Wandering Towards a Goal: The Key Role of Biomolecules by George F. R. Ellis

George Ellis

General comment: Jonathan Kopel has suggested the following very interesting addition to my essay (shown in italics below):

4.2 The link of physics to logic: the molecular basis

The logic of what happens is enabled by voltage gated ion channels in axon and dendrite membranes [3, 11]. They lead to controlled flow of sodium, potassium and chlorine ions into and out of the axons and dendrites. The ion channels implement logical operations with the following logic:

If voltage V > V0 then let ions flow, else not (6)

which is of the form (5).

It is the structural form of the ion channels - the detailed three dimensional molecular configurations characterized as tertiary and quaternary structures - that enables this logic to emerge out of physics in the brain at the lower levels, and so underlie emerging logic at higher levesl [10]. The relevant structure is that of incredibly complex proteins imbedded in the cell wall: see here and here for the structure of one particular family of these channels. Given the existence of the ion channels, Maxwell's equations (2,3) together with the equations of motion for particles (4) underlie what happens. The flow of ions through ion channels is governed by these physical laws and so has the physics form (1). The implication is that, at least in the brain, 5 Molecular basis of "IF ... THEN ... ELSE ...." logic in biology: Biomolecules perform logical operations. This applies equally in many other biological contexts (see below), where they can be combined to give the basic operations AND, OR, NOT.

However, it is incomprehensible how the thousands of synaptic inputs on any neuron could lead to coordinated actions involved in learning, memory, and higher level cognitive function. However, N-methyl-D-aspartate (NMDA) receptors are one such class of receptors capable responding to the high density of synaptic inputs on a single neuron. These receptors have a characteristic seven transmembrane domain coupled to G proteins that mediate numerous biological effects within neurons1. Most notable of these effects relate to learning and memory, particularly with respect to long-term potentiation (LTP) and synaptic plasticity in the hippocampus1. Unlike typical voltage-gated ion channels previously mentioned, NMDA receptors respond to the coordinated input from many synapses leading to global depolarization across the cell membrane before activating and allowing calcium entry into the cell1. Thus, NMDA receptors are linked to the function of higher level functions in humans. The integrative nature of NMDA receptors illustrates the holistic nature of biological systems expressed by the late developmental biologist, Paul A. Weiss. In his book, The Science of Life, Weiss wrote that,

"The complex [biological organism] is a system if the variance of the features of the whole collective is significantly less than the sum of variances of its constituents; or, written in a formula:

Vs тЙд (Va + Vb + тЛп Vn )

In short, the basic characteristic of a system is its essential invariance beyond the much more variant flux and fluctuations of its elements or constituents... This is exactly the opposite of a machine, in which the pattern of the product is simply the terminal end of a chain of rigorously predefined sequential operations of parts. In a system, the structure of the whole coordinates the play of the parts; in the machine, the operation of the parts determines the outcome. Of course, even the machine owes the coordinated functional arrangement of its parts, in last analysis, to a systems operation-that of the brain of its designer".

Similarly, there exists a dynamic interplay between single voltage-channel receptors and receptors responding to the global interplay of all synaptic inputs on postsynaptic neurons. Thus, the brain exists as a dynamic entity of intertwining top-down and bottom-up processes.

Energy is of course used in carrying out these logical processes, and local energy minimisation will occur as part of what is going on (e.g. in the protein folding that converts one-dimensional strings of amino acids to the very complex tertiary and quaternary structures of proteins [14]). But energy or entropy considerations will not by themselves produce the desired logical operations that enable the function and purpose characteristic of life [7] to emerge. Indeed the necessary energy usage for cellular function is controlled by complex metabolic regulatory networks [19] that determine what energy transactions will take place on the basis of logical operations; Figure 2 gives a simple example, showing how they rely on basic logical operations (5) mediated by transcription factors that can be "on" or "of". Thermodynamics and statistical mechanics are not by themselves enough to capture what is going on. In summary, biomolecules such as ion channels [3, 11] can be used to make logic gates, and the higher level physiological systems in which they are imbedded [2, 6, 15, 10] enable emergence of complex life logic and processes.

Nestler, Eric J., Steven E. Hyman, and David M. Holtzman. Molecular Neuropharmacology: A Fundation for Clinical Neuroscience. 3rd ed. New York: McGraw-Hill, 2015.

Weiss, Paul A. The Science of Life: The Living System - A System for Living. Mount Kisco, NY, Futura Pub. Co., 1978.

George Ellis

I should have added:

Jonathan J. Kopel is in the Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center (TTUHSC)

Rajiv Singh

Dear George,

Since you have continued to take the points forward, I trust, you are interested in settling the issue.

>> Therefore, either information has a reality of its own in the function of the universe, or it can never come about.

- Not sure I understand that. Once it is realised, say in DNA or a brain or a computer, it has come about in a physical sense and does indeed have a reality in the universe.

My comment was related to the fact that all states of matter naturally correlates with certain information. Consider this from my essay. "If an interaction among physical entities results in an observable state S of a physical entity P, then S of P must naturally correlate with the cause and the context of the transition to the state S. Otherwise, measurements do not have an interpretation relating to the cause. A cause-and-effect analysis of an observed state of a physical entity in a context results in associating certain definite information with the state. Therefore, it is generally accepted in the scientific community that association of information with a state is the consequence of an act of modeling by an intelligent interpreter. On the contrary, given the laws of natural causation, the observed state must naturally correlate with, or bear an association with, or represent, information about the contextual relation among the interacting states that caused the state."

It is not only the DNA, or the brain that happened to represent certain information, all state descriptions of physical entities correlates with certain definitive information. I can only refer to my essay for fuller description. The striking point is then that at each interaction, information processing takes place, then it is a matter of only organizing a system that carries out appropriate high level information processing, as I have worked out. Surprisingly, it is not IF THEN ELSE like.

>> Starting from an example of bacteria, the author lays down a physicalist scenario of how to create more sophisticated form of bacteria (higher level organism), which can deal with more complex contexts. But then, if the bacteria did not have 'aims and intentions' even though it could take right actions, the more sophisticated organism also would have only a sophisticated action selector without having to deal with 'aims and intentions'. Representation of the [abstraction of] information of the 'need' requiring action as a consequence is the key to the 'aims and intention'.

As you continued to take the point forward, it means that you saw the point. Yes, we could create larger and larger systems (brains) to carry out very complex IF THEN ELSE kind of computations in hierarchy, but then if bacteria did not have the sense of Aims and Intentions, at no level of such logical computation in higher order organism can also have that sense. So, it was not a non sequitur.

Top-down causation is discussed often, but without rationalizing exactly how it brings in the elements of abstraction or Aims and Intentions. You suggested a recent paper that challenges the reductionists' view, again without qualifying how it helps to understand the sense of goals. As you yourself showed, bacteria itself has goal oriented behavior, but does it have the sense of the goal? So the pure behavior (action) oriented claim does not meet the need of the sense of aims and intentions.

As you said, "Unlike typical voltage-gated ion channels previously mentioned, NMDA receptors respond to the coordinated input from many synapses leading to global depolarization across the cell membrane before activating and allowing calcium entry into the cell. ... The integrative nature of NMDA receptors illustrates the holistic nature of biological systems."

I can understand that it carries out more complex computation of IF THEN ELSE version, but again how does the information abstraction happen? Moreover, variance of a system with multiple variables would naturally be lower than the sum of variances of individual variables if the variables are correlated.

In all of these discussions, one establishes more and more strongly how a complex system may develop that may exhibit complex behavior (function), but the meaning, the semantics, the abstraction remain unqualified. In my essay, I have attempted to derive each of these objects from first principles of information processing. I would request then, sticking to the definitions there, since each of these terms have diverse senses.

Rajiv

George Ellis

Dear Rajiv

1. "all state descriptions of physical entities correlates with certain definitive information ... given the laws of natural causation, the observed state must naturally correlate with, or bear an association with, or represent, information about the contextual relation among the interacting states that caused the state... ..all state descriptions of physical entities correlates with certain definitive information."

- Indeed. But the processes carry on without worrying about whether anyone is making a description of the state or not. For example, physics textbooks describing Newton's laws of gravitation don't talk about information associated with that interaction. They just talk about either forces or potentials and the outcomes resulting from their influences - which take place regardless of whether any observer is present or not.

2. ". Yes, we could create larger and larger systems (brains) to carry out very complex IF THEN ELSE kind of computations in hierarchy, but then if bacteria did not have the sense of Aims and Intentions, at no level of such logical computation in higher order organism can also have that sense"

- You are assuming emergence of new kinds of properties cannot occur in a complex structure. It is my contention that they can and do.

3. "bacteria itself has goal oriented behavior, but does it have the sense of the goal?"

- No- it has no brain.

4. " So the pure behavior (action) oriented claim does not meet the need of the sense of aims and intentions."

- Exactly. You have answered your own comment 2. above.

5. "I can understand that it carries out more complex computation of IF THEN ELSE version, but again how does the information abstraction happen?"

- Through modularity of the hierarchical structures, with information hiding and modular interfaces that depend only on abstracted variables. This is described in depth by Grady Booch in his book on Object Oriented Programming.

6. " Moreover, variance of a system with multiple variables would naturally be lower than the sum of variances of individual variables if the variables are correlated."

- I don't understand that statement in the kind of highly non-linear situation we are faced with in life, nor what its implication is supposed to be.

George

Rajiv Singh

Dear George,

Your responses this time allow us to move towards heartening convergence.

1. "all state descriptions of physical entities correlates with certain definitive information..."

- Indeed. But the processes carry on without worrying about whether anyone is making a description of the state or not. ... They just talk about either forces or potentials and the outcomes resulting from their influences - which take place regardless of whether any observer is present or not.

What is heartening to see is that you agree that there is natural association of information with each description. This would mean that at every interaction information processing is taking place. Now, it is for me to construct the logical structure of how the interactions can be organized to build higher level abstraction from this correlation with information. And it is for me to show how this organization maps very well with the elementary neural connectivity structure in the brain. This is what precisely I have attempted in my essay.

2. "Yes, we could create larger and larger systems (brains) to carry out very complex IF THEN ELSE kind of computations in hierarchy, but then if bacteria did not have the sense of Aims and Intentions, at no level of such logical computation in higher order organism can also have that sense"

- You are assuming emergence of new kinds of properties cannot occur in a complex structure. It is my contention that they can and do.

Yet another heartening response. No, I do not mean that emergence does not take place, in fact, what is needed is to show how exactly emergence happens that may create the descriptions of high level abstractions as well as complex structures of semantics. Again I have to refer to my essay, which has laid down step by step in specific detail how the abstraction takes place and what exactly constitutes the step of concrete emergence. I do not prefer citing emergence without actually showing the step.

3. "bacteria itself has goal oriented behavior, but does it have the sense of the goal?"

- No- it has no brain.

Yes, it does not have the brain, but what difference the organization makes is something that needs complete elaboration. From the description of information processing and emergence of abstraction I show what kind of organization and information processing would make the specific difference.

4. "So the pure behavior (action) oriented claim does not meet the need of the sense of aims and intentions."

- Exactly. You have answered your own comment 2. above.

Thank you, it does not need any further discussion.

5. "I can understand that it carries out more complex computation of IF THEN ELSE version, but again how does the information abstraction happen?"

- Through modularity of the hierarchical structures, with information hiding and modular interfaces that depend only on abstracted variables.

I am not in the knowledge of Grady Booch's work, but if I have a mechanism to show how modularity in hierarchy builds the required information abstraction, it suffices. It is not through hiding of information, but rather via disjunction among multiple specific information that the abstraction emerges. Moreover, the states interact not the information represented; therefore, information cannot be directly probed anyway.

So, I may infer that we do not differ on any of the points, except that each point needs very well justified specific detail of emergence and organization. In case, if you do choose to peruse my essay, my request is to be patient, open, and very critical, while judging the meaning from the precise definitions of the terms stated at first use. This is extremely condensed version to fit in 25000 characters.

Rajiv

Rajiv Singh

Dear George,

Now that rating system and formal evaluation are out of context, we may take up issues between us informally. Of course, it is a bit disappointing that I could not receive your comments on my essay, in particular for the following reasons.

It seems, we agreed upon so many things, such as natural association of information with states of matter, information processing at each interaction, emergence of high level abstract semantics through such processing, and why a system like brain makes all the difference to show why bacterial actions may not have aims and intentions behind them. I am sure you did notice my claim of having dealt with precisely these issues; it then leaves me at loss to imagine why you could not find time to evaluate my claim which had the promise of fulfilling exactly what you demanded in your essay.

Here are the points of agreement, quoting from my last response.

1. What is heartening to see is that you agree that there is natural association of information with each description. This would mean that at every interaction information processing is taking place. Now, it is for me to construct the logical structure of how the interactions can be organized to build higher level abstraction from this correlation with information.

2. Yet another heartening response. No, I do not mean that emergence does not take place, in fact, what is needed is to show how exactly emergence happens that may create the descriptions of high level abstractions as well as complex structures of semantics. Again I have to refer to my essay, which has laid down step by step in specific detail how the abstraction takes place and what exactly constitutes the step of concrete emergence.

3. Yes, it does not have the brain, but what difference the organization makes is something that needs complete elaboration. From the description of information processing and emergence of abstraction I show what kind of organization and information processing would make the specific difference.

4. [If] I have a mechanism to show how modularity in hierarchy builds the required information abstraction [as you required], it suffices. It is not through hiding of information, but rather via disjunction among multiple specific information that the abstraction emerges. Moreover, the states interact not the information represented; therefore, information cannot be directly probed anyway.

Rajiv

Mark Pharoah

Responding to 1:

I think every action is a response to interaction, and that all such actions express a renewed equilibrium. So, fundamentally, I disagree with your position and we will have to leave it at that I think. Thanks for the exchange though.

Responding to 2:

"They translate"... same issue. I know that systems of cells do as you say, and that selection has made things as they are etc. What I am trying to express to you is that words like, reading, translating, transporting, and using, are all problematic because they require that a certain type of information can be accessed and utilised by a system in these meaningful ways. The issue is that in these contexts the concept of meaningful information, which is manipulated, has not successfully been explained by the physical sciences yet. I think of such terms as words of convenience where explanation is assumed as part of the mechanism of the relevant complex system actions.

Good luck with the competition... at least you are getting feedback which is more than I can say regarding my essay.

George Ellis

Dear Mark

1. "I think every action is a response to interaction, and that all such actions express a renewed equilibrium. "

- Yes we have to disagree. A lot of what goes on in life is not equilibrium.

2. "What I am trying to express to you is that words like, reading, translating, transporting, and using, are all problematic because they require that a certain type of information can be accessed and utilised by a system in these meaningful ways. The issue is that in these contexts the concept of meaningful information, which is manipulated, has not successfully been explained by the physical sciences yet"

- But that is just what I have been saying. Physics and biology are different, even though biology is ultimately based in physics. You need biological systems to have meaningful information.

regards

George.

Laurence Hitterdale

Dear Professor Ellis,

Thank you for your thought-provoking essay. Are there examples of information collection, processing, and utilization outside of living things? Or is the logic of life found only in living things, and perhaps also in artifacts, such as computers, which are devised by living things? I realize of course that there is no purpose in the existence of most inanimate objects, or in their behavior. Your opening sentences and quotation clearly state this. However, information storage and logical operations can be physically realised in a variety of ways. In view of this variety, the question arises whether there might be a few instances, though rudimentary ones, of informational logic outside of biological systems. But perhaps informational logic is not only distinctive of living things but wholly confined to them.

Laurence Hitterdale

George Ellis

Dear Laurence Hitterdale

>> Are there examples of information collection, processing, and utilization outside of living things? Or is the logic of life found only in living things, and perhaps also in artifacts, such as computers, which are devised by living things?

This is an excellent question. The problem here is that it is notoriously difficult to define "information". In a sense every interaction conveys information, for example light from distant stars tells us about the nature of those stars; but there is no device or organism that collects or uses that information, except those devised by scientists. It was not in some sense intended to be used. The information is just a byproduct of physical processes, and does not have a code in the following sense: a code is arbitrary, and could have been different. The spectral lines in star are what they are, and could not have been different. The second main difference is that in coded information, the energy released by use of the information to attain one of an intended range of purposes is independent of the energy conveying the information (separate energy sources are used to implement outcomes arising from the incoming signal, e.g. a battery in a remote control) whereas in physical interactions, the energy of the interaction is all that is available when any further consequences arise out of the information (although it may trigger instabilties in metastable systems). Let's call information in the biological sense "active information". Then information such as that in starlight is "passive information"

Taking all this into account, I think active information collection, processing, and utilization takes place only in living beings, or their artefacts such as computers.

>>> I realize of course that there is no purpose in the existence of most inanimate objects, or in their behavior. Your opening sentences and quotation clearly state this. However, information storage and logical operations can be physically realised in a variety of ways.

Yes indeed. Multiple realisability is a key feature of active information. It cannot occur in passive information.

>>> In view of this variety, the question arises whether there might be a few instances, though rudimentary ones, of informational logic outside of biological systems. But perhaps informational logic is not only distinctive of living things but wholly confined to them.

While I'm inclined to say that active information only occurs in biological systems or manufactured artefacts (as described in the excellent book The Sciences of the Artificial by H A Simon), obviously life emerged and somehow made the step up from no active information to being driven by active information. Some of the steps on the way to life must have had a rudimentary form of active information in order that the full thing could emerge. But we have no idea how that happened.

Regards

George Ellis

Alexey/Lev Burov

Dear George, dear Laurence,

Thinking about a difference between, say, a fire and a living cell, I see essentially only one well-defined parameter which make them dramatically different: their complexity. Fire is essentially described by ~ 10 parameters (volume, pressure, temperature, chemical constituents, seems that's it). The fire existence is not sensitive to infinite number of its specific details, which dynamically change; fire is simple in that sense. To describe the living cell, many orders of magnitude more crucial parameters are needed. If only one of them were wrong, the cell would be dead.

All the best,

Alexey Burov.

George Ellis

Dear Alexey

The difference is indeed complexity, but that is not easy to characterise in a meaningful way.

>>> The fire existence is not sensitive to infinite number of its specific details, which dynamically change; fire is simple in that sense.

Yes

>>> To describe the living cell, many orders of magnitude more crucial parameters are needed.

Yes. They relate to organised complexity - the parts have functional relations to the whole. They each serve a purpose.

>> If only one of them were wrong, the cell would be dead.

No. The cell is very robust - its mechanisms thrive on randomness, see Life's Ratchet: How Molecular Machines Extract Order from Chaos by Peter M. Hoffmann. It is digital computers that are sensitive in this way. The cell also has preferred range.

George

George Ellis

That got truncated. Should be,

"The cell also has a set of homeostatic systems keeping its parameters in a preferred range"

Alexey/Lev Burov

Dear George,

I agree with your comments/corrections; thanks for the reference.

A possible definition for the amount of information in any object can be taken in the Kolmogorov style, as a length of a minimal description for creation of that object. For a fire or even the Sun this length would be very small. For a living cell, it would be many orders of magnitude more.

Alexey.

George Ellis

Dear Alexey

Ah yes that is a good proposal: Lee Cronin has suggested essentially that same idea under the name "Pathway Complexity".

George

Alexey/Lev Burov

Many thanks, George!

Don't you have a reference to the general presentation of this Pathway Complexity? I have my own ideas on that (a bit more than just Kolmogorov-like); it would be interesting to compare with Cronin's. Did you review that in your new book? I am in the process of reading it. By the way, I like your list of attacks on the free will (your Table 7.2); I will show and comment it in my talk on the free will in my Fermi Society of Philosophy.

All the best, Alexey.

George Ellis

Dear Alexey

Cronin spoke about it at a meeting in Arizona a few months ago and has a preprint on with Stuart M. Marshall and Alastair R. G. Murray. It does not see to yet be publicly available, but I've asked him about that. It was completed after my new book.

Thanks for the comments on free will. It is a key issue that the different attacks on it contradict each other.

Best wishes

George

Tejinder Singh

Dear George,

Excellent essay, beautifully written.

Is it possible to identify physics principles which underlie adaptive selection? Why does life sustain itself? Could it be that that there are some physical quantities that a living system tends to conserve, despite being an open system? Naively, it seems that the purpose of reproduction is to create more low entropy states (progeny) as the entropy of the parent(s) increases due to aging and eventual death.

Thanks and regards,

Tejinder

George Ellis

Dear Tejinder

>>> Is it possible to identify physics principles which underlie adaptive selection?

I don't think so: its an emergent law that requires for its formulation the concept of a living being. That is not a physics concept.

>>> Why does life sustain itself? Could it be that that there are some physical quantities that a living system tends to conserve, despite being an open system?

Well it exchanges matter and energy with the environment all the time (we eat many times our own weight each year!), nevertheless maintaining its essential nature (the famous fact that each of us will be made of completely different molecules in 7 years time but will still in some sense be the same person). So it maintains its physiological systems including the brain despite these interactions. That is a dynamic stability maintained via homeostasis and developmental processes that for example heal wounds.

>> Naively, it seems that the purpose of reproduction is to create more low entropy states (progeny) as the entropy of the parent(s) increases due to aging and eventual death.

This is something like what Jeremy England claims. I find it contradictory to talk about a purpose in relation to entropy production. The core nature of entropy production, as explained beautifully by Eddington and Penrose, is that is has no purpose; it is an outcome simply of randomness together with the nature of phase space

Regards

George

George Ellis

Addendum:

>>> Is it possible to identify physics principles which underlie adaptive selection?

At a certain level, it is matter and energy conservation together with the 2nd Law of thermodynamics that underlie it, because we need usable energy and usable matter to live; we die without them. But this does not begin to take into account features such as predation on the one hand and reproduction on the other, which occur at the biological level.

Daniel Rocha

Dear Geogte

Yes, oscillation. Sorry, for taking long to answer here, but it seems we are not notified when someone else answers on other people's entries... But I would like you to comment there and see really what I wrote in the paper. Would mind? There are also many other things there...

http://fqxi.org/community/forum/topic/2846

Christopher Fiorillo

Dear Dr. Ellis,

Thank you for your interesting essay. I agree that the biological processes you describe are essential to the goals of biology. It is another matter whether they are essential to goals in general. It seems that you are only making an assertion when you state that goals are lacking in non-biological systems. You explicitly presented that as an assertion at the start, and I did not recognize a subsequent argument to support it. I am wondering if you consider it only an assumption that you use to reach conclusions about other issues, such as how intentions emerge from the level of proteins to cells to brains.

How do you define what it means to have a "goal" or "intention?" We can intuitively recognize intentionality in biology, but to draw strong conclusions about its relation to physical systems requires a precise definition that would allow us to judge whether or not a physical system does or does not have intentionality.

We can describe the state of an ion channel or other protein with logical statements (equations 5 and 6). However, any physical system, following any rule, can be described by logical statements. Relative to a 'free' particle than can quite readily accelerate in any direction, an ion channel or other protein tends to transition between only a small number of "discrete" states (although more than two, to be realistic). That is a very important difference between higher and lower structures, but it is not a dichotomy. In the most detailed and realistic model that we could make of a protein (a quantum model), it would be possible for its component particles to accelerate in any direction at any time, however unlikely that might be. Because of the forces binding particles within a protein, a configuration that we label as a 'protein' is "more nearly binary" compared to a configuration in which the same number of particles are "free" of one another (separated enough so that interactions are weak). But even a single particle could be described with a sufficient number of logical statements (for quantum or classical or any other rules). If you mean to identify logical statements with intentionality, then would it not follow that any physical system has intentionality? I draw that conclusion in my essay ("The making of mind: what is inherent to matter and what emerges with complexity?"), although I do not attach any special significance to logical statements.

"The key point is that the functions T(X), F1(Y) and F2(Z) are not determined by the underlying physical laws; they can be shaped by evolutionary or developmental processes in highly complex ways (as for example in the citric acid cycle), or planned by human thought to produce any desired outcome"

The above statement seems to say that inanimate matter follows the laws of physics but animate matter does not. I doubt that you intend that meaning, but I do not see any alternative interpretation. I argue that a person is a configuration of particles following the laws of physics. But that does not imply "merely a configuration of particles." A person is a very special and unique configuration of particles, with special and unique properties (physical and mental).

Though not of fundamental importance to your argument, or my criticisms above, I think I should point out that equation 6 is not correct (except as a very rough approximation that is never made in biophysics, as in the case that "greater" means at least 0.1 V greater). Neither a single ion channel, nor a population, has a "voltage threshold." As membrane voltage changes in a graded manner (on the scale of millivolts), the probability of channel opening will change in a graded manner, and thus the number of open channels will change in a graded manner. In order for a voltage-sensitive channel to transition from closed to open with near certainty requires a change of at least ~50 mV, and that is very large on the physiological scale (see Hille, "Ion Channels of Excitable Membranes").

Finally, I would like to draw attention to the fact that you are a physicist who appears to be arguing for a fundamental dichotomy between animate and inanimate matter, and I am a neurobiologist arguing that that there is no fundamental distinction. That makes us both rather odd. But I want to emphasize that I am not a materialist; in my essay I label my framework as "anthropomorphic reductionism" (which I intend to be both humorous and accurate). I believe that intentionality is a property of matter, although it certainly does emerge with complexity in a quantitative sense.

Regardless of our different views, I am very pleased to see a great physicist taking mental properties seriously. Science needs that. I will also take this opportunity to express my great respect and gratitude for your important contributions to social justice. We all need that.

Best wishes,

Christopher

George Ellis

Dear Christopher D. Fiorillo

Than you for your thoughtful comments.

>> It seems that you are only making an assertion when you state that goals are lacking in non-biological systems. You explicitly presented that as an assertion at the start, and I did not recognize a subsequent argument to support it.

Several others have raised similar issues; I am surprised by this. Perhaps you are thinking of something like energy minimisation. I do not classify that as a goal, as it is not the result of an intention or a purposeful mechanism: it is just the way purposeless laws work, and there is no option about it. Animals can and do change their goals according to circumstances.

>>> How do you define what it means to have a "goal" or "intention?" We can intuitively recognize intentionality in biology, but to draw strong conclusions about its relation to physical systems requires a precise definition that would allow us to judge whether or not a physical system does or does not have intentionality.

At a higher level, it is a potential outcome that is the result of choice: it could have been different. At a lower level, it is a potential outcome that is a result of interacting systems actively working to attain that outcome (which activity costs energy).

>> We can describe the state of an ion channel or other protein with logical statements (equations 5 and 6). However, any physical system, following any rule, can be described by logical statements.

Yes, but physical laws are not arbitrary - they are immutably given us by Nature, for example an inverse square law of repulsion of like electric charges. The key point in (5) is where I emphasize that the logical and mathematical functions can be anything. They are not fixed by physical laws.

>> Relative to a 'free' particle than can quite readily accelerate in any direction, an ion channel or other protein tends to transition between only a small number of "discrete" states (although more than two, to be realistic).

sure

>> That is a very important difference between higher and lower structures, but it is not a dichotomy. In the most detailed and realistic model that we could make of a protein (a quantum model), it would be possible for its component particles to accelerate in any direction at any time, however unlikely that might be. Because of the forces binding particles within a protein, a configuration that we label as a 'protein' is "more nearly binary" compared to a configuration in which the same number of particles are "free" of one another (separated enough so that interactions are weak).

It has a specific structural character that is preserved over time, even if conformation changes

>> But even a single particle could be described with a sufficient number of logical statements (for quantum or classical or any other rules).

See above: they are not arbitrary, they are fixed by fundamental physics.

>>> If you mean to identify logical statements with intentionality, then would it not follow that any physical system has intentionality?

No. Physical systems are constrained by the initial data to do just one thing. Biological systems alter the way they react according to environmental conditions.

>> "The key point is that the functions T(X), F1(Y) and F2(Z) are not determined by the underlying physical laws; they can be shaped by evolutionary or developmental processes in highly complex ways (as for example in the citric acid cycle), or planned by human thought to produce any desired outcome"

Precisely so

>> The above statement seems to say that inanimate matter follows the laws of physics but animate matter does not.

Not at all. Living matter is structured so as to channel the underlying physical laws, which are always true. in order to attain specific goals.

>> I argue that a person is a configuration of particles following the laws of physics.

Indeed

>> But that does not imply "merely a configuration of particles." A person is a very special and unique configuration of particles, with special and unique properties (physical and mental).

Yes again.

>> Though not of fundamental importance to your argument, or my criticisms above, I think I should point out that equation 6 is not correct (except as a very rough approximation that is never made in biophysics, as in the case that "greater" means at least 0.1 V greater). Neither a single ion channel, nor a population, has a "voltage threshold." As membrane voltage changes in a graded manner (on the scale of millivolts), the probability of channel opening will change in a graded manner, and thus the number of open channels will change in a graded manner. In order for a voltage-sensitive channel to transition from closed to open with near certainty requires a change of at least ~50 mV, and that is very large on the physiological scale (see Hille, "Ion Channels of Excitable Membranes").

Ok I agree. It is an approximate description. We can use a more accurate description as you point out. The point then is that that response function you describe is not determined by the underlying physics per se. It is determined by the structure of the ion channel, which provides the physical laws a context in which to function so as to achieve that outcome.

>>> Finally, I would like to draw attention to the fact that you are a physicist who appears to be arguing for a fundamental dichotomy between animate and inanimate matter,

Not the matter per se, which is identical at the particle level, but they way it is organised, which is very different at the molecular level

>>> I want to emphasize that I am not a materialist; in my essay I label my framework as "anthropomorphic reductionism" (which I intend to be both humorous and accurate). I believe that intentionality is a property of matter, although it certainly does emerge with complexity in a quantitative sense.

Ok then we agree on that

Thanks for the kind comments

Best wishes

George

Avtar Singh

Dear George:

FQXi is a unique forum to address key open issues related to science that impact humanity and life. The mainstream science has treated the universe, laws, and fundamental particles as inanimate entities devoid of life, consciousness, or free will. As a result, the mainstream theories of science are also devoid of consciousness or free will. While science, especially quantum mechanics, recognizes the spontaneous free-willed (without any cause) birth and decay of particles out of the Zero-point vacuum as a fundamental physical phenomenon, it refutes existence of free will via consciously labeling it as "Randomness" in nature. This vicious circle has failed science in two ways - first is its erroneous prediction of a purposeless universe and life in it making the science itself purposeless and meaningless from a deeper human perspective. Secondly, ignorance of consciousness or free will which is a fundamental dimension of the universe along with mass/energy/space/time leaves scientific theories incomplete leading to their current paradoxes and internal inconsistencies.

Just like a dead mother cannot nurture and give birth to a living baby, a dead universe governed by inanimate laws cannot support any living systems within it. Universal consciousness is fundamental to the emergence and sustenance of any living system - quantum or biological. The mathematical laws must be living to give rise to living aims and intentions. If the fundamentality of the consciousness of the universe and laws is not understood, a scientific theory would be like a castle built on sand.

FQXi forum is participated by brilliant and accomplished scientists representing in-depth knowledge and expertise in diverse fields. I would propose that the forum scientists take on a challenge to enhance and uplift science from its current status quo as an incomplete science of the inanimate (dead) matter to the wholesome science of the living and conscious universe. This would complete science and make it purposeful and meaningful adding to its current successes as a tool for enhancing material life alone. Science deserves its long-awaited recognition to address not only matter but mind as well and not only material but spiritual life as well. Considering the current political and economic threats to the basic survival of science and religious extremism/terrorism threatening the fundamental freedom (free will) of humanity, the role of a wholesome and genuine science has become even more vital to humanity.

I have forwarded a humble and example proposal detailing how a consciousness-integrated scientific model of the universe entailing matter-mind could be developed that resolves current paradoxes of science, predicts the observed universe, and offers a testable theory via future empirical observations. This proposal and theory are documented in my contest paper - FROM LAWS TO AIMS & INTENTIONS - A UNIVERSAL MODEL INTEGRATING MATTER, MIND, CONSCIOUSNESS, AND PURPOSE .

I would greatly appreciate any feedback as well as constructive criticism of the proposed approach to advance physics and cosmology.

Best Regards

Avtar Singh

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