at all.

  4. CharlieM: The German theoretical physicist Sabine Hossenfelder has a talk on YouTube, What’s Going Wrong in Particle Physics? (This is why I lost faith in science.). She seems to know what she is talking about, but I’m not sure how many people here would enjoy listening to it as her scepticism is running in the wrong direction.

    I do. I already watched that movie a while ago. Also, her book “Existential Physics” is in my pile of books yet-to-read.

  5. Alan Fox:
    “CharlieM: Chemical bonds are being made and broken all the time. And it might be too small to measure but the mass of these “particles” does not remain constant.”

    Alan Fox: It’s still a fact that particles, atoms, molecules carry no historical information. I wouldn’t put any store by the idea that particles might be distinguished my mass variation? How do you think the mass of an atom is measured?

    Hint.

    Let’s see where all of this is leading us.

    The image below is from your link. It shows the trajectories of carbon dioxide ions through the spectrometer. Are these trajectories not a historical record (however short) of the path of the ions from source to detector?

    What does it matter if all protons or atoms or molecules of the same type are mathematically identical in certain respects and we cannot distinguish one from the other? How does this stop them having their own history? Some of the molecules that pass through my body might have entered through my mouth and are now heading down a pipe towards the local sewage works. Being in some respect identical does not mean that they are not distinctly separate individuals.

    Returning to Heraclitus and the river I know that the physical substances passing through the river are transient. So the river is an entity which has more permanence than the physical substances. Form is more enduring than substance.

    You are correct, you can’t help but step into the same river. But only if you are aware that in essence the river is more than the molecules which pass through it.

  6. DNA_Jock:
    “CharlieM: Are we in agreement that that, at present on earth, urea is known to be created from two sources and both of them involve life?”

    “DNA_Jock: Well, you are still wrong about that, so agreement will not be forthcoming.”

    “CharlieM: Here we are discussing, what I consider to be a relatively simple compound, CO(NH2)2. (In the above quote they class urea as a “complex organic molecule” because it consists of eight molecules[sic].) Now picture all those other far more complex interacting compounds and chemical arrangements that are fundamental to life, and are only found to be produced by living systems. It’s no wonder that the origin of life from basic non-living substances is a theory that has never been demonstrated. And it’s not for the want of trying.”

    DNA_Jock: I encourage you to go and learn about all the research that is being done into abiogenesis. Although, for starters, you might want to internalize the difference between a molecule and an atom.

    Can you provide any specifics rather than vague generalizations?

    In your eagerness to discredit me you assume that I don’t know the difference between atoms and molecules just because I didn’t proofread my post with enough thoroughness to pick up the genuine compositional slip up due to my being in a bit of a rush .

    I live in hope for a touch more goodwill in reading my posts.

  7. Alan Fox: I’ve been dallying at Uncommon Descent lately (as much as their cranky softwarewill allow). In the process, I’ve realized RNA world ideas have led to some interesting research. I might try an OP if I find time.

    That would be great. I hope you can find the time.

  8. Corneel:
    “Corneel: If not, then why on earth did you use the phrase “products of life”, which apparently literally includes the kitchen sink?

    “Charlie: Because we are alive and we produce them. I don’t consider wood to be alive, even if it is the product of living trees.”

    Corneel: Your claim is that there is something that sets living beings apart from non-living objects. This claim extends to some of the molecules that make up living organisms, since you believe dynein motor proteins to be possessed by some “inner activity”. This is essentially a vitalist claim.

    This claim is challenged by the fact that we can artificially synthesize organic molecules such as urea, but also more complex ones like polynucleotides (DNA and RNA) and polypeptides. This demonstrates that there is no fundamental difference between organic and inorganic chemistry.

    I totally agree that there is no fundamental difference between organic and inorganic chemistry. In the same way there is no fundamental difference between naturally occuring chemical reactions and those reactions induced by chemists in a lab. It makes no difference whether it’s the behaviour of atmospheric processes, human chemists, or cells in an organism that instigates the chemical reactions; the reactions all occur in accordance within the laws of chemistry.

    Corneel: Now, unless you believe that manufactured objects are somehow relevant to your claim, I would very much like you to drop the obfuscating language such as the totally irrelevant and wildly confusing “products of life”. Thanks!

    And I would like you to try to understand what I am saying.

    “CharlieM: Getting down to basics. In the standard model all particles are excitation of fields and the vacuum excitation value, the total energy value of these fields averages out to zero. But physical existence relies on there being a break in this symmetry. This is where Higgs comes in. The vacuum expectation value, the lowest energy state, of the Higgs field isn’t zero, it’s 246GeV (giga electronvolts). For matter to exist as known by us it must have mass. And massive particles can only form because of the vacuum energy of the Higgs field. Precise measurements of the values associated with fundamental particles says nothing about why they have those values.”

    Corneel: ALSO, I would like you to stop spamming this discussion with random and completely irrelevant chunks of particle physics. If you don’t have any decent counterarguments, just say so.

    Then try to argue against what I actually mean and not a distortion of my meaning.

    “CharlieM: It is my belief that living matter condenses out of surrounding dynamic fields in like manner to the way crystals condense out of solution. In this way the complexity of life does not just suddenly poof by magic out of dead chemicals. The complexity is already prefigured in the dynamic life field.

    I believe this is a more parsimonious explanation than the reliance on so many serendipitous events coming into alignment which has allowed us to be here discussing this.”

    Corneel: If you like. But a belief is just a belief and I do not find your explanation with the completely unsupported “etheric life principle”, “formative fields”, “archetypes”, “point-wise radial forces” and “plane-wise peripheral forces” parsimonious at all.

    That is understandable from someone with your point of view.

  9. CharlieM: Can you provide any specifics rather than vague generalizations?

    I could, but I encourage you to educate yourself.

    In your eagerness to discredit me you assume that I don’t know the difference between atoms and molecules just because I didn’t proofread my post with enough thoroughness to pick up the genuine compositional slip up due to my being in a bit of a rush .

    In your eagerness to tone-troll, you completely misconstrued what I wrote. Actually, I assumed that you DO know the difference between an atom and a molecule. However, the fact that you wrote one when you meant the other indicates that you have yet to internalize the difference. Hence my comment; slow down and make fewer mistakes.

    I live in hope for a touch more goodwill in reading my posts.

    I am afraid that I have become somewhat jaded as a result of your ill-informed musings on basic Newtonian optics, visual perception, aural perception, organic farming, vibravision, high energy bonds, duck genitalia, and critically my left retina. Whatsoever a man soweth,…

  10. CharlieM: And I would like you to try to understand what I am saying.

    Do you actually believe that your difficulties in communicating are because of my unwillingness to understand what you are saying?

    CharlieM: Then try to argue against what I actually mean and not a distortion of my meaning.

    If you feel that I am distorting your position, then I apologize. I make a point of fairly representing other people’s point of view. Could you tell me where I have done so?

    Now this:

    CharlieM: I totally agree that there is no fundamental difference between organic and inorganic chemistry. In the same way there is no fundamental difference between naturally occuring chemical reactions and those reactions induced by chemists in a lab. It makes no difference whether it’s the behaviour of atmospheric processes, human chemists, or cells in an organism that instigates the chemical reactions; the reactions all occur in accordance within the laws of chemistry.

    is a distortion of your own making. There is no “life-force” or “inner activity” in regular chemistry, wheres you claim that this force or activity is involved in the catalytic activity of Taq polymerase and the motor activity of kinesin and dynein molecules.

    If you are going to argue that this inner activity is no part of chemistry, I swear, you never get to argue again that your failure to convey your point is because a fault on my part.

  11. DNA_Jock:
    “CharlieM: Can you provide any specifics rather than vague generalizations?”

    DNA_Jock: I could, but I encourage you to educate yourself.

    Your arrogance is noted. (Only from a superior educational standpoint would you be able to tell where my education is lacking.)

    “CharlieM: In your eagerness to discredit me you assume that I don’t know the difference between atoms and molecules just because I didn’t proofread my post with enough thoroughness to pick up the genuine compositional slip up due to my being in a bit of a rush .”

    DNA_Jock: In your eagerness to tone-troll, you completely misconstrued what I wrote. Actually, I assumed that you DO know the difference between an atom and a molecule. However, the fact that you wrote one when you meant the other indicates that you have yet to internalize the difference. Hence my comment; slow down and make fewer mistakes.

    The difference has been integral to my thinking for over half a century. I don’t mind getting things wrong occasionally. after all we learn by our mistakes. And I’ve learned that some people here will pounce on the slightest errors I make. 😉

    “CharlieM: I live in hope for a touch more goodwill in reading my posts.”

    DNA_Jock: I am afraid that I have become somewhat jaded as a result of your ill-informed musings on basic Newtonian optics, visual perception, aural perception, organic farming, vibravision, high energy bonds, duck genitalia, and critically my left retina. Whatsoever a man soweth,…

    If you are becoming tired of arguing with me then all I can suggest is you take a rest. Maybe then you will be able to return with renewed vigour, and you’ll be able to provide more constructive, detailed criticism. 🙂

  12. Corneel:
    “CharlieM: And I would like you to try to understand what I am saying.”

    Corneel: Do you actually believe that your difficulties in communicating are because of my unwillingness to understand what you are saying?

    In part, yes. For example, the products of life do not, themselves, have to be alive.

    “CharlieM: Then try to argue against what I actually mean and not a distortion of my meaning.”

    Corneel: If you feel that I am distorting your position, then I apologize. I make a point of fairly representing other people’s point of view. Could you tell me where I have done so?

    There is the example I gave above.

    Corneel: Now this:

    “CharlieM: I totally agree that there is no fundamental difference between organic and inorganic chemistry. In the same way there is no fundamental difference between naturally occurring chemical reactions and those reactions induced by chemists in a lab. It makes no difference whether it’s the behaviour of atmospheric processes, human chemists, or cells in an organism that instigates the chemical reactions; the reactions all occur in accordance within the laws of chemistry.”

    Corneel: is a distortion of your own making. There is no “life-force” or “inner activity” in regular chemistry, whereas you claim that this force or activity is involved in the catalytic activity of Taq polymerase and the motor activity of kinesin and dynein molecules.

    If you are going to argue that this inner activity is no part of chemistry, I swear, you never get to argue again that your failure to convey your point is because a fault on my part.

    All the activity makes use of chemical and physical forces but there is a higher purpose to this activity. Neither chemistry nor physics has anything to contribute to why a molecular complex should carry a cargo along a microtubule for the purpose of delivering it to where it is required to be. The laws of chemistry and physic do not allow for any purposeful activity, any teleology. Your activity in relying to me does not break any of these laws, but at the same time, these laws don’t account for your purposefulness in giving these replies.

  13. CharlieM: In part, yes. For example, the products of life do not, themselves, have to be alive.

    Nobody but you uses the phrase “products of life” to refer to artificial and synthetic products.

    CharlieM: There is the example I gave above.

    I cannot see it, sorry. Could you cite it and tell me how it misrepresents your position?

    CharlieM: All the activity makes use of chemical and physical forces but there is a higher purpose to this activity. Neither chemistry nor physics has anything to contribute to why a molecular complex should carry a cargo along a microtubule for the purpose of delivering it to where it is required to be. The laws of chemistry and physic do not allow for any purposeful activity, any teleology. Your activity in relying to me does not break any of these laws, but at the same time, these laws don’t account for your purposefulness in giving these replies.

    Then why not call it purpose? I do not believe “life force” exists but I do believe purpose exists.

    Purpose is not bestowed on living beings by any fields BTW, but we can discuss that later.

  14. Corneel:
    Corneel: Nobody but you uses the phrase “products of life” to refer to artificial and synthetic products.

    The beauty of language is that we can arrange phrases or sentences occasionally in unique ways and still be understood. I’ve used a simple phrase and the meaning shouldn’t be difficult to discern.

    I used “product” meaning something that is the result of a process, and that leaves life. “Life” according to Wikepedia:

    Life is a quality that distinguishes matter that has biological processes, such as signaling and self-sustaining processes, from matter that does not, and is defined by the capacity for growth, reaction to stimuli, metabolism, energy transformation, and reproduction. Various forms of life exist, such as plants, animals, fungi, protists, archaea, and bacteria.

    I think it is safe to say that we fall within the category of life.

    According to Richard Tarnas in his book, “The Passion of the Western Mind”, “the human mind is ultimately the organ of the world’s own self-revelation”. And through science and technology more and more is being revealed.

    So we need not stop at saying human inventions are the products of life, we can say they are the products of the world as a whole.

    “CharlieM (on a distortion of my meaning): There is the example I gave above.”

    Corneel: I cannot see it, sorry. Could you cite it and tell me how it misrepresents your position?

    I was being a bit unfair, but it seemed that you were arguing that I had intended “product of life” to be some sort of obscure, ambiguous use of words. I thought my meaning was quite clear.

    “CharlieM: All the activity makes use of chemical and physical forces but there is a higher purpose to this activity. Neither chemistry nor physics has anything to contribute to why a molecular complex should carry a cargo along a microtubule for the purpose of delivering it to where it is required to be. The laws of chemistry and physic do not allow for any purposeful activity, any teleology. Your activity in relying to me does not break any of these laws, but at the same time, these laws don’t account for your purposefulness in giving these replies.”

    Corneel: Then why not call it purpose? I do not believe “life force” exists but I do believe purpose exists.

    I suppose I could call it the teleological principle, because purpose is a major factor in what separates the living from the non-living. Teleology is not accounted for by any laws of chemistry or physics. So what I call a life force you are welcome to call an inner purposeful principle or something like that. But whatever it is, it is an active principle which is exclusive to life.

    Purpose is not bestowed on living beings by any fields BTW, but we can discuss that later.

    It doesn’t matter what we believe, fields are fundamental to reality. I have just read an article in New Scientist, 8 April 2023. A cover story written by Jon Cartwright which is listed as “A Quantum Guidebook”. In it he asks a question, “Is reality made of particles or fields?” He then goes on to say:

    We talk of particles, which is to say things that occupy points (more or Less) in space-yet particles are just energetic spikes, or “excitations”, in underlying quantum fields. A photon, say, as the carrier of electromagnetism, is an excitation of the underlying electromagnetic field.

    These fields permeate the entire universe, which means that there is some residual photon-ness everywhere-so-called virtual particles, which appear fleetingly and then vanish-even when there isn’t enough energy around to manifest a particle proper.

    Fields, then, are usually considered more fundamental. The maths simply doesn’t work without them. But the ambivalent quantum nature of a field means that it can’t be observed directly: any observation requires a dose of energy that, in effect, forces the field to show its hand and produce a particle. For this reason, particle talk seems unavoidable. Particles are what we see.

    I suppose that depends on what he means by “particles”. We can observe objects such as dust particles dancing in the sunlight, but we can no more see fundamental particles than we can see fundamental fields.

    So the assumption that purpose is bestowed on living beings by matter, can be taken a step further. Matter is produced by the excitation of fields, so it can be logically concluded that, purpose becomes the product of fundamental fields. 🙂

  15. CharlieM: The beauty of language is that we can arrange phrases or sentences occasionally in unique ways and still be understood. I’ve used a simple phrase and the meaning shouldn’t be difficult to discern.

    Let me recommend you go back to the place where you introduced the term and ask yourself whether you really wanted to know whether I would file “cells, cytoplasm, proteins and tissues” in the same category as dog poo and strap-on dildos.

    CharlieM: I was being a bit unfair, but it seemed that you were arguing that I had intended “product of life” to be some sort of obscure, ambiguous use of words. I thought my meaning was quite clear.

    Well, I am pretty sure that I invest way more energy than the average visitor here on this site to try and make sense of your writings and I still get the impression you are being deliberately vague on occasion.

    No, you didn’t make yourself clear, and I don’t think it is just because of me.

    CharlieM: I suppose I could call it the teleological principle, because purpose is a major factor in what separates the living from the non-living. Teleology is not accounted for by any laws of chemistry or physics. So what I call a life force you are welcome to call an inner purposeful principle or something like that. But whatever it is, it is an active principle which is exclusive to life.

    Active in what sense? Does it affect the outcome of chemical and physical processes in living beings?

  16. Corneel:
    “CharlieM: The beauty of language is that we can arrange phrases or sentences occasionally in unique ways and still be understood. I’ve used a simple phrase and the meaning shouldn’t be difficult to discern.”

    Corneel: Let me recommend you go back to the place where you introduced the term and ask yourself whether you really wanted to know whether I would file “cells, cytoplasm, proteins and tissues” in the same category as dog poo and strap-on dildos.

    No, I don’t think you would file them in the same category. And that is why I gave you the choice of two categories. You can categorize them as living, the products of life, neither or both. (You seem to have a problem with the term ‘products of life’, so you can use ‘products of living beings’ as an alternative.)

    “CharlieM: I was being a bit unfair, but it seemed that you were arguing that I had intended “product of life” to be some sort of obscure, ambiguous use of words. I thought my meaning was quite clear.”

    Corneel: Well, I am pretty sure that I invest way more energy than the average visitor here on this site to try and make sense of your writings and I still get the impression you are being deliberately vague on occasion.

    No, you didn’t make yourself clear, and I don’t think it is just because of me.

    It is rare to get straight-forward, yes/no answers to the questions we are asking. Looking for answers invariably leads to many more questions. And, personally I prefer when questions make me think and the answers don’t come easily.

    “CharlieM: I suppose I could call it the teleological principle, because purpose is a major factor in what separates the living from the non-living. Teleology is not accounted for by any laws of chemistry or physics. So what I call a life force you are welcome to call an inner purposeful principle or something like that. But whatever it is, it is an active principle which is exclusive to life.”

    Corneel: Active in what sense? Does it affect the outcome of chemical and physical processes in living beings?

    Integral activity which has its source within the entity. Computers have integral activity, but its source is in human design. I have integral activity, but its source is within me whether it is bodily functions or acts of will. There is a dynamic organizing principle within me maintaining my life.

    When I make a decision to act it sets off a multitude of chemical and physical processes within my body. As far as I’m aware, the processes I instigate all obey the laws of physics and chemistry.

    My body has an integral self-organizing principle.

    When the body of an animal fossilizes its cells and tissues lose their integral organizing ability and succumb to external environmental forces. The body is acted upon by physical and chemical forces, rather than itself using these forces to sustain an active life. It has lost its self-sustaining organizing principle.

  17. CharlieM: And, personally I prefer when questions make me think and the answers don’t come easily.

    Ah, another “multitude of questions you would like to find answers to”?

    CharlieM: When I make a decision to act it sets off a multitude of chemical and physical processes within my body. As far as I’m aware, the processes I instigate all obey the laws of physics and chemistry.

    They sure do. Even better: dynein and kinesin motor proteins do their thing just fine in organisms without any conscious decision making and even in vitro. It’s almost as if chemical and physical processes are themselves sufficient to endow proteins with purpose.

    CharlieM: My body has an integral self-organizing principle.

    So you keep saying, but that doesn’t follow from any of the stuff you wrote. You just keep closing your eyes to the alternative explanation that self organisation and purpose are emergent properties.

    Is the purpose of a dynein motor protein not to transport cellular cargo? Is the purpose of a DNA polymerase not to assemble a chain of nucleotides? Can you think of a process in populations of living organisms that maintains such molecular functions? And if it maintains them, could that same process not also be responsible for their creation?

    Was one of your questions among the ones above? I bet not!

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