Control in a living cell

[lateralsuz]

I was first drawn to this site by some topics, which I can no longer find, that seemed to ask about the nature of control in a living cell. It was a issue that niggled at my mind during my studies, and which has never been explained.

Cells do not have brains within them. Nor do they seem to have extensive neural networks that could act as a pseudo-brain.

Cells can also exist in isolation, so they do not need to be controlled by outside influences. Yet they are regularly seen to adapt to changing circumstances in appropriate ways.

As was pointed out in the other posts, there are many cellular functions such as adapting internal structures during the reproductive cycle, (while expanding or contracting); or DNA repair; which seem to go far beyond the inevitability of a chemical reaction.

Is anyone aware of factors that could explain what is observed?
(Sorry if this is covered by the other topics - but I can't find them)

[SciameriKen]

Hi Lateralsuz - I was not sure what you mean by your question? Could you clarify?

[lateralsuz]

Hi SciameriKen

I have been ill which is why I haven't been on the forum for a while.

DNA is a mechanism which seems to initiate the production of various polymers, (principally proteins, RNA etc).

This is believed to happen because the chemical components of DNA act as a code, as well as a template. In combination with various enzymes and other chemicals, different sections of the DNA code can be switched on or off at different times, in what is believed to be a relatively fixed sequence, in order to produce a living being. The development of that sequence is believed to be the result of trial and error by natural mechanisms over millions of years until a working version emerged.

As some books have pointed out, there is a difference between these 'structural' mechanisms / processes and those which 'react to the moment' - which cannot be pre-coded in the same way because they represent dynamic circumstances that require actions to resolve issues, not just construct things to a fixed template. There's a long list of these activities within individual cells.

By focussing on individual cells rather than an entire body we see the real difficulties with these matters when we try to explain such levels of control without a brain - just relying on chemical processes.

As was pointed out in the other posts, some of these processes are very involved because they do seem to 'investigate' problems before determining an appropriate solution out of many possible responses. Yet conceptually the most sophisticated chemical control mechanism we have thought of is the 'feedback loop' where concentrations of a chemical that get out of balance, can trigger a chemical-based response which regulates those concentration. That hardly seems to deal with these circumstances.

In terms of some cell processes, it has been suggested that codes are used to direct activity, and such chemical codes do seem to be observed, (say on vesicles), but a code that is used in this way suggests a level of purpose that goes beyond whether a chemical reaction occurs or not. Something has to deploy them and then respond them in different ways.

As the other posts tried to point out, we can imagine how a computer chip might regulate complex activity like this, but there is no known computer equivalent in a cell - so what is the latest thinking on how these effects are achieved?

Has there been any more progress in this research?

[edy420]

Maybe not a computer chips equivelent, but most definitely machines.

[lateralsuz]

I think you're right about the notion of machines in cells edy420.

Whether we consider motor proteins or ribosomes, there is a level of sophistication that goes beyond what we might expect from a chemical reaction - even with trial and error.

You went for the motor proteins (above) and how they transport cargo (vesicles) to very different but specific destinations around a cell - apparently reading and using a code. However in putting the destination code on a vesicle something must determine an end location and the code relevant to that destination. The motor proteins must also read the code and work out how to navigate the many criss-crossing pathways around the cell. How?

This goes way beyond the simple bumping of two chemicals that then react in an inevitable way.

What gives the control if there is only chemistry?

There are many other examples - and as cells can operate in isolation in a test tube, it can't be direction from a larger brain.

[TheVat]

https://www.ncbi.nlm.nih.gov/pmc/articl ... rt=classic

Hope this help.

[lateralsuz]

Thank you for the link, but this article merely acknowledges the problem - it doesn't offer any solutions, or even pointers to solutions.

As was pointed out on the previous posts on this forum, (which I still can't find), various cell mechanisms (again - working within an isolated single cell within a 'test tube'), such as homologous re-combination, do genuinely seem to analyse a problem, search out relevant factors, and then determine and implement a complex solution out of a myriad of possible options.

This is obviously how we interpret what is happening in these chemical processes but there is every indication that problems are being worked out in a dynamic situation - which seems to be impossible on a fixed pre-coded basis, without a computer/pseudo-brain program, using just chemical reactions.

However, if we do begin to see possible solutions, could this start to give us the beginnings of an idea about the underlying nature of thought? Conversely, if thought is indeed based on quantum mechanical principles rather than 'pure chemistry' could we start to argue that it might be applicable at any level of life?

The one thing that the article didn't seem to mention were ideas based on quantum theory.

[Dave_C]

However, if we do begin to see possible solutions, could this start to give us the beginnings of an idea about the underlying nature of thought? Conversely, if thought is indeed based on quantum mechanical principles rather than 'pure chemistry' could we start to argue that it might be applicable at any level of life?

Here’s an interesting article regarding single cellular “slime mold”. They seem to not only be capable of problem solving:

Traditionally, simple organisms without brains or neurons were thought to be capable of simple stimulus-response behavior at most. Research into the behavior of protozoa such as the slime mold Physarum polycephalum (especially the work of Toshiyuki Nakagaki at Hokkaido University in Japan) suggests that these seemingly simple organisms are capable of complex decision-making and problem-solving within their environments. Nakagaki and his colleagues have shown, for example, that slime molds are capable of solving maze problems and laying out distribution networks as efficient as ones designed by humans (in one famous result, slime molds recreated the Tokyo rail system).

They also appear to be capable of memory:

But Dussutour wanted to push further and see whether that habituating memory could be recalled in the long term. So she and her team put the blobs to sleep for a year by drying them up in a controlled manner. In March, they woke up the blobs — which found themselves surrounded by salt. The non-habituated slime molds died, perhaps from osmotic shock because they could not cope with how rapidly moisture leaked out of their cells. “We lost a lot of slime molds like that,” Dussutour said. “But habituated ones survived.” They also quickly started extending out across their salty surroundings to hunt for food.

Right away, I wonder what molecular mechanism is responsible for this 'memory'.

Some thoughts are provided on how slime mold might accomplish this but you’ll need to dig into the research papers for more:

Scientists have no idea what mechanism underpins this kind of cognition. Baluška thinks that a number of processes and molecules might be involved, and that they may vary among simple organisms. In the case of slime molds, their cytoskeleton may form smart, complex networks able to process sensory information. “They feed this information up to the nuclei,” he said.
…
Chris Reid and his colleague Simon Garnier, who heads the Swarm Lab at the New Jersey Institute of Technology, are working on the mechanism behind how a slime mold transfers information between all of its parts to act as a kind of collective that mimics the capabilities of a brain full of neurons. Each tiny part of the slime mold contracts and expands over the course of about one minute, but the contraction rate is linked to the quality of the local environment. Attractive stimuli cause faster pulsations, while negative stimuli cause the pulsations to slow. Each pulsing part also influences the pulsing frequency of its neighbors, not unlike the way the firing rates of linked neurons influence one another. Using computer vision techniques and experiments that might be likened to a slime mold version of an MRI brain scan, the researchers are examining how the slime mold uses this mechanism to transfer information around its giant unicellular body and make complex decisions between conflicting stimuli.

https://www.quantamagazine.org/slime-mo ... -20180709/

Regarding thought, if neuroscience had all the answers to how phenomenal consciousness (and thought) arise in a brain, there would be an uncontroversial theory. But there is no such thing. Chalmers pointed out the hard problem, but I’d suggest the even harder problem is for everyone to understand all the issues surrounding the ‘hard problem’… As Chalmers puts it, why don’t all the neuron interactions and chemical reactions simply occur WITHOUT any experience or feeling or whatever? Clearly, there’s no need to have experiences or feelings for chemical and neuron interactions to occur. In fact, the problem arises BECAUSE there’s an experience of something. This leads us to the problem of epiphenomenalism. But there are many more problems. The symbol grounding problem is a very serious issue we’ve not resolved. And counterfactual sensitivity seems to violate everything we know about physics. So the problem is not just the ‘hard problem’ of how experience arises in a brain, the really really hard problem IMHO is getting people to understand why it’s so hard. People simply don’t understand why it should be hard and what the logical problems are with the existing theory of computationalism.

If you’re interested, feel free to read and comment on a paper I’ve written (and intend to finish some day before I croak) which provides answers to these even harder problems and does seem to dovetail nicely into those mechanisms single cellular organisms might use (on a quantum scale) to do such things as learn and create memory. Long story short, I believe our experience must supervene on our DNA or something very much like it. In the nucleus of each neuron and each slime mold, the DNA reads and interprets the surroundings. Single cellular theories of mind are rare but have garnered attention from biologists and neuroscientists. There are a few out there. And I think they make sense. Neurons had to evolve somehow. If things such as thoughts and qualia were in fact phenomena that could be ‘discovered’ by cells/DNA rather than some sort of phenomenon that was ‘created’ (think of math being discovered or created) then we should expect cells to discover these phenomena long before brains develop.
viewtopic.php?f=39&t=34944

Per the above link:

But some mainstream biologists and neuroscientists are critical of the results. “Neuroscientists are objecting to the ‘devaluing’ of the specialness of the brain,” said Michael Levin, a biologist at Tufts University. “Brains are great, but we have to remember where they came from. Neurons evolved from nonneural cells, they did not magically appear.”

[TheVat]

...in one famous result, slime molds recreated the Tokyo rail system).

Without unions, they will continue to be exploited. If the slime molds need an organizer, we have many slime balls in my country.

The cytoskeleton idea, for complex processor networks, with DNA as a central processor, is fascinating. And a bit Penrosian. Be funny if Penrose and Hamerof were onto something after all, after being poo-poohed for the last couple decades.

[lateralsuz]

Be funny if Penrose and Hamerof were onto something after all, after being poo-poohed for the last couple decades.

There have been quite a few experiments on cognitive processes which have been shown to relate to quantum mechanical influences, (such as navigation in some birds), and there are other theories (like Pribram & Bohm's Holononmic Brain Theory) which might dove-tail into Penrose Hamerof as well. Following the links on the earlier posts I read Finipolscie's 2nd Book and found it to be an interesting summary of the options.

However, I still think the key lies in individual cells. Brains are multi-celled organs, whereas the apparent logic being applied within a single cell has to be self-contained and not part of a collaborative process.

[lateralsuz]

Clearly, there’s no need to have experiences or feelings for chemical and neuron interactions to occur. In fact, the problem arises BECAUSE there’s an experience of something.

I totally agree.
It may be argued that an 'occurrence' generates a feedback loop, (ie. in some way adapting a chemical circumstance to an experience/occurrence), but when chemical processes seem to initiate an investigation of something, (as in the case of DNA repair), then that implies much more than a chemical response, because it is initiating something for the purpose of a recognised objective (eg. apparently working out how to fix a particular type of break while preserving and not distorting the complex code that DNA represents).

In the nucleus of each neuron and each slime mold, the DNA reads and interprets the surroundings.

I haven't read any theory about DNA which suggests that it actually thinks. It is a fixed code that essentially prescribes a relatively fixed sequence (especially when engaged in cellular reproduction). Individual genes can be triggered to generate new proteins and RNA - but that doesn't require logic. I haven't heard of any DNA-related process which indicates logic or experience.

I think Finipolscie made a valid point by distinguishing pre-determined processes (generally based around DNA), from those mechanisms which generate responses to dynamic circumstances, (which are therefore not structured and therefore less likely to be pre-coded).

Not sure about whether the slime mould experiments deal with individual cells or groups of cells.

[Dave_C]

Paul Stamets likes his mushrooms and other fungi. He talks about the Tokyo train thing and has some film of the fungus that designed the underground (better than people could). The info about mushrooms and our evolution from them is cool too. All sorts of crazy gems in this piece. Take 11 minutes, it's worth it.
https://www.youtube.com/watch?v=Nxn2LlBJDl0

[Event Horizon]

By far my favourite organelle is called the Golgi Body.
Its basically like a parcel delivery hub, packing proteins in lipids and sending them on to their destinations.
I do love cell biology. If intelligent design has but one prop, the workings of a cell would be a good shout!

[lateralsuz]

Hi Event Horizon

The Golgi Body, as I understand it, is the main centre which initiates targeted delivery.

Would you agree that this requires a measure of analysis and control by the Golgi - and perhaps a route map too?

[hyksos]

This goes way beyond the simple bumping of two chemicals that then react in an inevitable way.

Yes, the manner of operation in a cell goes way beyond the simple bumping of two chemicals. It goes way, way beyond that.

There is something called the electron transport chain, where a ligand carries around an electron that is bumped up in energy levels through stages. When it arrives to its destination in the outer layers of a mitochondrion, the high-energy electron is used to run a circular pump channel that synthesizes ATP using phosphorylation. Micheal Behe is impressed by flagella. In my opinion, the electron transport chain is far more impressive.

The mere bumping of chemicals can't do things like this. Only some kind of control could engage these kinds of orchestrated actions effectively.

Therefore do we have proof that an elan vital participates in the inner dynamics of cells?

Is this proof-positive of a vital essence that undergirds all of physical reality?

No and no.

The reason why living cells engage in dynamics that far exceed "mere inert matter" is because they are not in thermal equilibrium with their environment. They are open thermodynamic systems. They can exhibit dynamics that looks like they are becoming more ordered over time. And physically speaking, they are actually doing that.

To our best understanding of nature, order is allowed to increase in living cells, provided the order in the larger environment decreases to offset it.

[lateralsuz]

Hi Hyksos - only just seen your note. Apologies.

I am not sure there is a life force either, (if that' s what you mean by 'vital essence'). There is certainly no evidence for it, as such.

I hadn't heard of the electron transport chain before - but I will try to find out more about it.

However I am most intrigued, (as stated in earlier posts), by processes which are seemingly not driven the pre-programmed activities of DNA or other inherent structural features of developed cell components. I would prefer to focus on processes which react to unforeseeable events of the moment, in a manner that to all intents and purposes analyses and then resolves complex issues. These are the ones which illustrate true control.

Consciousness has not been explained by mechanical/chemical means, nor feelings, nor even basic awareness, yet we know they exist as every moment of our entire existence exhibits that capability. The surprise is that such things also appear to apply at the level of single cells, and indeed, processes within single cells - with a reasonable level of sophistication.

Even accepting your outline description of electron transport chains, there is nothing that seems to come close to explaining that capability through mechanical/chemical means - (eg. the process of homologous recombination).

Where do you think the search might take us ?

When people say that it is a natural thing for chemicals to organise themselves and become ever more sophisticated, that may be valid for crystalline structures and even the shapes achieved by protein strands but there is not logic to say how such an explanation goes beyond that.

[hyksos]

Consciousness has not been explained by mechanical/chemical means, nor feelings, nor even basic awareness, yet we know they exist as every moment of our entire existence exhibits that capability.

While this is all true, your thread here has digressed into a different topic from living cells. Consciousness is so complicated a topic that books on it can fill a shelf. Tweed jackets hold entire symposiums just on this topic alone.

Technically you could make a forum like this one that is just dedicated to consciousness.

The surprise is that such things also appear to apply at the level of single cells, and indeed, processes within single cells - with a reasonable level of sophistication.

I need clarification of these pronouns. What is the "such things" which also apply to single cells and within cells?

[Forest_Dump]

I'd probably suggest starting with S. Pinker's book on how the mind works and work from there.

[lateralsuz]

Hi Hyksos

I'm not sure what it is that you want me to describe.

My point was that we cannot deny that consciousness, awareness, and the application of logic through thought are real. They are not an illusion, even if we can't explain how they are achieved through physical means.

If you can explain how Homologous Re-combination can work (even in concept) without applying some basic level of awareness, assessment, and co-ordination, (given the steps that have been observed by scientists), then I and many biochemists would love to hear it.

If you are not familiar with this cellular DNA repair process, then it means the repair of a double break in DNA - ie. a break in both strands of the DNA ladder at the same point. It might be an uneven break with pieces missing - where the ends cannot simply be stuck together, but the missing pieces need re-creating exactly.

A single strand break can use the opposite side of the DNA ladder as a template, but that cannot happen with a double strand break.

We observe that the 4 damaged ends of the DNA are cleaned up and then the nature and size of the damage/break seems to be assessed. Enzymes hunt for a template (an entirely different but complete DNA strand). They then search for a section along it that would appear to match the break (finding a match to the bits that remain on either side of 4 break points). Given the length of the DNA chain, how do they know which bits to use?

The sizes of breaks vary radically from single rungs on the DNA ladder to potentially thousands.

If a suitable template is found from a separate strand of DNA, it is manoeuvred alongside the break in the original DNA chain and the strands from the damaged DNA are re-built by copying the template, until they reach a point when the original breaks could be connected perfectly - without any additions or omissions in the amino acid sequence.... not one.

The alignment in itself would cause any human to apply considerable logic, while the knowledge of when to stop and which strands of the DNA should be re-connected are potentially even more testing to our brains, let alone an unthinking chemical which can only attach to one of the 4 strands.

And yet cells do it all the time.


If these logical steps were part of a mechanism with a brain, our rationalised explanations would probably be accepted at face value, but when we see such things within a cell with no apparent brain/computer as a means of control, chemistry alone does not seem up to the task.

We are obviously still looking for an unthinking chemical way to achieve this, but given what we observe, is it unreasonable to ask whether the unknown mechanisms which must exist to create awareness, might also be working here, (even if such a suggestion doesn't conform to some people's perceptions of how things should be)?

Control within a cell, at this level of sophistication, is probably a way to unravel the secrets of life itself, as opposed to just chemistry.

[TheVat]

"just chemistry"

heh

[hyksos]

If you can explain how Homologous Re-combination can work (even in concept) without applying some basic level of awareness, assessment, and co-ordination, (given the steps that have been observed by scientists), then I and many biochemists would love to hear it.

I have no idea what the basis of this claim is. There are six RAD51 proteins that operate during HR , and the 7th one operates only during meiosis. This is perfectly understood by science. Biochemists don't need my help, as they already know the mechanisms.

Control within a cell, at this level of sophistication, is probably a way to unravel the secrets of life itself, as opposed to just chemistry.

I agree with this approach in principle, but the unraveling of the secrets of life involve abiogenesis. They don't involve whatever this thing is about DNA repair.

But to concede the point, there is the intron/exon system that produces fully-matured mRNA starting from RNA that was just freshly transcribed in the nucleus. While this genetic stage exists in all our cells, the reason why we have it at all, in the first place, is a mystery to science. (Some suggest RNA splicing evolved as a mechanism to fight a kind of virus that causes cancer. The debate rages on.) In my humble opinion, RNA splicing is significantly more complicated than HR.

but given what we observe, is it unreasonable to ask whether the unknown mechanisms which must exist to create awareness, might also be working here,

It is reasonable and fine to do that -- provided you subscribe to a certain ontology about consciousness to begin with. The way you have phrased your question implies that you think I already subscribe to dualism, which happens to not be true.

By mentioning any of the following ontologies, I don't mean to act as an advocate of any them, and all of them have their own weaknesses in some ways. {I gave a short synopsis and definition of all these. I erased them because it came off as too preachy.}

1. Epiphenomenalism. (I had to add this comment for completeness). An Epiphenomenologist would disagree that there is any mechanism to be found at all, whether known or unknown.

2. Heterophenomenology.

3. Eliminative Materialism. I'm not a huge fan of this position, and so the people who like it would probably get angry at me.

4. Hylozoism. Ancient and fairly mystico-religious. Google it if you have free time.

5. Panpsychism.

6. Dualism. Dualism is a wide class of ideas like souls, vital essences (vitalism), Hegelianism, and maybe some German Idealism. Your repeating of this mysterious "Control" all over the forum leads me beleive you might be far into the dualist corner.


Consciousness has come up in chat rooms recently several times. Feel free to start a whole new thread on consciousness!

[lateralsuz]

Hi hyksos

There are six RAD51 proteins that operate during HR , and the 7th one operates only during meiosis. This is perfectly understood by science. Biochemists don't need my help, as they already know the mechanisms.

Even if this is a list of all the mechanisms at work in Homologous Recombination, (and I'm not sure it is), scientists merely see proteins (which they deem to be just a bunch of chemicals) doing things - but without any explanation of how they do them.

Once again - let's not confuse observation and description, with explanation.

If there is an explanation of how they do those things - then please present it.

On the assumption that nobody has explained how the Homologous Recombination actions summarised in my earlier posts are achieved in chemical terms, then it is not a deviation to ask the question whether such levels of control require something beyond chemistry.

I am open to any potentially viable explanation, but when we get into mysticism there is again no real explanation - only description and hope.

Eliminative Materialism at least has the beginnings of an interesting idea which may be part of the answer.

When you say that

Dualism is a wide class of ideas like souls, vital essences (vitalism), Hegelianism, and maybe some German Idealism.

I don't think that's correct. Dualism merely says that two types of stuff underpin reality, instead of the one which we can identify and test at the moment. Souls are something that might emerge from such other stuff, but they are not the other stuff itself.

Vitalism may suggest that something is the essence of life - but if you can't define what those distinguishing characteristics are, then is a road to nowhere.

Consciousness and control are factors that we do know exist, and the higher forms of them display characteristics that we can identify - and they go well beyond the defined parameters of Matter/Energy. So either the perceptions of Matter/Energy have to change, or something else is contributing to the effect.

The same could be said of entanglement and the 'faster than light communication' experiments done by Nicholas Gisin.... or indeed the dual slit experiments which can only be sensibly explained by the presence of another hidden type of stuff underpinning reality, unless we resort to something even more bizarre like wave-particle duality with the awareness to sense in advance when a change might be required!

There may be other explanations of course, but if you asked me to choose between a 2nd type of stuff or wave particle duality, I'll go with the other stuff every time on the KISS principle if nothing else!

We could potentially add Dark Energy into the evidence pool for other stuff, but the thing for me would be to define the characteristics it should display.

If awareness and consciousness are simply not present in a bunch of amino acids it is entirely valid to look at the other possibilities without having to subscribe to a particular ideology - but those ideologies may point to where the answers may be found - and to me that is valid.

When you can tell me how amino acids can do the steps in 'HR' then I will start to believe that it is possible, but as you can't - I would argue that the evidence is pretty strong that they cant and therefore, that such levels of control must be coming from somewhere else.

[hyksos]

Even if this is a list of all the mechanisms at work in Homologous Recombination, (and I'm not sure it is), scientists merely see proteins (which they deem to be just a bunch of chemicals) doing things - but without any explanation of how they do them.

Once again - let's not confuse observation and description, with explanation.

I am neither confusing nor am I conflating description with explanation. I understand the difference clearly, and my understanding of the difference is exhibited in my posts made to you on this forum already.

An "explanation" would mean that we have a clear history of the evolution of homologous recombination. I understand that we don't have that explanation for HR, as I also included the example of RNA splicing, which we also have no "explanation" for why living cells have it in the first place. Completely outside of the book-keeping that goes into describing a physical system in cells, "explanation" also entails we understand the purpose of something end-to-end. There are selective ion channels found in cells that science does not know what their purpose is. Such strange ion channels can be described in a stack of papers 8 inches thick, without a single mention as to what they are doing there to begin with (i.e. the "explanation" )

If there is an explanation of how they do those things - then please present it.

There is that word "explanation" again. This has been addressed. HR is mediated by 6 RAD51 proteins, and our best current understanding is that it is a defense against some cancers.

Eliminative Materialism at least has the beginnings of an interesting idea which may be part of the answer.

I'm flabbergasted by your interest in that particular approach versus the others I gave you. An eliminative materialist would disagree with 99% of the things you have written on this forum.

Dualism merely says that two types of stuff underpin reality, instead of the one which we can identify and test at the moment. Souls are something that might emerge from such other stuff, but they are not the other stuff itself.

This is word salad.

Vitalism may suggest that something is the essence of life - but if you can't define what those distinguishing characteristics are, then is a road to nowhere.

This is not true of the history of vitalism. Vitalism could have been totally true -- even scientifically true. It had to be debunked through careful experiment.

Consciousness and control are factors that we do know exist, and the higher forms of them display characteristics that we can identify

"We"? Do not include me in this false assertion.

You are conflating consciousness with this neologism you are using all over this forum, "Control". You are not allowed to do that , and I won't let you do it for reasons I already submitted to you. Now I will repeat them and we will go in circles.

Consciousness is such a deep and wide and complex topic, that you need to make a whole new thread on it. As I have already pointed out, (and you apparently ignored) one could literally build an entire forum of this size just dedicated to consciousness alone. By conflating your "Control" thing with consciousness you are running roughshod over a century of work by highly respected thinkers, some of which I am quite a fan of, some of which I have interacted with personally in interactions that spanned years. This is not a semantic or typographic complaint. Conflating consciousness with "Control" is bordering on a personal insult.

Please do make a new thread on consciousness. I spent years interacting with a panpsychist who is now a faculty at a university in California. I spent over a year discussing and sharing mutual fanboyism with a friend in Kansas City. At that time we were both really into Gerald Edelman. But yes.. if you are interested, do make a thread.

Consciousness .. {snip} .. characteristics that we can identify - and they go well beyond the defined parameters of Matter/Energy.

Consciousness goes beyond the defined parameters of matter and energy. Yes. I agree with this.

So either the perceptions of Matter/Energy have to change, or something else is contributing to the effect.

Well, maybe. That is one plausible angle-of-attack at the Hard Problem of Consciousness. There are others.

Make a thread.

If awareness and consciousness are simply not present in a bunch of amino acids it is entirely valid to look at the other possibilities without having to subscribe to a particular ideology

The very assertion that goes , "consciousness is not present in a bunch of amino acids" is itself a statement in a particular ideology (!!)

Make a thread.

[lateralsuz]

Hi hyksos

I have to admit that I am getting very annoyed with this site, when I spend a considerable time writing responses, and then, when I come to post them, the system bombs; requiring me to log in again, but in doing so, it then loses all of my work.

However - to the topic in hand....

I am neither confusing nor am I conflating description with explanation. I understand the difference clearly,

Really? When you then go on to say things like this....

There is that word "explanation" again. This has been addressed. HR is mediated by 6 RAD51 proteins, and our best current understanding is that it is a defense against some cancers.

Then why do you persist in offering observations about proteins doing things (ie. descriptions) as explanations?

An "explanation" would mean that we have a clear history of the evolution of homologous recombination. I understand that we don't have that explanation for HR,

No!! What we need is a chemical explanation about how a bunch of Amino Acids can achieve the logical steps being observed. It has nothing to do with 'the history of evolution'. That is a separate question altogether.

Me : Eliminative Materialism at least has the beginnings of an interesting idea which may be part of the answer.
You : I'm flabbergasted by your interest in that particular approach versus the others I gave you. An eliminative materialist would disagree with 99% of the things you have written on this forum.

Why? I have always said that we should be open to all ideas if they may lead to a valid explanation, even if, in this case, I feel it might only apply to a tiny/obscure part of the puzzle we seek to explain.

Me : Dualism merely says that two types of stuff underpin reality, instead of the one which we can identify and test at the moment. Souls are something that might emerge from such other stuff, but they are not the other stuff itself.
You : This is word salad.

That is both insulting and inaccurate. Dualism does only claim that there is a 2nd type of stuff underpinning reality. That is why it is called Dualism instead of Pluralism or anything else. You mentioned the souls not me. And if people wish to believe in them, it is a logical extension of that possibility which says that things might develop from such other stuff in much the same way as our universe has emerged from Matter/Energy.

You may not agree with it, but it is certainly not 'word salad' as you described it.

Me : Vitalism may suggest that something is the essence of life - but if you can't define what those distinguishing characteristics are, then is a road to nowhere.
You : This is not true of the history of vitalism. Vitalism could have been totally true -- even scientifically true. It had to be debunked through careful experiment.

I think we are both right here. Historically, Vitalism wasn't very clever at identifying reliable characteristics that pointed to capabilities beyond what Matter/Energy could deliver. Their argument was unpicked when biological chemicals were synthesised in the lab, (although that began with urea (which was not an example provided by the Vitalists). However your point is well made.... but I would suggest, with limits.

The underlying point of Vitalism was that you put a full set of such biological chemicals in a bag and they still wouldn't come alive. I am not a Vitalist, but if Vitalism was active today, its exponents would probably be cleverer - pointing to things such as consciousness and control as the distinguishing factors, that may not be achievable in Matter/Energy alone.

Me : Consciousness and control are factors that we do know exist, and the higher forms of them display characteristics that we can identify
you : "We"? Do not include me in this false assertion.

I am not conflating anything. I am merely pointing out that these undeniable things have characteristics which we can identify - unlike the Vitalists. But if you are actually denying the existence of Consciousness and Control, that would be quite interesting!


I do not wish to be distracted by consciousness on this thread, as you seem to be trying to do. I wish the topic to remain as stated - "Control in a living Cell."

So I would ask you again to address the point of how a bunch of chemicals (like amino acids) can perform the logical tasks which they appear to be doing?


I do think that a thread on consciousness would be good, but I can't think how to phrase it in a sensible but focussed way. However that is not the subject at hand.

[hyksos]

So I would ask you again to address the point of how a bunch of chemicals (like amino acids) can perform the logical tasks which they appear to be doing?

These proteins are definitely performing mechanical procedures that are logical. They "identify" portions of a DNA strand, bind to them, and perform cleaving and rejoining actions. This is all true, and the coordination is simply impossible to believe. For all intents, a restriction enzyme appears to be able to "read" DNA. In some sense it is doing just that. From my experience with them in lab, they identify binding sites with the precision of a computer.

There are also organelles whose 'job' it is to go around the cell and act like a garbage truck collection service. They go around scooping up all the left over "trash" from previous processes and bring it back to a "recycling center".

Among these proteins that perform these logical procedures on RNA introns and exons, and on the DNA in the case of HR, these proteins do not show up randomly in nature. You won't find them on the surface of Mars, and you won't find them just floating around in the water of the oceans or lakes. They are not found in comets or asteroids.

The answer to how proteins perform logical operations is that they are the products of evolution. Evolution can take something extremely rare and then multiply its occurrence in nature by reproduction. This is a theory after all, and what this theory would predict is that these molecular machines will only exist in tight proximity to the DNA strands that encode them. This is what is observed.

We have no reason to believe that lysosomes nor RAD51 proteins violate the laws of physics. If you have found them doing that , you don't need to be on this forum. You should contact a scientist at a university.

But if you are actually denying the existence of Consciousness and Control, that would be quite interesting!

I am not denying the existence of consciousness at all.

I do deny your continued conflation of this "control" stuff with consciousness. I denied your conflation in such clear english. You then turned around and conflated them again right in my face.

I do think that a thread on consciousness would be good, but I can't think how to phrase it in a sensible but focussed way. However that is not the subject at hand.

If it is not the subject at hand, then stop using the word.

[lateralsuz]

Hi hyksos

I have spent very little of my communications on this thread talking about 'consciousness', and most of the bits that I have done were in response to your much bigger diatribes on that subject, (which missed the very simple point I had originally been making). So I am very happy if we both now focus entirely on matters of control.

I described (above) the apparent logical steps that various proteins and enzymes perform in Homologous Recombination. If you consider the logic within each of those steps, you have to ask how chemicals can perform those steps which require :
- the assessment of non-standard situations and deployment of a suitable repair option (out of several) - not merely performing the first chemical reaction that a protein was capable of.

To say....

The answer to how proteins perform logical operations is that they are the products of evolution.

misses the point entirely, and does not explain how these chemicals perform their seemingly analytical tasks.

If we were to discover how these chemicals 'work things out' then we can go back to evolution to see how the origin of those proteins/enzymes might have come about...

But the reality is that nobody can explain how any chemical could do these things, even at a conceptual level! That is the point! Their actions seemingly go beyond the capabilities of Matter/Energy.

There is no apparent computer programming capability within a protein or enzyme. Neither can we say that any DNA code in the vicinity could act like an instruction manual - because such instructions would be massive in themselves, and the code would have to be reproduced thousands of times to be close to every possible break point. From what we can tell - that isn't the case.

(Indeed, the redundant code that we can observe is from old versions of protein templates that have been 'flagged' as obsolete - nothing more).

Such an analytical capability would also break our concept of DNA because it is believed that is is little more than a pre-set template for cellular reproduction, which includes a few pre-cursor triggers to generate an appropriate sequence of activity. In other words it prescribes a fixed routine, rather than responding to dynamic and non-standard situations requiring complex solutions.

That is not to demean the status of DNA in any way, as it is an astonishing evolutionary development, but I do say that we shouldn't push the capabilities of DNA into mysticism.

Let's focus on the control that must be exercised by the chemicals themselves.

[hyksos]

But the reality is that nobody can explain how any chemical could do these things, even at a conceptual level! That is the point! Their actions seemingly go beyond the capabilities of Matter/Energy.

You are speaking in abstract terms now "any chemical" and "not even at a conceptual level".

We might lack a conceptual level understanding for RAD51 in its particular context, but in the general context this is not true. Living cells create more order than they start out with. To our best understanding (at the conceptual level) living cells are not at thermal equilibrium. They take in energy from their environment, and then release energy back into the surrounding environment. This allows them to create more order within their membrane than previously existed.

While this behavior might look like a violation of the laws of physics at first glance, if we add up all the entropy inside the cell and outside it as well, that total entropy actually increased.

A more provincial example is the giant causeway rocks on Ireland's coast.



They appear that they must have been created by a stone mason. Because the patterns exhibits intent, and "mere matter" cannot have intent. How did the molecules in these rocks "know" they were supposed to form into this large shape? What was guiding them to do this other than CONTROL --- shouldn't we amend our understanding of matter in light of these findings?

No.

These formations were created by totally natural processes of deep sea lava being cooled very quickly near the ocean floor. They exhibit order because open thermodynamic systems can become more ordered over time.

Such an analytical capability would also break our concept of DNA because it is believed that is is little more than a pre-set template for cellular reproduction, which includes a few pre-cursor triggers to generate an appropriate sequence of activity. In other words it prescribes a fixed routine, rather than responding to dynamic and non-standard situations requiring complex solutions.

I'm sure it would break somebody's concept of DNA as a preset template. But not mine. Freshly transcribed RNA is taken through a complex process of RNA splicing involving introns and exons before this dynamic, non-standard process creates a fully-matured mRNA to leave the nucleus. The purpose of this is hotly debated to this day. If DNA is just a template, then why all this run-around with the splicing?

There is no apparent computer programming capability within a protein or enzyme. Neither can we say that any DNA code in the vicinity could act like an instruction manual - because such instructions would be massive in themselves, and the code would have to be reproduced thousands of times to be close to every possible break point. From what we can tell - that isn't the case.

After a restriction enzyme is produced by a cell, the enzyme acts on its own to identify a binding site and latch onto it. It does not consult the DNA further as a manual as it goes about these "reading" behaviors.

There is nothing intrinsic to the behavior of these particular proteins in their context where they perform these feats. If we saw information-processing in rocks on Mars, we would likely be revising our outdated conceptions of molecules in a huge way. These rare RAD51 proteins are products of evolution means they will act in a way that suggests "intent" towards a goal.

Normally we would say that a large molecule does not think, and cannot plan towards the future, and should not be endowed with abilities like "reading". Homologous Recombination looks like molecules are planning towards a future by doing things in the present. Inert matter cannot predict, but this matter is not inert, it is an open thermodynamic system, and it was "tuned" to be effective at its job by evolution.

[hyksos]

I'm going to add some additional reply to this thread, even though all the participants are not engaging with it.

But the reality is that nobody can explain how any chemical could do these things, even at a conceptual level! That is the point! Their actions seemingly go beyond the capabilities of Matter/Energy.

There is no a priori gaurantees to us that processes in nature should be conceptual-izable for human minds. By the mid 1940s, it was apparent that there are optimization problems whose solutions cannot be found on paper. These optimization/planning problems involve things as provincial as how much land a farmer should allocate to various crops, given the probability of seasonal climate. Mathematicians knew that the solution to such problems actually lies in 9-dimensional spaces. In fact, any real-world , "interesting" problems will go to much higher dimensions like 50 dimensions or more. No human will ever do this on paper armed with a hand calculator. These optimization problems can only be automated by computers. In the 1940s these sorts of discussions were practically "futurism" at the time, since computers were only owned by military departments and took up an entire room.

This is one of many examples where human conceptualization fails, because the human mind has no intuition of what is happening in 50-dimensional spaces. I would say most people can't conceptualize spaces above about 5 dimensions.



The animation above shows 3-dimensional "shadows" of a 4-dimensional cube.

Vis-a-vis laterlsuz's demands that biochemistry in cells must proceed by a manner that is "conceptual" in, otherwise we "must" face the possibility that matter and energy contain an ephemeral Control component : I will point at the best example I know of. Protein folding.

Protein Folding

A ribosome will translate a messenger RNA to a protein stand of amino acids, and at some particular point along the process, the ribosome will be activated to cut off the growing amino strand and let it flow freely in the cytoplasm.



What happens next is the strand of amino acids will fold up like origami paper into a final molecular shape. The process of amino acid chain --> to ---> protein is called protein folding.



The chain of amino acids will fold according to a collection of forces that include,

• electrostatic
• magnetic
• thermodynamic
• quantum mechanical

The cluster of various forces operating on the chain cannot be visualized, nor conceptualized by the human mind. Protein folding is not only something which must be automated by computers, but supercomputers are employed to do this calculation.



https://embnet.vital-it.ch/MD_tutorial/pages/MD.Part1.html

Okay so now that we have the above material "under our belts" as it were. Let me turn to what laterlsuz is demanding that I do.

But the reality is that nobody can explain how any chemical could do these things, even at a conceptual level! That is the point! Their actions seemingly go beyond the capabilities of Matter/Energy.

as homologous re-combination, do genuinely seem to analyse a problem, search out relevant factors, and then determine and implement a complex solution out of a myriad of possible options.
{snip}
in a manner that to all intents and purposes analyses and then resolves complex issues. These are the ones which illustrate true control.
{snip}
the damaged DNA are re-built by copying the template, until they reach a point when the original breaks could be connected perfectly - without any additions or omissions in the amino acid sequence.... not one. The alignment in itself would cause any human to apply considerable logic, while the knowledge of when to stop and which strands of the DNA should be re-connected are potentially even more testing to our brains, let alone an unthinking chemical which can only attach to one of the 4 strands.

At a legal level, what is being demanded here is that I produce a conceptual description of homologous recombination to laterlsuz, in a way which she finds personally satisfying. And if I do not produce this conceptualization, then I am "forced" in some way to revise the laws of physics that operate on matter and energy. That is the challenge. That is the gauntlet thrown on the table.

My first response is that there is no a priori gaurantee that a physical description be conceptualizable by human minds. To my understanding, there are no forces or energies operating in Molecular Dynamics simulations that are in violation of the laws of physics. (I cannot state this with any confidence, as I have never written the sourcecode for one of them. )

My direct response to this exact --> That is the point! Their actions seemingly go beyond the capabilities of Matter/Energy.

Their actions do not go beyond the capabilities of Matter/Energy. Their actions go beyond human conceptualization.

Telos
A similar argument is that the processes of protein folding appear to be preparing the protein for a function much farther downstream in its lifespan, and even very much farther away from where the protein is originally created. Many of these proteins are eventually delivered to a different place in the body altogether by riding on red blood cells. How could the ribosome located at this part of the body "know" that it should prepare a protein for its use at its future delivery site?

That looks like purpose... that looks like teleology. In academic contexts, the professors refer to this as "telos" particularly those who ascribe to panpsychism.

https://www.rep.routledge.com/articles/thematic/telos/v-1

I am certainly open to such arguments, particularly since philosophers tend to speak of things in terms of principles, rather than in physical detail. Example would be referring to "the spirit of the Law" without making any claim about the existence of spirits and ghosts (that you could hold seances with or what have you.)

A curmudgeon could say "The spirit of the Law doesn't exist because spirits don't exist." Such a curmudgeon is missing the point or committing a category error.

This is an interesting direction to go in, but I worry it exceeds the scope of this thread.

[lateralsuz]

Hi hyksos - and 'wow' to the effort you have put into your last two responses.

I'm not sure that I can respond to all of your points in one go, as there are so many things that I lose track of them. However.....

The major flaw in the 2nd Law of Thermodynamics & the principle of increasing entropy is that you cannot disassemble something before it has first been assembled.

I have seen in other threads on this site that people almost always talk about disassembly (almost as if that's the only thing they have been trained to do), and the thrust of their arguments are very rarely about the wonder of assembly, (especially in living things).

I see comments which suggest that chemical bonds only form in the 'accidental' moment when circumstances are perfect and then cannot be undone.... effectively rendering the formation of complex biological chemicals as a happy accident, which somehow occurs on a massive scale!

There should be more constructive discussion about assembly.

Yes - it is well known that a significant part of the way that proteins/catalysts etc work is through their shape, which places the active elements in a position where only the desired partner reaction can occur.

It is also well known that the different energy levels within the structure of proteins (ie. different combinations of amino acids) can be a major determinant of how a protein can can fold into exactly the right shape. (There are also many instances where the cell processes effectively incorporate a temporary 'scaffolding mechanism' to help achieve shape). All of these were stunning pieces of research.

However they all demonstrate how a single task can be performed - not multiple options selected appropriately. There is no sequence of such chemical steps (that I am aware of) which unpicks that apparent logic.

Equally, when people pretend that there is an explanation through energy levels by hiding behind probabilities, they are kidding themselves. As we are debating elsewhere, probabilities admit that there are multiple outcomes without explanation.

It is not the case that you have to satisfy my whim. The questions that I pose are valid for everyone.
I do not even demand an explanation now.

But I do demand honesty in the findings achieved to date and the ceasing of false and overblown claims by the scientific community

[hyksos]

However they all demonstrate how a single task can be performed - not multiple options selected appropriately. There is no sequence of such chemical steps (that I am aware of) which unpicks that apparent logic.

I understand the claim. We cannot deduce, in principle, why forces acting on chemistry would perform analysis and selection of a particular option from among several of them. At the very least, there would be something happening in the molecule requiring it it to remember what it had "perceived" at an earlier time, rather than just latching on like a machine and performing detachment or splicing.

I don't know the details of HR well enough to speak with any confidence in these claims. But I would presume that something in the RAD51 protein is changing in order to facilitate something like memory. It would be loss of a chemical bond, or the twisting of some branch to another configuration. But I'm just guessing.

I do know about ligand gated ion channels. They go into open and closed states, and the states are returned to after they "count" the number of ions that pass through them. It is possible that complex proteins and enzymes can be in discrete states, and change between states in response to an event in the past.