Mechanisms and Organisms

[CharlieM]

From here: https://www.khanacademy.org/science/bio ... to-viruses

Because they can't reproduce by themselves (without a host), viruses are not considered living. Nor do viruses have cells: they're very small, much smaller than the cells of living things, and are basically just packages of nucleic acid and protein.

So the minimum requirement for reproduction is a cell. It doesn't matter how you slice up the energy allocation or how smart you think virus strategy is. The fact of the matter is that cells are an essential part of the process. Take the cell away and tell me what happens.

Tapeworm anyone. Tapeworms can't reproduce without a host, therefore...

Therefore what? Have you had a look at tapeworm life cycles and reproduction? Get back to me when you discover any form of tapeworm reproduction that doesn't involve egg cells.

Trying to describe life is something exobiologists have a lot of fun with.
https://www.space.com/22210-life-defini ... rview.html

Some notable remarks in that interview, to be sure. For instance:

"Darwinian evolution" has an associated property list: You can’t have Darwinian evolution without self-replication or reproduction. You can’t have it without mutability, heritability, and variation of form and function. And metabolism is in there too. You can’t have Darwinian evolution without, at some level, a flux of higher-energy starting materials to lower-energy products that drive the processes of replication and whatever is necessary to support replication...
A single individual might seem to be capable of undergoing Darwinian evolution, but may in fact be dead, or a fossil remnant, or about to die, or unable to find a mate. So it is the system that is said to be capable, not the individual.

Self-replication in the case of viruses necessarily involves the whole system. This system includes the host cell as a minimum requirement.

They even state as much in your link, so thanks for that:

The viral genome only evolves in the context of the host cell...Something within the system, within the collective system, must provide all of the information necessary to bring about Darwinian evolution... The virus alone can’t achieve this, but the virus plus the host cell can.

I couldn't have put it better myself.

Your whole argument boils down to a logical fallacy:

argument from incredulity

My only incredulity is in the fact that you would link to an interview that confirms my point.

[Johnny Blade]

I don’t give it a lot of thought.

Well, me neither until now.

To say a virus isn’t alive is a problem, though.

I’d consider a grain of sand to be not alive. Viruses do quite a few more tricks than grains of sand do.

So does my cell phone.

From what little I know, viruses seem to be more like bits of corrupted DNA. Maybe a bit of what should have been a normal, fully developed cell that got hit by a radioactive particle during a specific phase of cell division? Probably I am wrong. I have no idea.
We all shed DNA, leaving traces of our identity practically everywhere we go. Forensic scientists use DNA left behind on cigarette butts, phones, handles, keyboards, cups, and numerous other objects, not to mention the genetic content found in drops of bodily fluid, like blood and semen (Van Oorschot & Jones, 1997).

Anyway, there seems to be an agreement in the mainstream literature that viruses are not living. So criticizing CharlieM for a citing a source that also says the same thing, but is maybe not mainstream, is kinda pointless.

[CharlieM]

From here: https://www.khanacademy.org/science/bio ... to-viruses

Because they (without a host), viruses are not considered living. Nor do viruses have cells: they're very small, much smaller than the cells of living things, and are basically just packages of nucleic acid and protein.

can't reproduce by themselves
So the minimum requirement for reproduction is a cell. It doesn't matter how you slice up the energy allocation or how smart you think virus strategy is. The fact of the matter is that cells are an essential part of the process. Take the cell away and tell me what happens.

Khan Academy? You are using Khan Academy for your authoritative definition of life?

Who is trying to define life? Not me.

You do know their target audience, don’t you? Students. Children. You do know Sal Khan has absolutely no qualifications in pedagogy, don’t you?

Did you notice the lack of peer review in that article to which you linked?

Now you are accusing me of arguing from non-authority. That makes a change! As the link that romansh provided shows, I could have picked from any number of sites to make my point. I didn't quote from Khan Academy because of who they are, I quoted them because of what they said. If you have evidence that some viruses can reproduce by themselves then share it.

“they’re very small”, eh? So small, in fact, they couldn’t possibly make off with a whole leg. How small is very small, Charlie?

Ask Khan Academy. It was them who wrote that. Their size makes no difference to my argument.

Which came first, Charlie, the virus or the cell?

There has been a lot of discussion about that. I'd put my money on the cell.

[The_Metatron]

Charlie, you can’t reproduce by yourself, either.

[CharlieM]

Charlie, you can’t reproduce by yourself, either.

Why would I want to? That would take all the fun out of it.

But seriously, these are obvious but wise words you have given us. For reproduction the whole system of essential parts must be present. The parts must come together and cooperate in a coordinated manner if any living system is to produce viable offspring which can then potentially continue in like manner. It is only through the cooperation of a woman's ovum that a man's sperm is able to penetrate its outer layers and continue the cycle of reproduction. Likewise it is only through the cooperation of the host cell that viruses are able to reproduce.

If you wish to witness any Darwinian evolution within physical earthly life, cells are a minimum requirement.

[CharlieM]

Masculine forcefulness and feminine receptivity are just two of the polarities that abound in nature.

"The Plant Between Sun and Earth" is a fairly old book which examines the polarities within plant life from a Goethean perspective and the complete book can be found here: https://www.aetherforce.energy/the-plan ... chapter-1/. Whatever anyone thinks about the website that contains this book, I would recommend reading it for its detailed examination of living, dynamic, expansions and contractions that feature heavily in plant life and for its spectacular images.

[The_Metatron]

Yeah, like the receptive female praying mantis.

[CharlieM]

Yeah, like the receptive female praying mantis.

The female mantis shows her receptivity by releasing pheromones which males eagerly follow. You're being fairly anthropomorphic if you think that getting his head chewed off bothers the male mantis or puts him off from his objective. He can continue to mate for hours even without his head. Mission accomplished.

He may lose his head for love but that's not important because the brain that matters is in his proverbial pants.

[CharlieM]

about polarities.

Speaking of polarities, when Goethe eventually began making observations of light through a prism, he noticed the polar nature of edge spectra. And in order for green to be produced the prism had to be turned to allow both edge spectra to overlap. Looking at any edge between darkness and light produced a red/orange band over the light part and a blue/violet band over the dark part. And thus he disagreed with Newton that colours are contained in "white" light. He believed that colours appeared as the interplay of light and darkness. He saw that Newton had to set up the conditions in a particular way to get the seven colours of the spectrum he was looking for.

Instead of Newton's static set up, Goethe used the prism in a dynamic way and observed the effects. He realised that the production of overlapping bands could be achieved in two ways, one produced the central colour green and the other magenta. Newton focused on the spectra that contained green while Goethe gave both spectra equal consideration.

Goethe saw spectral colours as forming from the interplay of light and darkness, but the eye of the observer was also an essential component of this process. With his work on complementary colours he noticed that we are always trying to make things whole. Thus staring at a coloured surface will always give an afterimage of its complementary colour.

Another effect that demonstrates this is the observation of coloured shadows. as seen in the following video:


An easy experiment to do at home to study the effect of matter on light. Take a glass of water that's been made cloudy with a drop of milk into a dark room. Shine a light through the glass and watch the colour of the liquid change from having an orange appearance to a blue appearance as the light is moved round from back to front. Goethe explains this phenomenon well.

Goethe remained with the observation of colours while Newton was looking for the mathematics behind light and colours.

[The_Metatron]

Yeah, like the receptive female praying mantis.

The female mantis shows her receptivity by releasing pheromones which males eagerly follow. You're being fairly anthropomorphic if you think that getting his head chewed off bothers the male mantis or puts him off from his objective. He can continue to mate for hours even without his head. Mission accomplished.

He may lose his head for love but that's not important because the brain that matters is in his proverbial pants.

You wouldn’t be so cavalier if it were your head getting chewed off.

[CharlieM]

What works for mantis evolution would be totally inappropriate for humans and that is why there have been no recorded instances of it happening during the astonomical number of human copulations throughout our history. So I think I'm safe enough. One of the perks of being humans, we can have a sex life without fear of having our heads chewed off.

It probably became a habit among preying mantises when one male happened to remark to his partner, "Don't bite my head off but the sex could be better!"

[Johnny Blade]

Well, as they say, "There is no such thing as bad publisity"

Well I have to say a lot of what you have posted here just blows my mind. Very enjoyable and informative. I was not expecting it to be so.

[Rumraket]

Well, as they say, "There is no such thing as bad publisity"

Well I have to say a lot of what you have posted here just blows my mind. Very enjoyable and informative. I was not expecting it to be so.

Did you find out how to calculate any of these things yet?

[CharlieM]

Well, as they say, "There is no such thing as bad publisity"

Well I have to say a lot of what you have posted here just blows my mind. Very enjoyable and informative. I was not expecting it to be so.

I'm glad you're getting something from it. I'm just thankful that the technology of today allows us to search out the hard work done and shared by others. Although we all no there's a lot of dodgy stuff out there.

[Rumraket]

Now we are getting into intrinsic and extrinsic teleology. Do you consider magnets to have goals?

They have exactly the same goals the macrophage and bacterium do: None. So it's not a property of them, it's as property of our minds when we look at them. It's a view in our minds. That's it.

From Nature.com: https://www.nature.com/articles/nature12034

Macrophages, the most plastic cells of the haematopoietic system, are found in all tissues and show great functional diversity. They have roles in development, homeostasis, tissue repair and immunity. Although tissue macrophages are anatomically distinct from one another, and have different transcriptional profiles and functional capabilities, they are all required for the maintenance of homeostasis.

This quote indicates some of the reasons why macrophages exist within organisms. It is very unlikely that they have any goals of which they are aware, but they do have various functions which contribute to the continued health of the organism. They have a reason to exist and it is for the sake of the whole.

Nobody would dispute that there are reasons for (as in causes that explain) their existence. But again, I would just offer the simple clarification that to perceive goals for their behavior is merely an interpretation.

We can return to the screwdriver again. Does the screwdriver have a goal? As an idea in the mind of it's user/creator, sure. Is it intrinsic to the screwdriver itself? No. There is no reason to think the macrophage is any different.

Do you think they demonstrate intrinsic teleology?

Nothing demonstrates intrinsic teleology. All anyone can actually demonstrate is to report that they themselves have conceived of, or perceived of a goal for themselves or in others.

I looked up "teleology" here: https://en.wiktionary.org/wiki/teleology and from there I found "teleophobia" here: https://en.wiktionary.org/wiki/teleophobia#English. Maybe in some people mechanistic reductionism has induced an irrational fear of teleology in nature.

That's funny but ultimately of no probative value. Anyone can label a viewpoint they disagree with as being motivated by some sort of phobia. But all I am offering is really a way to make sense of the concept of teleology so that it can be applied consistently across basically any topic. I am simply explaining what I think goals really are, not denying that they exist. They do exist, but as ideas in the minds of sentient creatures.

You seem to want it to be more than this. As if that is just not enough for you. That an idea in your mind isn't real enough, and if I don't join you in saying macrophages (or whatever) act towards certain ends, as if they have goals, beyond merely as an idea in our minds, then you think I am somehow denying, or missing, something about what they're doing.
It just isn't clear to me what you're even trying to achieve here, or what you think is missing, or what behavior I can't make sense of given how I describe and characterize what we mean by teleology, or goal-directed behavior.

[Rumraket]

The end point is indeed something that is in our minds. That is because we have observed the processes involved. We see that an end point of nest building is the laying of eggs, caring for the young, and thus ensuring the continuation of the species. We see the facts unfolding before us. To be consistent your position applies equally to Darwinian evolution. Is it just an idea in our minds, an interpretation?

Rumraket: That's deeply confused. The process of building a nest is a physical reality, the idea that it is a goal, an endpoint, is not a physical reality. That is an idea in your mind (well, unless you want to say the neurological processes that would correspond to you holding that idea in your mind is a physical reality of a kind). But I would just say it is what you alluded to earlier, a kind of higher-order explanation. Explanations are also ideas in our mind.

The process of evolution—that is the transgenerational inheritance of traits and the accumulation of changes in populations of organisms—is a physical reality too. It really does physically happen that populations change over time. We describe this process as evolution. If you were to say evolution has some end or a goal, that too would just be an idea in your mind. And of course evolution as an explanation is also an abstract concept, and so is also an idea in our minds. It is not an interpretation though, because the process really can be observed.

Most of us have witnessed newborn babies develop into full grown adults. Indeed it is also a personal memorable experience from the point where we begin to retain memories. These are directed processes which we observe and not just ideas in our minds.

We observe the process, but the claim that they are "directed" is just an interpretation. An idea in our minds.

The actions of living systems achieving ends is something that can be observed.

No. It is interpreted. There's no observation of any ends. The fact that you can see some particular entity or event transpire doesn't make it a goal. That is you interpreting that way. Like with the screwdriver. Whatever anyone does with a screwdriver doesn't make that it's goal or end or purpose. That will only ever remain an idea in the mind of the observer or the one who uses it. It isn't observed, it is interpreted. Rose colored glasses analogy again.

Michael Levin brings up the subject of the emergence of novel agents and the goals of these novel agents. He is researching the emergence of basal intelligence, goal directedness, some competency, and asks, "Where do the goals of novel complex systems come from?

He mentions William James who contrasted living systems with magnets. If two magnets are put together with a block of wood separating them, then they remain fixed in that position. Levin's experiments on systems which, unlike the magnets will manoeuver to positions which are less favourable in order to then get into a more favourable position.

Yes and organisms are also much more complex than just two magnets of course. They have systems that respond to local circumstances to bring them out of, for example, having got stuck somewhere. Organisms can follow a concentration gradient through the chemotaxis system, for example (what the macrophage and bacterium is doing, moving against and along a concentration gradient, respectively). A purely reflexive and mechanical (basically algorithmic) reaction system that, as you would say, gives the appearance of being "directed." But we understand it's entirely mechanical and physical basis.

Here I am, screwdriver in hand. The plan is to take this thingumabob in front of me apart. It is held together with screws. The only problem is there are caps over the screw heads. I scratch my head, "How do I get to the screws?" I use the screwdriver to lever off the caps and then use the screwdriver as intended to dismantle the thingumabob. The goal which I had in mind has now been physically achieved. I observe the pieces in front of me and satisfied with my work I make myself a cup of coffee as a reward. Meanwhile the screwdriver sat on the bench wondering what just happened, feeling embarrassed and violated, subjected to such inappropriate behaviour.

Then someone else picks up the screwdriver and stabs you with it. New goal for the screwdriver, another "end" achieved. Was that it's goal all along, or is that just an idea in the head of whoever perceives it being used, or uses it themselves?

Serious question by the way. And I think my view of what goals are can make perfect sense of it. Ideas in the minds of sentient beings and nothing more.

[Rumraket]

In the case of this maze demonstration we must remember that it was only possible because of the way that humans prepared the setup.

That's just an assertion.

[CharlieM]

A good source of information on Goethe's theory of colours is his youtube channel here: [url]https://www.youtube.com/@PehrSall[/url

Here is one video from his channel: "Colour and Physics - On the compatibility of Goethe's theory of colour with that of Newton's", a talk by Pehr Sällström of Stockholm University

Convention colour theory talks of impossible colours, chimerical colors and the like according to their relationship to wavelengths. Goethe was interested in the way colour behaved for visual experiences without thinking about anything lying behind the colours themselves.

[Rumraket]

Living forms such as organisms, however basic, can only be envisioned as complex, functional wholes. Evolutionary processes have not added complexity piece by piece in the same way that human produced mechanisms have evolved. Instead the novelty emerges from the whole.

This is so vague so as to be basically meaningless. Novelty emerges from the whole—What does that even mean? We can look at specific examples of evolutionary novelty to see how they have evolved. Gene duplication followed by divergence, for example, is how a novel functional component can evolve and be added to an existing system to increase it's complexity.

I don't see what we gain from having to engage in this mealy-mouthed "the novelty emerges from the whole" way of speaking when we start looking at the specifics. I some times get the sense that you're not even sure of what you're trying to say, you just have this strange but actually ill-considered attraction to "holistic", "dynamic", "living", "fluid" interpretations.

They're buzzwords, really. You just have buzzwords in the end. We must see the whole. We must see the ends. The teleodynamics. The whole, the living, the dynamics, goal-directedness. For universal love and peace on Earth. We must consider the relationship across time and space, it's all it's multiple facets and nuances.

Like back when you wrote:

It has been ingrained in our thinking minds to see the living world as no more than machines produced by evolutionary processes. We need to move on from this repressive, stultified, dead thinking to a more dynamic, living way of studying nature.

"More dynamic", "living way" of studying nature. And if we don't engage in this (whatever the fuck it really is) then we're being repressive, stultified, and showing dead thinking.

Yawn.

[Rumraket]

Oh look, it's yet more outings for more tedious apologetic variations on the theme of "I don't understand how testable natural processes can achieve the requisite results, therefore Magic Man did it".

Except that we have evidence by the supertanker load for testable natural processes, and ZERO evidence for magic poofing by a cartoon magic man.

Of course, I'm aware of how testable natural processes might look like magic to the scientifically illiterate, but that doesn't validate fantasies about magic poofing.

The only "elephant in the room" here, centres upon the apologetic desperation and dishonesty of magic man fetishists.

Sounds like to you, this more about trying to prove there is no God, rather than explaining a secular theory of origins in a logical manner. If there is no conceivable way to bridge the gap, logically, between your secular theory of the cosmos with your secular theory of life, then what good is either theory really?

Can you explain what this "secular theory of the cosmos and secular theory of life" is? I still don't know what you're asking for when you speak in this way.

Are you asking for a theory of the origin of life? As in, a scenario for how life could have originated somewhere in the universe?

Are you claiming it is not possible to offer even a hypothetical account of how life could have originated?