Cell Intelligence in Physiological & Morphological Spaces

[Federica]

Ok, Cleric, Ashvin,

Thanks for your replies above. I will not say all that I would like to say, otherwise the most crucial thing I want to say will inevitably be snowed under the mass of text (Ashvin, yes, this is also what happened on the transhumanist topic, and it's the sole reason for the unaddressed Steiner quotes).


So, I want to make one single point for now. The following is a question that, to me, exemplifies 'using the concepts from the simulations as a way to probe the inner experience':

QUESTION: What kind of spiritual insights can be gained by observing attempts to ‘understand life’ that move from the bottom up, i.e. inductive, i.e. computational, through guessing a molecular or cellular geometry through analysis of databases, versus simulations that start from empirically determined geometry - i.e. measured/observed on natural or artificial molecules/cells - and then apply the laws of chemistry on top of that initial picture to predict the life dynamics of the entity? Is it in both cases the exact same mesmerization by scientific superstition that ignores the etheric nature of life, trying to understand it as configuration of material dynamics only, or not?

I have a sense that it is not so, but to make it short I am currently struggling to articulate that. So, I would think that asking questions like this one would be one possible proper way not to remain ignorant and fearful and avoidant (needless to say it's never been my attitude), while also offering that necessary resistance to Ahrimanic momentum (I picked the word from Steiner, but we can use another one).

Federica,

I agree that the question as you stated above, assuming of course we are interested in exploring the answers with an open mind, is a great way to engage the topic in a spiritually healthy way. I know that Cleric will offer a much more helpful and detailed answer to that question so I will keep my observation very general and brief.

By observing these patterns of thinking-feeling and trying to imitate the thinking gestures, so to speak, and observing the results, we are seeking to resonate with the underlying intentions that structure our epoch, both the spirits of progress and those of hindrances. At the same time, because our own individual soul-structure (higher and lower) is a microcosmic image of all the patterns of thinking-feeling-will that are embedded in the forms and activities of culture and nature, we are learning more about the depth structure of our be-ing and maturing spiritually in that way. In other words, we are not gaining insights through the materialistic conclusions of the research i.e. life is just an epiphenomenal manifestation of mindless and mechanically interacting particles, but through the way in which the research is carried out and the results that manifest from it. The scientists cannot help but stumble on valuable insights embedded in the results because, whether they know it or not (and usually not), their thinking activity is a lawful continuation of Cosmic spiritual activity and is therefore probing the very meaningful contours of reality. In that sense, when we approach the results with living thinking that doesn’t forget its own activity, we are mining insights from the results that could not possibly be mined when spiritual activity remains in the blind spot.

Ashvin,

I understand your comment as a premise to the question. The expectation is to gain insights from "descending" in thinking patterns similar to those that allow for the conception and execution of such projects (to the extent that it is possible at any given state of conventional understanding of the details) and clearly not from the research results taken at face value. This is the point of departure, but thanks for making it extra clear and properly articulated.

Correspondingly, it seems to me that a question of the sort that you asked, Ashvin, which is: “How fascinating, so does it make sense that we will then be able to 3D-print liver cells to heal the poor at low costs?” goes into a slightly different direction compared to the question above. A direction that leans towards what Steiner calls “illusions of a mathematical nature about the universe", that are especially illusory "when we transpose them into our daily environment” as per the quote in my post just above, more than towards relating the simulation to our "deepened and delaminated experience".

I never asked that question, but I can see how you may have misconstrued it in that way. In that post, I was pointing to how things could go in one or two directions, or most likely in both.

1) The etheric forces remain unconscious and therefore the capacity for regeneration and healing remains concentrated in a small segment of the population with material resources because it is mediated through the mineral-technological element and people are generally unaware of this mediation.

2) The etheric forces are brought into consciousness by inner attunement and harmonization of the full-depth spectrum, i.e. inner moral transformation and elevation of cognition, and then individuals can find creative pathways to regenerating their own diseased organism, or helping others at minimal to no cost, without mediation by the mineral-technological element that requires the concentration of material resources. Practically, we are speaking of prayer, meditation, and all sorts of creative and moral ways of interacting with our environment and fellow beings. Most of these ways of interacting are completely unsuspected for the average person who is ignorant of the spiritual influences that surround us (including me). Eventually, this interaction will also take on a more artistic and scientific character and it already has to some extent, for ex. the Anthroposophical work in the medical field, such as Are Thoresen’s work with the elemental beings or healing via Eurhythmy, or Rolfing, etc. Just like with any science, we should expect these things to become more integrated and systematic and effective over time, and for new creative developments in the healing sciences that we can scarcely imagine now.

What a fantastic overview! Indeed, this is not at all what I gathered from that post. I haven't re-read it now, but sorry if I didn't get the intended meaning out of it. One question: if that's the extent of the misunderstanding, why have you waited until the third or fourth mention of that post before clarifying?

[AshvinP]

Ok, Cleric, Ashvin,

Thanks for your replies above. I will not say all that I would like to say, otherwise the most crucial thing I want to say will inevitably be snowed under the mass of text (Ashvin, yes, this is also what happened on the transhumanist topic, and it's the sole reason for the unaddressed Steiner quotes).


So, I want to make one single point for now. The following is a question that, to me, exemplifies 'using the concepts from the simulations as a way to probe the inner experience':

QUESTION: What kind of spiritual insights can be gained by observing attempts to ‘understand life’ that move from the bottom up, i.e. inductive, i.e. computational, through guessing a molecular or cellular geometry through analysis of databases, versus simulations that start from empirically determined geometry - i.e. measured/observed on natural or artificial molecules/cells - and then apply the laws of chemistry on top of that initial picture to predict the life dynamics of the entity? Is it in both cases the exact same mesmerization by scientific superstition that ignores the etheric nature of life, trying to understand it as configuration of material dynamics only, or not?

I have a sense that it is not so, but to make it short I am currently struggling to articulate that. So, I would think that asking questions like this one would be one possible proper way not to remain ignorant and fearful and avoidant (needless to say it's never been my attitude), while also offering that necessary resistance to Ahrimanic momentum (I picked the word from Steiner, but we can use another one).

Federica,

I agree that the question as you stated above, assuming of course we are interested in exploring the answers with an open mind, is a great way to engage the topic in a spiritually healthy way. I know that Cleric will offer a much more helpful and detailed answer to that question so I will keep my observation very general and brief.

By observing these patterns of thinking-feeling and trying to imitate the thinking gestures, so to speak, and observing the results, we are seeking to resonate with the underlying intentions that structure our epoch, both the spirits of progress and those of hindrances. At the same time, because our own individual soul-structure (higher and lower) is a microcosmic image of all the patterns of thinking-feeling-will that are embedded in the forms and activities of culture and nature, we are learning more about the depth structure of our be-ing and maturing spiritually in that way. In other words, we are not gaining insights through the materialistic conclusions of the research i.e. life is just an epiphenomenal manifestation of mindless and mechanically interacting particles, but through the way in which the research is carried out and the results that manifest from it. The scientists cannot help but stumble on valuable insights embedded in the results because, whether they know it or not (and usually not), their thinking activity is a lawful continuation of Cosmic spiritual activity and is therefore probing the very meaningful contours of reality. In that sense, when we approach the results with living thinking that doesn’t forget its own activity, we are mining insights from the results that could not possibly be mined when spiritual activity remains in the blind spot.

Ashvin,

I understand your comment as a premise to the question. The expectation is to gain insights from "descending" in thinking patterns similar to those that allow for the conception and execution of such projects (to the extent that it is possible at any given state of conventional understanding of the details) and clearly not from the research results taken at face value. This is the point of departure, but thanks for making it extra clear and properly articulated.

Yes, but I want to emphasize that we should approach those thinking patterns as phenomena that point toward the intentional activity of higher beings that is on the 'same side' as our thinking, unlike the people who are conceiving and executing the projects, who feel they are confronting some external forces 'behind' the sensory spectrum on the 'other side' of their inner activity. Thereby we are also gaining intimate insight into the structuring of our own thinking activity.

The results should be taken at face value in the spiritual sense, whereas the materialistic interpretations are something added on top of the given results, due to the externalization of spiritual activity, and therefore are not “face value”. Studying the way a living cell functions with our living thinking, for example, gives us real insight into the activity of the spiritual Cosmos, even through the use of dead technology.

Correspondingly, it seems to me that a question of the sort that you asked, Ashvin, which is: “How fascinating, so does it make sense that we will then be able to 3D-print liver cells to heal the poor at low costs?” goes into a slightly different direction compared to the question above. A direction that leans towards what Steiner calls “illusions of a mathematical nature about the universe", that are especially illusory "when we transpose them into our daily environment” as per the quote in my post just above, more than towards relating the simulation to our "deepened and delaminated experience".

I never asked that question, but I can see how you may have misconstrued it in that way. In that post, I was pointing to how things could go in one or two directions, or most likely in both.

1) The etheric forces remain unconscious and therefore the capacity for regeneration and healing remains concentrated in a small segment of the population with material resources because it is mediated through the mineral-technological element and people are generally unaware of this mediation.

2) The etheric forces are brought into consciousness by inner attunement and harmonization of the full-depth spectrum, i.e. inner moral transformation and elevation of cognition, and then individuals can find creative pathways to regenerating their own diseased organism, or helping others at minimal to no cost, without mediation by the mineral-technological element that requires the concentration of material resources. Practically, we are speaking of prayer, meditation, and all sorts of creative and moral ways of interacting with our environment and fellow beings. Most of these ways of interacting are completely unsuspected for the average person who is ignorant of the spiritual influences that surround us (including me). Eventually, this interaction will also take on a more artistic and scientific character and it already has to some extent, for ex. the Anthroposophical work in the medical field, such as Are Thoresen’s work with the elemental beings or healing via Eurhythmy, or Rolfing, etc. Just like with any science, we should expect these things to become more integrated and systematic and effective over time, and for new creative developments in the healing sciences that we can scarcely imagine now.

What a fantastic overview! Indeed, this is not at all what I gathered from that post. I haven't re-read it now, but sorry if I didn't get the intended meaning out of it. One question: if that's the extent of the misunderstanding, why have you waited until the third or fourth mention of that post before clarifying?

Well, I'm not sure if that is the extent of the misunderstanding But I'm glad we at least reached some common understanding. Hopefully there is more of that to follow with Cleric's post.

[Federica]

Ashvin,

I understand your comment as a premise to the question. The expectation is to gain insights from "descending" in thinking patterns similar to those that allow for the conception and execution of such projects (to the extent that it is possible at any given state of conventional understanding of the details) and clearly not from the research results taken at face value. This is the point of departure, but thanks for making it extra clear and properly articulated.

Yes, but I want to emphasize that we should approach those thinking patterns as phenomena that point toward the intentional activity of higher beings that is on the 'same side' as our thinking, unlike the people who are conceiving and executing the projects, who feel they are confronting some external forces 'behind' the sensory spectrum on the 'other side' of their inner activity. Thereby we are also gaining intimate insight into the structuring of our own thinking activity.

The results should be taken at face value in the spiritual sense, whereas the materialistic interpretations are something added on top of the given results, due to the externalization of spiritual activity, and therefore are not “face value”. Studying the way a living cell functions with our living thinking, for example, gives us real insight into the activity of the spiritual Cosmos, even through the use of dead technology.

Yes, I understand the emphasis. If I try to follow that approach, these are the thoughts. The computational approach seems more reliant on space, compared to the deductive. The predictive behavioral pattern is extracted out of itself, so to say, whilst in the deductive approach based on natural laws, the future pattern is predicted through a theory. The computational approach bypasses theories, it fully externalizes logical reasoning, it deflates it into the flatness of space. I can't decide if it's useful or not, spiritually. In a way, it could, because it frees science from getting engulfed in the illusion of cause and effect. It's almost a sort of materialistic meditative technique which frees the intention from the multiplicity of intellectualized time layers - through extreme manyness! It's a sort of paradox. The deductive method appears more meaningful, but bears the same old problem of complete imprisonment in the sensory spectrum and conventional time. The computational approach renounces causal logic and maybe is an advancement in spiritual sense? It doesn't enter the spiritual by withdrawing from space, but it could achieve something similar by doing the opposite, by exhausting space, once it is refined further… It is a methodological disruption, but I'm not sure if the vacuum of theory points to an even deeper unconsciousness, or to an opening where more vertical patterns of experience may appear with new clarity...

[AshvinP]

Ashvin,

I understand your comment as a premise to the question. The expectation is to gain insights from "descending" in thinking patterns similar to those that allow for the conception and execution of such projects (to the extent that it is possible at any given state of conventional understanding of the details) and clearly not from the research results taken at face value. This is the point of departure, but thanks for making it extra clear and properly articulated.

Yes, but I want to emphasize that we should approach those thinking patterns as phenomena that point toward the intentional activity of higher beings that is on the 'same side' as our thinking, unlike the people who are conceiving and executing the projects, who feel they are confronting some external forces 'behind' the sensory spectrum on the 'other side' of their inner activity. Thereby we are also gaining intimate insight into the structuring of our own thinking activity.

The results should be taken at face value in the spiritual sense, whereas the materialistic interpretations are something added on top of the given results, due to the externalization of spiritual activity, and therefore are not “face value”. Studying the way a living cell functions with our living thinking, for example, gives us real insight into the activity of the spiritual Cosmos, even through the use of dead technology.

Yes, I understand the emphasis. If I try to follow that approach, these are the thoughts. The computational approach seems more reliant on space, compared to the deductive. The predictive behavioral pattern is extracted out of itself, so to say, whilst in the deductive approach based on natural laws, the future pattern is predicted through a theory. The computational approach bypasses theories, it fully externalizes logical reasoning, it deflates it into the flatness of space. I can't decide if it's useful or not, spiritually. In a way, it could, because it frees science from getting engulfed in the illusion of cause and effect. It's almost a sort of materialistic meditative technique which frees the intention from the multiplicity of intellectualized time layers - through extreme manyness! It's a sort of paradox. The deductive method appears more meaningful, but bears the same old problem of complete imprisonment in the sensory spectrum and conventional time. The computational approach renounces causal logic and maybe is an advancement in spiritual sense? It doesn't enter the spiritual by withdrawing from space, but it could achieve something similar by doing the opposite, by exhausting space, once it is refined further… It is a methodological disruption, but I'm not sure if the vacuum of theory points to an even deeper unconsciousness, or to an opening where more vertical patterns of experience may appear with new clarity...

Federica,

I think what you are saying makes sense, although it is sort of hazy for me right now. What are you saying is kind of similar to abstract philosophy in the modern age, insofar as philosophical thinking removed itself from the confines of the sensory spectrum and started investigating the laws of thinking itself, as we see in the German idealism of Kant et al. Perhaps the computational models can provide further insight into the way our thinking works in a similar way.

But in terms of insight into the deeper layers of spiritual reality which are ‘outside’ our normal thinking space, we actually need to reintegrate the sensory spectrum and its natural movements but at the deeper level of the life and soul forces involved, so cause-effect is not only horizontal but also vertical. I don’t think that can be even outwardly grasped through any sort of mathematical computation because we are speaking of qualitative movements, i.e. the living, aesthetic, and moral laws of Karma. So the dynamics of living cell biology need to be understood in their soul-spiritual aspect which can only be discerned through higher cognitive research across the threshold.

For us right now, however, it seems the most value is in either giving us insight into the way modern thinking is developing – the sort of soul-factors currently steering it - and/or kindling our intuition for the principles that go into the structuring of human psycho-physical organization and how we encounter those principles in our conceptual thinking, similar to Levin’s morphic spaces model. My higher thinking is not developed enough to really discern the relevant connections, especially since I lack basic technical familiarity with human biology to begin with. If I had confronted Levin’s model before, I doubt it would have occurred to me how it applies to the sevenfold bodies, realms, planes, etc. of esoteric science. But once Cleric presents the connections in an essay, then there is the feeling, “oh yes of course, it fits so well!”.

Cleric already shared a few insights he gleaned, such as how the simulations act as a ‘testing bench’ that controls for the variable of life spaces ‘taking over’ the cellular machinery. Whatever results from the simulation is only a result of the mechanical algorithms, unlike the direct use of cellular components. And I’m guessing not much more success will be had from such simulations more than the 20 min., but that’s just my uneducated guess. But I’m not even familiar enough to rephrase what Cleric wrote in any more helpful way or elaborate on what it means. So right now, I am in a holding pattern, waiting for Cleric to explore the full paper (which I am not even attempting to decipher) and share his insights with us Perhaps that is also a reflection of my laziness.

At the same time, though, there is no doubt in my mind that there are such insights because that’s the way spiritual reality always works - thinking that stays somewhat connected to concrete phenomenal dynamics is always unveiling a more holistic tapestry of spiritual influences that can help clarify the overarching principles involved (which are basically those of the elementary kingdoms outlined in Kurten’s book), even though it is mostly unaware of doing so.

[Federica]

For us right now, however, it seems the most value is in either giving us insight into the way modern thinking is developing – the sort of soul-factors currently steering it - and/or kindling our intuition for the principles that go into the structuring of human psycho-physical organization and how we encounter those principles in our conceptual thinking, similar to Levin’s morphic spaces model. My higher thinking is not developed enough to really discern the relevant connections, especially since I lack basic technical familiarity with human biology to begin with. If I had confronted Levin’s model before, I doubt it would have occurred to me how it applies to the sevenfold bodies, realms, planes, etc. of esoteric science. But once Cleric presents the connections in an essay, then there is the feeling, “oh yes of course, it fits so well!”.

Cleric already shared a few insights he gleaned, such as how the simulations act as a ‘testing bench’ that controls for the variable of life spaces ‘taking over’ the cellular machinery. Whatever results from the simulation is only a result of the mechanical algorithms, unlike the direct use of cellular components. And I’m guessing not much more success will be had from such simulations more than the 20 min., but that’s just my uneducated guess. But I’m not even familiar enough to rephrase what Cleric wrote in any more helpful way or elaborate on what it means. So right now, I am in a holding pattern, waiting for Cleric to explore the full paper (which I am not even attempting to decipher) and share his insights with us Perhaps that is also a reflection of my laziness.

At the same time, though, there is no doubt in my mind that there are such insights because that’s the way spiritual reality always works - thinking that stays somewhat connected to concrete phenomenal dynamics is always unveiling a more holistic tapestry of spiritual influences that can help clarify the overarching principles involved (which are basically those of the elementary kingdoms outlined in Kurten’s book), even though it is mostly unaware of doing so.

Ashvin,
Thanks for your answer. Would you please reformulate the blue? I don’t understand the difference you are making between two types of insights. Besides, I also lack familiarity with biology, but I think it’s still important to take a look at the article. Many concepts may be unfamiliar but some may be DIY:ed (not to minimize the level of technicality and intellectual refinement behind them) and some may be put in standby for later deepening and better understanding.

Regarding the green, I think the question should be looked at from the other edge. If you had had enough familiarity with biology, you would maybe have encountered the ML research, and then the connection between theories of biological spaces and architecture of reality at large would have occurred to you. By the way, if you reviewed state-of-the-art research from other knowledge fields that you are more familiar with, constitutional law as an example, you would surely find immediate insights into the nature of reality and evolution of thinking, don't you think?

What I understood from the reference Cleric made to simulation as a bench test is that he encourages us to ask: “What is a simulation?” and “What is our thought that interprets the simulation?” It seems like there are two different levels of third person perspective maybe? I guess that eventually the test will succeed for longer than 20 minutes, because (I believe) they regularly feed the model with deterministic data, sort of they put it back on track, in case the algorithm deviates too much from a combined pattern of behavior that is compatible with life / that sustains itself through reproduction and beyond. So I imagine that eventually they will find how to exactly fill the gaps in between deterministic "data injections", with finer tuned algorithms. But, as you say, with Cleric’s help, things will start to make more sense.

[AshvinP]

For us right now, however, it seems the most value is in either giving us insight into the way modern thinking is developing – the sort of soul-factors currently steering it - and/or kindling our intuition for the principles that go into the structuring of human psycho-physical organization and how we encounter those principles in our conceptual thinking, similar to Levin’s morphic spaces model. My higher thinking is not developed enough to really discern the relevant connections, especially since I lack basic technical familiarity with human biology to begin with. If I had confronted Levin’s model before, I doubt it would have occurred to me how it applies to the sevenfold bodies, realms, planes, etc. of esoteric science. But once Cleric presents the connections in an essay, then there is the feeling, “oh yes of course, it fits so well!”.

Cleric already shared a few insights he gleaned, such as how the simulations act as a ‘testing bench’ that controls for the variable of life spaces ‘taking over’ the cellular machinery. Whatever results from the simulation is only a result of the mechanical algorithms, unlike the direct use of cellular components. And I’m guessing not much more success will be had from such simulations more than the 20 min., but that’s just my uneducated guess. But I’m not even familiar enough to rephrase what Cleric wrote in any more helpful way or elaborate on what it means. So right now, I am in a holding pattern, waiting for Cleric to explore the full paper (which I am not even attempting to decipher) and share his insights with us Perhaps that is also a reflection of my laziness.

At the same time, though, there is no doubt in my mind that there are such insights because that’s the way spiritual reality always works - thinking that stays somewhat connected to concrete phenomenal dynamics is always unveiling a more holistic tapestry of spiritual influences that can help clarify the overarching principles involved (which are basically those of the elementary kingdoms outlined in Kurten’s book), even though it is mostly unaware of doing so.

Ashvin,
Thanks for your answer. Would you please reformulate the blue? I don’t understand the difference you are making between two types of insights. Besides, I also lack familiarity with biology, but I think it’s still important to take a look at the article. Many concepts may be unfamiliar but some may be DIY:ed (not to minimize the level of technicality and intellectual refinement behind them) and some may be put in standby for later deepening and better understanding.

Federica,

There are certainly no clear lines that separate types of insights and they all overlap to some extent. In the first case, I would say we are seeking insight into the way that Earthly evolution into the etheric realm is feeding back into the average intellectual consciousness that is still steeped in materialistic habits of thinking (and most of us still are to some extent, even if on the esoteric path). We are seeking deeper resonance with the modern soul life that confronts the unfamiliar and unknown. It is similar to when we watch a movie or observe some other artistic development and try to discern how the physicalized narrative expressions point towards imaginative themes that are anticipating future developments (or likewise recalling long past developments). I am reminded of all the various movies surrounding ‘time travel’ and/or encounters with ‘aliens’ (for ex. the movie Arrival is a great imaginative and surprisingly lucid integration of both). So this deeper resonance could help us become more intimate with our individual and collective patterns of thinking and also help us interface with others when introducing them to the spiritual path, since we have better insight into how people are thinking through the increasingly transparent spiritual reality.

In the second case, it is more about illuminating the ways in which the life space, or the 2nd elementary Kingdom, works into and structures the physical space, or the 1st elementary Kingdom. Perhaps we also gain some insight into the 3rd and 4th kingdoms, since after all it is human beings carrying out these simulations and experiments with their desires, feelings, and thinking activity. For ex. by comparing a temporally extended plant form with a crystal form, we can already mine some insights in that respect. It could be similar to how Levin's research may give insight into the interaction of the various morphic spaces. We should remember that none of these technologies were around in Steiner's time (or the few Anthroposophists who also did original spiritual research), so they provide a level of resolution that could stimulate further conceptual exploration and spiritual research across the threshold. It is here where a lack of familiarity with cell biology or computational technology-methods makes it difficult to mine the results or the method that produced the results for deeper insights.

I did read the short article, but I was referring to the full paper which I started reading and then quickly gave up But I do agree it would probably be easier than I imagine to get accustomed to if I devoted more time and effort to it.

Regarding the green, I think the question should be looked at from the other edge. If you had had enough familiarity with biology, you would maybe have encountered the ML research, and then the connection between theories of biological spaces and architecture of reality at large would have occurred to you. By the way, if you reviewed state-of-the-art research from other knowledge fields that you are more familiar with, constitutional law as an example, you would surely find immediate insights into the nature of reality and evolution of thinking, don't you think?

Yes, that’s definitely true and I think it goes to show how higher cognition can only serve its intended function when it also descends into the normal sensory-conceptual spectrum and becomes intimately familiar with phenomenal dynamics. Without prior familiarity of cell biology, there are simply no conceptual slots for my higher intuitions about the architecture of reality to resonate with when exploring that topic. Although perhaps the amount of familiarity I would need to obtain such a resonance would be less than the average person who has not worked on deepening their thinking activity. Put another way, I could condense the time it would take to become familiar with the basic phenomenal foundation that is necessary for my spiritual activity to work through. Nevertheless, I need to be able to take a keen and effortful interest in the way the Spirit expresses itself in diverse domains of phenomenal experience for those domains to yield greater insights.

What I understood from the reference Cleric made to simulation as a bench test is that he encourages us to ask: “What is a simulation?” and “What is our thought that interprets the simulation?” It seems like there are two different levels of third person perspective maybe? I guess that eventually the test will succeed for longer than 20 minutes, because (I believe) they regularly feed the model with deterministic data, sort of they put it back on track, in case the algorithm deviates too much from a combined pattern of behavior that is compatible with life / that it sustains itself through reproduction and beyond. So I imagine that eventually they will find how to exactly fill the gaps in between deterministic "data injections", with finer tuned algorithms. But, as you say, with Cleric’s help, things will start to make more sense.

Right, those are important questions to understand why the simulation is fundamentally different than using existing cells or cell components to generate new cells. The latter already started off with the life space in a certain harmonic resonance with the physical space, while the former clearly starts from only the dead physical space.

Yes, that seems plausible to me as well, in which case they are practically obviating the bottom-up approach to life as ‘emergent phenomena’ from Earthly physical forces and substituting themselves and their top-down ‘data injections’ for the cognitive life energy of the Sun that works in from the periphery.

[Federica]

Ashvin, I was referring to the paper too (ther is not much to 'concept-DIY' in the short article).

[AshvinP]

Ashvin, I was referring to the paper too (ther is not much to 'concept-DIY' in the short article).

Oh ok, well I might try to 'concept-DIY' through it again soon. In general, I think you're right that it's good to extend our spiritual activity into these domains in a flexible and fluid way, seeking to gain some holistic sense of what is being attempted and how, especially when we initially feel hesitant and uncomfortable.

[Cleric K]

Cleric,

Does the following article and associated journal paper suggest you need to reassess your assertion I have bolded? Personally I'm unsure as I don't have the biological training to fully understand what the researchers actually achieved. But on the face of it, it seems like they were able to reproduce many of the features of a living cell.
https://blogs.nvidia.com/blog/2022/01/2 ... imulation/

I went through the paper. As expected, the simulation doesn’t work on the particle level. And this is not surprising. Presently it is still not possible to calculate the folding of a single protein molecule, what’s left for a whole cell where there can be millions.

I’ll try to give a simple overview of what the simulation actually does. It is actually implemented in two levels. The first is based on the so-called kinetic model. Here the important thing is that these models don’t calculate interactions between individual particles. Instead, they work with statistical concentrations of certain reactants. The equations define the properties of reactions such as A + B -> C. Here A, B, C could be any chemicals – a simple atom, simple molecule or even complex macromolecules. These models basically pose the question: if I have a volume of chemical A with a certain concentration and I mix it with volume of chemical B, how would the reaction proceed through time? Graphically it looks something like this:



When the equations are solved we can see that as the two chemicals react, they are converted into C. Thus the concentrations of A and B decrease, they convert into C whose concentration increases. While the concentration of A and B is still high, the chance of reaction is also high (it’s more likely that particles can bump into each other, so to speak). As the reactants are used up and diluted, the speed of reaction also slows down.

The most important thing to understand is that at this level of abstraction we don’t deal with the physics of the atoms, we don’t have to know anything about electron orbitals, chemical bonds and so on. It’s all statistical modeling. We can reach the kinetic equations through experimentation.

Now the first level of simulation of the cell uses such an approach. The difference is that there are many possible chemicals in the cell and ways in which they can react. These can be presented graphically as reaction pathway diagrams.






Here every dot in the diagram represents a chemical. It can be something simple but also something very complicated such as a protein, enzyme, segment of DNA (a gene) and so on. The arrows represent the possible ways in which chemicals can react. This is the heavy work in such a model because all these possible reactions have to be described with their kinetic equations. This model doesn’t understand what the different dots (chemicals) are made of at the physical level. It doesn’t care if they are made of a few atoms or thousands. The model operates on a higher level of abstraction. We only care that when X and Y are present in certain concentrations, Z can be produced with such and such dynamic properties.

Our first example with A + B -> C was very simple because it is a one way reaction. But with more chemicals it is possible to achieve more complex behavior. Chemical oscillators are a good visual example.



Here concentrations change in such a way that the whole system goes through rhythmic alterations of concentrations.


(different colored curves are the concentrations of different chemicals)

Now imagine something like this but with thousands of chemicals and thousands of ways in which they can react. This is what a kinetic whole-cell model does.

Once again, the crucial thing to realize is that such a model treats the system statistically (so-called ‘well-stirred’ model). This means that the model doesn’t know nor cares about individual particles and their positions in space. The information it works with are concentrations of the different chemicals. They are spread out, superimposed as it were. This model can be accurate only if we assume that all chemicals in the cell are perfectly mixed, diffused. We can most easily imagine how such a simulation would work (and this is the most common way it is actually calculated) if we move in small timesteps and calculate possible reactions for every combination of chemicals (for which we have a reaction pathway). At every timestep we reduce the concentration of the reactants and increase the concentration of the products according to the corresponding (experimentally discovered) dynamics. Then we repeat the process with the updated concentrations and so on. The result is very complicated increases and decreases in the concentrations of the thousands of chemicals.

Obviously, such an approach can not be universally applicable for simulating cells. To some extent it makes sense for prokaryotic cells, such as the one simulated. I remind that the paper works with the version of Mycoplasma Genitalium, which was created by Venter by progressively reducing the genome until reaching a minimal version with which the cell could still live and reproduce: “JCVI-syn3A is a genetically minimal bacterial cell, consisting of only of 493 genes on a single 543-kbp circular chromosome with 452 genes coding for proteins”.

The interior of such a cell can be considered ‘well-stirred’ to some extent because most of the chemicals are indeed more or less uniformly diffused. Of course, this assumption can’t be made for everything. For example, the larger molecules, such as the ribosomes (the complexes that synthesize proteins) are so big that there are actually 503 of them in the scanned cell that they work with. Such a number is low enough that we can’t easily ignore the positions of the individual ribosomes. We can’t simply assume that they are spread out everywhere. Nevertheless, the first level of the simulation does work with that assumption. Everything is taken to be fully diffused – even the circular chromosome of the cell (the DNA).

To alleviate such shortcomings, there’s a second level of the model which partitions the volume of the cell in 64x64x64 lattice.


(see images B, C, D, E)

The idea is simple. Each of these small cubes is simulated by the very same kinetic model above. The difference is that these cubes can have their own concentrations of chemicals. After simulating each cube individually, they are allowed to diffuse with each other – every cube with its six neighbors. In this way a spatial model is achieved, where there’s some notion of position of the chemicals.

It’s important to note that the authors have made some simplifications in the spatial model. The membrane, the DNA and the ribosomes are fixed. That is, the concentration of these chemicals is not allowed to diffuse to other cubes. Why is that? Well, here we begin to see that at a certain stage we can’t ignore the spatial structure of the molecules. Many prokaryotic organisms (like the one simulated) have a single circular chromosome. Yet in reality it doesn’t look like a simple ring but more like a very large loop of rope that has been tangled in a ball:



The tangled chromosome can also be seen in the lattice in the color cubes on C image. The yellow balls are the ribosomes. It’s obvious that if these were allowed to diffuse into adjacent cubes, a nonsensical result will be obtained. It would be as if the DNA molecule is chopped into pieces and diffused around. It’s clear that this model cannot easily account for the structural properties of the long DNA molecule. For this and other reasons, the spatial model has to be simplified by assuming the DNA is immobile.

The latter in itself shows that the spatial model can’t simulate cell division in detail. In real life, the DNA molecule is replicated in place.



Then the two new chromosomes have to be pulled in the opposite parts of the dividing cell. There are many problems with this. For example, the replication itself tenses the braiding as explained with the rope analogy here:



Such topological features are completely beyond the reach of the model in question. They simply don't exist at the level of abstraction that only deals with concentrations of chemicals - even if compartmentalized into a lattice.

So as we can see, saying that a full cell has been simulated is an overstatement. Technically, a full cell has indeed been simulated but it has to be explained what exactly has been simulated. The authors of course speak very clearly about this. As usual, the deviations occur when scientific works are reported by the media. When things are simplified such that they can be digestible by the general public, the message is very often twisted (often intentionally, to make for more bombastic headlines). In our case, if we read only the media article, we get the impression that a full simulation at the particle level has been achieved.

All said doesn’t aim to criticize the work of the scientists. They are well aware of the limitations of the model and they have listed them in the paper.

Returning on the main question – is physics enough for life – I don’t think we can answer based on these simulations. They operate on a quite high level of abstraction. Basically they show that the concentration of metabolites increases, DNA is replicated (not structurally but simply by increase of concentration), proteins are synthesized, etc. What they call cell-division in this model is simply the doubling of the concentration of the ingredients. It is one thing to simulate statistically that the amount of DNA doubles but quite another to simulate the topological structure (and we see how incredibly complicated this is). In other words, just because the kinetic simulation shows that statistically the amount of ingredients doubles, it doesn’t mean that the chromosome will be properly replicated, unentangled and both daughter chromosomes pulled in the opposite sides of the dividing cell.

I still think that if a full particle simulation was possible (without higher order orchestration), it would gradually lead to chaos. The present simulations suggest to me that maybe this degradation won’t be as rapid as I imagine but who knows. In any case, it is still amazing to see the mind boggling details of these cellular processes.

[AshvinP]

Cleric,

Does the following article and associated journal paper suggest you need to reassess your assertion I have bolded? Personally I'm unsure as I don't have the biological training to fully understand what the researchers actually achieved. But on the face of it, it seems like they were able to reproduce many of the features of a living cell.
https://blogs.nvidia.com/blog/2022/01/2 ... imulation/

I went through the paper. As expected, the simulation doesn’t work on the particle level. And this is not surprising. Presently it is still not possible to calculate the folding of a single protein molecule, what’s left for a whole cell where there can be millions.

Cleric,

Thank you for this clear and lucid analysis of the paper. It made it relatively clear to me at least the methodology that the researchers are pursuing in these sorts of simulations, at a level of abstraction that is not practically useful for actually shedding light into how physical mechanisms can support the living functions of even the simplest cell. The most important function of life being that of cell reproduction, which is completely beyond the scope of the model.

Here every dot in the diagram represents a chemical. It can be something simple but also something very complicated such as a protein, enzyme, segment of DNA (a gene) and so on. The arrows represent the possible ways in which chemicals can react. This is the heavy work in such a model because all these possible reactions have to be described with their kinetic equations. This model doesn’t understand what the different dots (chemicals) are made of at the physical level. It doesn’t care if they are made of a few atoms or thousands. The model operates on a higher level of abstraction. We only care that when X and Y are present in certain concentrations, Z can be produced with such and such dynamic properties.

Our first example with A + B -> C was very simple because it is a one way reaction. But with more chemicals it is possible to achieve more complex behavior. Chemical oscillators are a good visual example.



Here concentrations change in such a way that the whole system goes through rhythmic alterations of concentrations.

As an aside, this section and the video reminded me of a passage that I was reading recently in a book about the poet, Percy Shelly. It's very interesting to consider how much of natural science can act as a vast symbol for how psychic energies convey themselves into physical manifestation through the etheric medium (such as the ‘chemical-ether’).

Later, whilst an undergraduate at Oxford, Shelley continued his studies of a scientific, especially chemical-alchemical nature. His friend Hogg has left a description of Shelley's rooms in University College worthy of a stage-design for the first scene of Faust, the poet brooding timelessly amidst a confusion of retorts and other instruments:

"as if the young chemist, in order to analyse the mystery of creation, had endeavoured first to reconstruct the primeval chaos. The tables, and especially the carpet, were already stained with large spots of various hues, which frequently proclaimed the agency of fire. An electrical machine, an air-pump, the galvanic trough, a solar microscope, and large glass jars and receivers, were conspicuous amidst the mass of matter.... There were bottles of soda water, sugar, pieces of lemon, and the traces of an effervescent beverage. Two piles of books supported the tongs, and these upheld a small glass retort above an argand lamp. I had not been seated many minutes before the liquor in the vessel boiled over, adding fresh stains to the table, and rising in fumes with a most disagreeable odour. Shelley snatched the glass quickly, and dashing it in pieces among the ashes under the grate. increased the unpleasant and penetrating effluvium."

Upon examination it turns out that poetry and alchemy have frequently lived as close neighbours. Like earlier experimenters, Shelley must certainly have noticed how the chemical processes in his retort- subtle, startling, violent or imperceptibly slow by turns were suggestive of ideas and analogies for the workings of the human heart. Indeed, Charles Nicholl points out, there had always been a side to alchemy according to which the alchemist's probing, purifying, transforming operations became a kind of mirror for psychic discoveries and changes. His meditations on the astonishingly complex physical occurrences inside the Hermetic egg, or glass vessel, were a way of contacting those 'obscure parts' of the mind, as was Shelley's interest in the power of alchemical and other symbols. The alchemical transmutation of the psyche depended, not on understanding the chemistry of the Work, but on the play of images and inner forces released within the adept during his long vigil at the athanor where the incubation took place. Shakespeare and Ben Jonson had drawn upon its imaginative resources long before Shelley, though they had not both treated it with equal solemnity; Donne and Vaughan had reveled in its potentialities for far-flung metaphor and hidden interconnections. A contemporary European parallel to Shelley again suggests itself in Goethe, whose strange Novelle Elective Affinities brought the chemistry of interacting characters strictly up to date in terms of the latest scientific theories; but the background in his case was alchemical too.