Mechanisms and Organisms

[Rumraket]

I think he has made a rather convincing argument so far actually.

Argument for what, specifically?

I understand that because the earth is constantly receiving energy from the sun, then it can be said that locally on earth we might be able to say we have an endless power supply. But CharlieM has shown that even the most fundamental and "primitive" living life components seem to require much more information and "purpose" than most of us realize.

That is incredibly confused. You speak of the quantity of energy supplied by the sun, then turn around and peak of information and purpose. These are not the same. Charlie also hasn't "shown" anything about how much information or purpose anything "requires", nor how much of it anyone has realized is required.

Where has CharlieM shown how much information is required by primitive life? Nowhere.
Where has CharlieM shown how much "purpose" is required by primitive life? Nowhere.
Where has CharlieM shown how much purpose or information most of realize that primitive life "requires"? Nowhere.
Where has CharlieM shown what he thinks the relationship is between energy, the second law of thermodynamics, information, and purpose? Nowhere.

Which makes it less likely that you have a efficeint mechanism to convert solar heat energy into the information required to create or sustain life.

In order to determine that some thing A is less likely than another thing B, you must be able to show what the probabilities are of each. No probabilities have been calculated, nor even as much as asserted, anywhere by CharlieM.

Please show where he calculated the probability that we have "an efficient mechanism to convert solar heat energy into the information required to create or sustain life", and please also show where he calculated "the information required to create or sustain life."

The probability that life has evolved on earth is 1.

How is that a response to what I am asking of Johnny Blade? He seems to have hallucinated a number of things of what you have shown and/or calculated, that you nowhere showed or calculated. And he appears to want to characterize this as some sort of win for him or you, for some unexplained purpose.

Even worse is I asked him to clarify his last response to me, but he stopped responding entirely. It's really odd behavior, as is your response. It looks like a sort of damage control taking the form of flailing wildly with text.

As far as I can tell the probability of humans creating life from scratch in the near future is zero.

Yes I agree. We are far from creating life from scratch. But is there some sort of conclusion you wish to draw from that? Presumably Johnny boy thinks this is of great significance, because if we haven't solved it already then (he thinks, I take it) we never will, and then that is somehow a sort of proof that God exists or whatever.

If that really is the inference he wants us to make, then sadly for him none of the logic checks out, but shh don't look too closely.

What about some researchers in a lab producing life in the next month or two.? I will stake my life on claiming that the probability is so low as to be for all intents and purposes zero, of researchers producing living systems from basic chemicals without the use of molecules already produced by life.

And what a brave bet that would be. Two months? Maybe it'll take two centuries, but then you won't be around to lose money. A truly pointless bet to make, of no actual value or consequence. I can make the bet that God won't perform a miracle in my apartment over the next 2 years. Let's bet all you own. Deal?

Which points to the fact that the production of life from relatively simple chemicals is complex enough to be beyond the capabilities of present day researchers with all their means and expertise. And not an insignificant amount of means and expertise at that.

How do you measure the significance of their means and expertise?

The probability of life on earth reaching a stage in which self-conscious, creative beings capable of abstract thinking is 1.

So if humans do eventually create life from basic chemicals it will still have been life coming from life.

That's silly. By that standard a natural process can't be experimentally confirmed, because any imaginable experiment performed by scientists will necessarily involve scientists setting up the experiment.

Scientists posit friction of air molecules and aerosols can create static discharges in the atmosphere. So they perform an experiment by setting up a chamber to mimic the atmosphere, and show that under certain conditions static discharges are observed. Then you say they haven't shown it was a natural process because the scientists set up the chamber etc.

Who do you think is being fooled by such a silly response?

If humans simulate a natural pre-biotic environment, such as a volcanic lake, in a laboratory setting, and life evolves in it from the sorts of molecules that would have existed on Earth before life existed, then that would be life from non-life. Any rational person should be able to agree with this.

And life from life is all that we have ever witnessed.

I can reasonably infer that my nephew took some cookies if there's crumbs on his shirt and so on. I don't need to observe him take the cookies.

The fact is, we can have evidence that show life must have, at some point in the past, nevertheless arisen from non-life. Heck, even if you are a theist you must still concede the point that life could not have always existed, and that if we go back far enough, life must have arisen in a way that is different from how cells divide into new cells today. Creationists would assert the first lifeforms were divinely created, which is of course a radically different "mechanism" of origin than binary fission of already existing cells. And creationists believe this without having actually witness divine creation of the first cell (or creation of humans, plants, and animals) themselves.

There's more to science than what we have directly observed. We throw people in jail on so-called circumstantial evidence, if we have enough of it. It's called an inference to the best explanation. We can have a body of data for which the best explanation we can come up with (a theory) is so compelling we would consider it irrational to deny it, and that is despite us not having directly observed the explanation take place.

[Rumraket]

Organisms remain alive even when the constituents of their bodies are being constantly replaced. So the initial conclusion to draw from this is that organisms are more than the material of their bodies.

This is no more significant an observation than the statement that a house is more than the bricks used to build it. Obviously it is at least also how they are positioned relative to each other in space. Nobody claims a pile of bricks on a pallet is a functional house any more than anyone claims that the molecules that make up an organism, neatly arranged on a long line, would make for a functional lifeform.

But that doesn't mean life isn't a physical phenomenon, or that there is a "ghost in the shell."

Yes life is made of molecules, but it is also their arrangement into higher-order structures and the physical and chemical reactions that take place between them in time, in relation to some surrounding physical environment.

Why do you have so many of these easily rebutted statements that seem superficially profound, but are really just a sort of appeal to quasi-mysticism in the end?

"Life is more than it's constituents." Whoah really? Tomato soup is more than a list of it's ingredients. It's magic now?

[CharlieM]

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.

The screwdriver has no ends to achieve. It's an inanimate object.

And now for some mental meanderings inspired by Johnny Blade's kind words of encouragement. (If my wife was to post here, she would have given you some sound advice, "Don't encourage him!)

Fond flagellar memories of tales being spun in sites like this. The helix is a wonderful winding form existing in the micro molecule, cochlear curves in floral phyllotaxis and in gargantuan galaxies in the depth of space. Seemingly screw has a more mundane meaning with possible roots in porcine procreation.

And now to the point of the simple screwdriver.
Pythagoreans played at producing screws. It was inevitable that an Archimedes would come along and adopt and adapt the form for practical purposes. And Hero promoted pressing practicalities.

The bright sparks of modern industry saw the potential and automatically turned to screws for a fixating future. Thinking minds matched slotted heads with flat-blade drivers designed for human hands. Inventing innovated heads like torx became a trend. A strive and drive for the perfect head. A grip that would not slip. Ratchets and rotary motored drivers were advanced additions to techies toolkits.
All inventions of human ingenuity and intent.

For more info on some of my sources see here: https://www.cambridge.org/core/services ... ws-div.pdf, and here: https://www.researchgate.net/publicatio ... Wine_Press, and here: https://languageofcarpentry.com/languag ... -say-screw

Moving along with macrophages and microphages; microscopic marvels on a mission. Fighting the good fight, living legends.
The adaptable plasticity of macrophages working as part of a team. They are an immensely important inclusion in any self-respecting immune system. An ally to all the other members of the group. How could any eukaryote have survived and thrived without these defenders of life at large?
There are microphages, macrophages, neutrophils, eosinophils, basophils. lymphocytes, monocytes. All of these are constantly coming into being, morphing, living and dying within our bodies for our benefit. Phagocytes and their friends rule. O.K.!

Some more relevant sources:
https://www.youtube.com/watch?v=aVd7OnG4c3c, and
https://www.superfoodscience.com/blogs/ ... microphage
and
https://www.youtube.com/watch?v=9NRvh_URY2s

Humans invented screwdrivers for a purpose. We control their uses. We did not invent phagocytes and we do not control the path of a phagocyte pursuing its prey. We watch in wonder. (At least I do).

And finally, back to the bacterial flagellum. The helical winding of the flagella/flagellum propels the bacterium on a straight path towards its destination. In order to disrupt this path the flagella/flagellum reverses direction so there is no longer a coordinated helical propellor and this causes the organism to tumble randomly. After the tumble the flagella/flagellum then resumes its original coordinated spin propelling the organism in a new direction. The organism can either move towards a source of nutrients or move away from danger by combining directed motion with random changes in direction. These are automatic moves that are made by the creature, but no less wise because of this.

[CharlieM]

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.

Can you explain how that particular demonstration could have been set up without human involvement?

[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.

Can you explain how that particular demonstration could have been set up without human involvement?

Since when am I required to disprove your assertion? You're the one making the claim, I am pointing out that is all it is. Please explain how you know it was only possible through human intervention?

What prevents me from saying, for example, that scenario like this is possible in principle(?): First an earthquake happens that splits rocks in just the right shape, that then fall onto the ground in the arrangement of a labyrinth, then the wind blows in just the right way and a body of water dissolves minerals of just the right type to result in these solutions, and it happens to fall into the labyrinth etc. etc.

There isn't anything impossible about a scenario like this. So, how do you know is only possible because the way that humans prepared the setup?

Actually more importantly, what is even the point you are trying to make by this assertion in the first place? I dispute the assertion because it's clear to me it's false and that you couldn't possibly support it, but why are you even making it? What are you trying to achieve by declaring that the experiment is only possible because of human activity?

[Rumraket]

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.

The screwdriver has no ends to achieve. It's an inanimate object.

Nothing is truly "inanimate" of course. The distinction animate and inanimate is purely synthetic and really only applies because there's a scale of movement too tiny to the naked eye and most common optical microscopes. There are chemical reactions occurring in/on screwdrivers, it physically moves ever so imperceptibly slightly as a result of the energies contained in it's chemical bonds breaking over time, the forces acting on it, Brownian motion etc.

Same goes for a ribosome (it's activity at the molecular scale just occur at a higher rate than those in a screwdriver's atomic constituents), and yet you would use teleological language to characterize the ribosome. One could say the same for a single drop of rain forming high in the atmosphere and eventually falling "to make a small dent in a patch of dirt" (just another end conceived of in my own mind for the effect an "inanimate object" has on the world). Of course lacking sentience, neither object truly have goals "of their own". Goals or ends are ideas in the heads of those who perceive them, like us.

Humans invented screwdrivers for a purpose. We control their uses.

We did not invent phagocytes and we do not control the path of a phagocyte pursuing its prey. We watch in wonder. (At least I do).

Yes, and this demonstrates what purposes really are. Ideas in our own minds that we project on to things and their behavior (including mere existence).

[CharlieM]

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?

A plant seed with its cotyledon is functional living whole as are the growing shoots and roots, and the mature plant with roots, leaves and flowers. It is a functioning whole throughout its development. An object such as a bicycle is not formed in the same way. It is built up from external parts that are added and cannot be said to be a whole functioning unit until all the essential parts are put together. The frame prior to the assembly of wheels, pedals etc. is non functional.

[CharlieM]

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.

The V-ATPase proton pump is a very sophisticated molecular complex. From here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8294626/

A primary function of the H+-ATPase (or V-ATPase) is to create an electrochemical proton gradient across eukaryotic cell membranes, which energizes fundamental cellular processes. Its activity allows for the acidification of intracellular vesicles and organelles, which is necessary for many essential cell biological events to occur. In addition, many specialized cell types in various organ systems such as the kidney, bone, male reproductive tract, inner ear, olfactory mucosa, and more, use plasma membrane V-ATPases to perform specific activities that depend on extracellular acidification. It is, however, increasingly apparent that V-ATPases are central players in many normal and pathophysiological processes that directly influence human health in many different and sometimes unexpected ways

According to Wikipedia: https://en.wikipedia.org/wiki/V-ATPase it is "a highly conserved evolutionarily ancient enzyme with remarkably diverse functions in eukaryotic organisms."

The paper you linked to gives examples of variations in a component of this complex between different groups of eukaryotes. The configuration of fungal V-ATPase is thought to have come about by gene duplication followed by mutations. This implies the differences occurred due to fortuitous circumstances. I don't believe these things come about fortuitously. I think the general form of this sophisticated enzyme is adapted to suit whichever kind of organism and specific membrane it is active in. From the publication, "Vacuolar-type ATPase: A proton pump to lysosomal trafficking", https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751294/

Consistent with its diverse physiological roles and unique localization, the seven subunits of V-ATPase have 2–4 isoforms that are organelle- or cell-specific.

Image from publication:


We should keep in mind that this image is an extremely simplified and static representation of what is in reality a very dynamic, complex arrangement of far from solid substances.

V-ATPase is just one multitasking complex among a host of active complexes within cells. Individual organisms and cells can use the flexibility of protein production to individualize the general forms within the proteome to achieve specific tasks. The proteome within each organism is equivalent in variability to the different kinds within organisms and the individual differences within populations of organisms.

The organized complexity at all levels is staggering! I think I should post something on proteomics. For those who have not looked into this but are interested, a brief introduction can be found here: https://en.wikipedia.org/wiki/Proteomics

[Fenrir]

Argument from incredulity

[Rumraket]

(...)

That's a long-ass post seemingly with no point behind it that seems relevant to what you are responding to. Why are you telling me these things?

[CharlieM]

Argument from incredulity

This response lacks any understanding of my position.

[Fenrir]

Your posts largely appear to consist of "look at this marvelous bit of biology. Its so wonderfully complicated. I can't see how it could possibly have arisen by accident".

Your last post, the one on which i commented, is precisely in that mould. How else is one to interpret "This implies the differences occurred due to fortuitous circumstances. I don't believe these things come about fortuitously."

So yes, argument from incredulity is exactly how your posts generally come across to me.

[CharlieM]

(...)

That's a long-ass post seemingly with no point behind it that seems relevant to what you are responding to. Why are you telling me these things?

I'm not trying to tell you anything. The reason for my response was not to argue against you just for the sake of it. Your link inspired me to take a closer look at V-ATPase and its role in cellular life. With the help of what's available on the 'net I'm trying to inform those who might not be aware of these things in an attempt to stir up interest. Who knows? Some readers might find this as fascinating as I do.

The only disagreement I have with paper you linked to is that it implies that increases in complexity is totally governed by blind chance. In my opinion the increase in complexity inherent in living processes is a fact which can't be denied.

[The_Metatron]

Sure it’s an observable fact. What we take issue with is your penchant for assigning “goddidit” to things you can’t figure out.

[CharlieM]

Your posts largely appear to consist of "look at this marvelous bit of biology. Its so wonderfully complicated. I can't see how it could possibly have arisen by accident".

Your last post, the one on which i commented, is precisely in that mould. How else is one to interpret "This implies the differences occurred due to fortuitous circumstances. I don't believe these things come about fortuitously."

So yes, argument from incredulity is exactly how your posts generally come across to me.

My argument would only be from incredulity if I had no alternative proposal as to blind chance. You haven't even asked if I had any alternative ideas before accusing me of incredulity.

[CharlieM]

Sure it’s an observable fact. What we take issue with is your penchant for assigning “goddidit” to things you can’t figure out.

Likewise you haven't even asked if I had any alternative ideas before accusing me of assigning “goddidit” to the evolution of life.

[The_Metatron]

Sure it’s an observable fact. What we take issue with is your penchant for assigning “goddidit” to things you can’t figure out.

Likewise you haven't even asked if I had any alternative ideas before accusing me of assigning “goddidit” to the evolution of life.

Do I need to?

[CharlieM]

Likewise you haven't even asked if I had any alternative ideas before accusing me of assigning “goddidit” to the evolution of life.

Do I need to?

Not if you don't want to. I wouldn't dream of telling you what to do.

[Cito di Pense]

You haven't even asked if I had any alternative ideas before accusing me of incredulity.

If you had any worthy ideas at all, you wouldn't keep them to yourself, would you? Instead, that is, of churning out agitation and fabulism as you have done. What you do in between a bunch of ridiculous interpretations of what you find is cite facts that anyone with access to the internet can easily locate with focused search terms and search engine recommendations. If you had any worthy ideas, we'd be discussing them now.

[CharlieM]

The human genome project was going to be a means to understand and the ability to cure much of our illnesses. What happened? It turned out that life is much more complex than was imagined. That is a phrase that gets used quite often.

Through focusing on the genome many further complexities came out of the periphery into the centre of our vision. Beyond the focus on genomics came proteomics and mRNAomics and epigenomics and microbiomics. And now there is a relatively new field arising that I will call exosomics.


What are exosomes? From here: https://bmcbiol.biomedcentral.com/artic ... 016-0268-z

That is a very good question. Since the original description of exosomes over 30 years ago, the term has been loosely used for various forms of extracellular vesicle, muddying the field and contributing to the scepticism with which the research has sometimes been met. Exosomes are best defined as extracellular vesicles that are released from cells upon fusion of an intermediate endocytic compartment, the multivesicular body (MVB), with the plasma membrane. This liberates intraluminal vesicles (ILVs) into the extracellular milieu and the vesicles thereby released are what we know as exosomes...
The presence of membranous vesicles outside cells was first recognized 50 years ago, although these were originally assumed to be waste products released via shedding of the plasma membrane...
it was not until 1987 that the term ‘exosome’ was coined for them.
Even then, however, these extracellular vesicles were largely ignored, forgotten or, again, dismissed as a means of cellular waste disposal. It is only in the past decade that interest in exosomes has exploded, with a nearly tenfold increase in publications in as many years (115 in 2006, 1010 in 2015).

Junk DNA was superseded by another candidate thought to be destined for the scrap heap, junk vesicles!

Image from the YouTube video, "Exosomes: nanoparticles offering a new future to cure disease", by Shivani Sharma, TED talk at Manhattan Beach: https://www.youtube.com/watch?v=NOJzeb32590



Even an electron microscope is too crude an instrument to capture exosomes in any detail. This zoomed in view was taken using an atomic force microscope (AFM).

Exosome activity is a method of intercellular communication. They contain mRNA, microRNA and protein and their types are unlimited. So they can take the message in a string of mRNA produced in one cell, transport it to other cells and from that mRNA produce the required proteins in those other cells. They are found in blood, milk, amniotic fluid and urine.

I would like to know how all of that complex activity is regulated.