Vast Complexity of Immune Pattern Recognition Receptors

PD sheets of dendritic cell capture HIVLiving among trillions of microbes, it is necessary to determine which are going to cause disease. This is done by recognizing patterns with special receptors on immune cells—pattern recognition receptors or PPRs. Once triggered, receptors activate powerful mechanisms to cause inflammation that is life saving but, also, can attack our own cells with chronic inflammation and autoimmune diseases. In fact, as with every other critical aspect of physiology, pattern recognition receptors have elaborate regulation and signaling. One regulation mechanism is elimination of the receptors themselves. Other processes move them into specific cellular compartments. Others increase and decrease their effects in complex cascades.  

A very complex set of unique pathways determines the outcome of the critical balance between enough versus too much inflammation. The risk is very great in either direction—run away microbe invasion versus excessive attack on our tissues. It is another very intelligent cellular system that is based on the vast complexity of immune pattern recognition receptors.

B0007289 White blood cellsVast arrays of pathways influence many factors determining the outcome of receptor activity. The receptors can self regulate. There are many different ways that receptor activity is amplified and suppressed. One involves receptors working together; others amplification or inhibition of two different signals; while many of the mechanisms use feedback both positive and negative.  

This post will describe current views on this very vital, but extremely complex subject. As with many other posts, the regulation is so complex and distributed among so many different cells at the same time, it is hard to envision how it can be directed.

Pattern Recognition Receptors

Healthy_Human_T_CellSeveral types of innate immune cells, including macrophages and dendritic cells, scour for dangerous microbes where they shouldn’t be in the body. Using pattern receptors they recognize specific molecules known as pathogen-associated molecular patterns (PAMPs). These receptors, also, pick up damaged tissue or cells—called damage-associated molecular patterns (DAMPs).

There are three large families of proteins that form a wide range of pattern receptors. They are triggered by proteins, nucleic acids, sugars, and lipids from a wide range of different microbes. They, also, can be triggered by anything that is completely unknown. Toll-like receptors (TLRs) have at least 13 types; RIG-I-like receptors (RLRs) have three types; and NOD-like receptors (NLRs for nucleotide-binding oligomerization domain proteins or NODs). There are now known to be many other structures in the cell made of multiple complex proteins that pick up random RNA and DNA in the cell.

PD NFKB_mechanism_of_actionStimulating TLRs produces the cytokine nuclear factor-κB (NF-κB) or interferon (IFN) that stimulates inflammation against microbes. RLSs are enzyme proteins that respond to genetic material from viruses in the cytoplasm. They, also, produce different interferons to fight viruses. NLR receptors pick up bacterial invasions.

With so many different receptors, it is necessary for a great amount of coordination and regulation to avoid over reactions that cause damaging autoimmune diseases. Responses of the various receptors involve cascades of molecules that trigger a variety of cytokines and immune cells. The regulatory machinery includes many molecules that influence various different steps in these cascades.

Molecules that tag DNA and histones are critical for the epigenetic regulation of a wide variety of genetic processes. There are now more than forty different types of genetic tags identified. Some of these same tags are used in the regulation of protein receptors. Also, transcription factors directly trigger and inhibit genetic actions related to the receptors. Enzymes involved with tags that are used for pattern receptors include kinases and phosphatases, as well as ubiquitin related proteins. Ubiquitin and sumoylation have been described in previous posts as a very complex molecule tagging system used for all types of cellular purposes (such as transport to particular locations in the cell). They described how microbes and cells manipulate these tags in their warfare with each other.

Regulation of Pattern Receptors

B0004343 Organelles in a pancreas cellMany different receptors operate at the same time, often different TLRs. These signals can increase or decrease the signal for immune factors. Interactions can occur through alteration of the sensing abilities of the receptors, and change of the cascades produced by the signals.

Once the receptors have triggered immune responses, there are at least five different ways that pattern receptors are regulated. The receptor can be transported to organelles for decomposition. A second is cycling the receptors, which is accomplished by helper chaperone molecules. The recycling can go between an organelle and the membrane or between organelles. There are many specific factors that affect this process.

A third way is the alteration of molecules that occur in the signaling cascade started by the receptor. This creates negative feedback to stop the effect of signals on cytokines. The fourth way is tagging of the receptors and other molecules by high-energy phosphates and ubiquitin enzyme tags. These enzymes can increase the impact on cytokines increase or decreasing inflammation. The fifth mechanism includes many inhibitors that remove the signals that have been placed.

The interaction of all of these techniques is extremely complex.

Pattern Receptors Can Self Regulate

B0008190 Organelles in spiral ganglion neuronOne type of regulation involves the alterations to the protein receptors themselves including elimination and movement into compartments. TLRs are cut by special enzymes and then brought into particular organelles, which can stop the signaling for more inflammation. As well as the Toll-like receptors, there are many associated proteins including special lipoproteins that are necessary for the receptor function. These can be placed in vesicles (endosomes) or into the Golgi and then sent to lysosomes where they can be destroyed. (See post on secretory pathway). Special enzymes are involved in taking apart the receptors, which stop the inflammation signaling. This process stops many important cytokines tumor necrosis factor TNF, interleukin-6 IL-6 and IFNβ.

Some TLRs and RLSs are altered by the ubiquitin system, which can stimulate, inhibit or alter their function. There are, in fact, a large number of different types of ubiquitin tags with unique enzymes that regulate some of the TLRs. These processes use atypical pathways for the ubiquitin system. Other newly discovered protease enzymes stimulate and cancel the effects of multiple different TLRs.

Movement of Pattern Receptors

B0008518 Rough endoplasmic reticulumPattern receptor proteins are moved, taken apart and rebuilt through many different cellular compartments. The endoplasmic reticulum (ER) has many different factors that interact with TLRs, creating vesicles that move and eliminate them.

When a TLR receptor protein is first created in the ER and then folded into the correct shape, special factors for each of the different TLRs help transport them to the membrane for their working position. Special lipoproteins and immune factors are necessary for this complex process. A different set of factors are necessary when the receptor needs amplification of its stimulus of cytokines to initiate inflammation. Special immune factors like CD14 are necessary for this process, which can occur in special vesicles called endosomes.

Stimulation of lipopolysaccharides (LPS) plays a significant part of this process in bringing more receptors from the ER and Golgi to the membrane. This is absolutely necessary to fight against microbes and its regulation is necessary to avoid autoimmune disease.

Many Different Regulators

From Vojtěch Dostál

From Vojtěch Dostál

Both the TLR and RLR receptors can create more of their own receptors by many different processes. These mechanisms, using epigenetic tags, alterations of proteins and changes in the metabolic signaling cascades, can increase the immune response when necessary.

Epigenetic alterations that create more receptors include methyl tags on DNA and other tags on histones, as well as special RNAs. All of these complex mechanisms create feedback loops. The enzyme that transfers methyl groups to DNA (methyltransferases DNMTs) are critical in a response to virus attacks. These mechanisms are just being discovered but there are many specific types and locations where they operate. Others use deacetylase enzymes on histones (HDACs) that affect proteins that promote and inhibit gene actions. When inflammation is strong it can affect the stimulation of particular genes in response to these processes.

Histone methylation, also, is a critical regulator of TLR actions by both inhibiting and stimulating particular genes in the immune response, including making cytokines, enzymes and transcription factors. There are large numbers of different versions of these cascades that are just now being discovered, making the feedback regulation extremely complex. These tags affect each of the different immune cell actions in complex ways

From Jacopo Werther

From Jacopo Werther

The interactions of various genetic signals affect both the responses to viruses and bacteria. The conversations that occur between the immune cells through these pathways appear to be related to how virus infections can stimulate larger bacterial infections.

It becomes even more complex when other factors and regulators of the TLR receptors are, also, affected by histone tags. When these factors are increased or decreased, it affects the inflammation responses. These involve the whole range of epigenetic tags and ubiquitin. Cascades can cause multiple different switches to regulate immune responses. These epigenetic enzymes work with acetyls (histone acetyltransferases HAT and deacetylase HDAC) are vital for many of the cytokines such as NF-κB.

Previous posts have described how the 3D structure of chromatin in the nucleus is increasingly critical in the regulation of genes. Long RNAs that do not make proteins (long non coding RNAs or lncRNAs) influence the 3D structure and can have wide effects in many parts of the genes at the same time. Recently, hundreds of different long RNAs have been found that are part of this pattern receptor process and are critical in immune response. They have influences increase and decreasing different kinds of immune cytokines. They, also, determine which immune cells are produced for the situation.

Altering Proteins for Regulation

From Stillnotelf

From Stillnotelf

Proteins are tagged with phosphates and ubiquitin molecules by kinases, phosphatases and other enzymes. Surprisingly, methylation and acetylation that is used in DNA and histones are, also, used in this special immune regulation. They occur through special enzymes. One particular factor stimulates interferon, the vital molecule that helps fight DNA viruses and bacteria. This factor is produced in ER and Golgi and activates multiple ubiquitin tags that work for and against the inflammation.

Adding methyl groups to lysine amino acids in part of the NF-κB molecule, also, regulates pattern receptors. This process can be modified in many different ways as well. Protein factors are, also, acetylated triggering a cascade that takes off phosphorus tags in other molecules that inhibits innate immune responses. These methylations and acetylations of proteins are very unusual and are critical feedback that regulates the immune responses.

Regulation by Metabolic Signaling

From Agrotman

From Agrotman

Previous posts have shown how what are considered ordinary metabolic cycles, such as respiration and glycolysis, can have many of the materials in the cycle serve a second function as triggers for cascades that signal to the nucleus and regulate genes. In dendritic cells, for example, when TLR receptors are triggered, they radically alter glycolysis pathways to produce much more energy and breakdown of materials. These changes help dendritic cells and other immune cells.

A previous post showed how these metabolic signals are a critical part of the way T cells can alter their functions so dramatically. In this case, succinate stimulates inflammation, triggering IL-1β. This alters cell compartments by providing different lipids in the membranes and structures. Similarly, other factors regulate increased and decreased inflammation, like lipoproteins LDL and CD36 modulating the inflammasome structure (the inflammasome is a large complex multi protein structure that is machinery to maintain inflammation). Omega-3 fatty acids inhibit the inflammasome and NF-κB and increase programmed cell death (autophagy). Prostoglandin E2 (well known to be involved in pain and inflammation) is involved in response to virus infections.

There are many other examples of metabolic cascades in the immune process providing more complex feedback loops. Ketone bodies (acetone, aceto-acetic acid and beta-hydroxybutyric acid) come from fatty acids and provide energy during starvation, lack of carbohydrates, extreme exercise and diet. The stimulate cytokines IL-1b and IL-18, which work against inflammation. (This may be why less calories lowers inflammation).

Inhibitors of Receptors

From Taraxacum

From Taraxacum

Special factors take off the phosphate and ubiquitin tags or stop signaling in other ways. These are enzymes involved in other processes that are stimulated specially for this task to stop inflammation that can be damaging. These enzymes, such as ubiquitin ligase and neuroregulin degradation protein (NRDP1) stop infections aimed at viruses, but at the same time stop many other cytokines that can be harmful. There are many different types that regulate the TLR receptors and maintain the general tissues from harm. There are other factors triggered by the pattern receptors that specifically stop cytokines such as IFNb

Amplifiers of Receptor Effects

From Muessig

From Muessig

Along with the many negative feed back loops and competing processes, there are specific mechanisms that increase the signal from the pattern receptors. One of these is a phosphatase enzyme.

Several pathways both strengthen and decrease the signals for cytokines in multiple ways. Some can increase the fight against viruses while limiting the over use of inflammation in the tissues. A large number of ubiquitin ligases (TRIM) have various ways that they increase the strength and length of the cytokine response.

Another mechanism involves LPS using MHC class II molecules (see post on immune and nervous system). These increase the signals in other complex pathways. There are transcription factors that also perform this function.

Many Different Signals for Innate Immunity

N0013888 HIV virus budding from T lymphocyteThere are a very large number of different dangerous particles that are picked up by pattern recognition receptors, and an even larger number of possible reactions. With all of these overlapping cascades, regulation is extremely important for the organism. In fact, these have to work together.

Cooperation: There are many examples where pathways work together to increase the response. One way this occurs is by building bundles of different proteins that have similar effects but can be modified for particular situations. Some combinations work with particular bacteria others with fungus. This can work both through altering the receptors effects as well as altering the cascades that are triggered before they stimulate the cytokines.

From TimVickers

From TimVickers

Augmentation: These different signals can work together and greatly increase the signal. When it is determined that an even greater response is necessary these multiple pathways increase the force of the inflammation. This, most often, happens through altering specific parts of the cascade that is triggered by the receptors.

The inflammasome structure is influenced in various ways from the receptors. An example is when NF-κB is stimulated it increases the gene products of IL1B, which increases pro-IL-1β. At the same time another process alters pro-IL-1β to IL-1β. These same pathways can produce many other results. Some create a pathway where an inflammasome is established outside of the cell. These may, on their own, continue to stimulate inflammation. Communication between various inflammasomes is an important way that the signals stay enhanced.

Inhibition: The various types of receptors have ways of influencing each other in different ways. Communication between TLR and NLRs, for example, can suppress each other’s signals by complex feedback loops. Each can, also, produce states where the immune cells allow inflammation to continue or to become more careful of reactions against tissue that can be too strong. LPS is vital in these regulatory cascades that affect many different cytokines in diverse mechanisms. Most commonly, the NLR signal inhibits the TLR signal, but not always. Colitis is the result of faulty mechanisms of this type involving NF-κB cytokine.

PD FEATURE WIK 800px-SalmonellaNIAIDAnother example is when flu virus increases bacterial infections through complex interactions. The response to the virus with interferon suppresses the NF-κB cytokine through a complex pathway. Also, other mechanisms contribute to this by inhibiting the ability of the tissue to fight off damage.

Positive Feedback with Complement: The complement system is a complex cascade that independently activates responses to invasion of microbes for innate immunity. The pattern receptor pathways work by themselves much of the time, but, also have interactions with complement usually with positive feedback to increase the responses. TLR can stimulate complement and complement can increase TLR responses. Some have considered that they form a complex together, but in fact the interactions are much more complex and variable including many factors that mediate both.

In one example, LPS molecules that trigger TLRs, also, stimulate complement, especially at 5a (one of the many steps of the complement cascade). The 5a and LPS work together increase many cytokines together such as TNF, IL-1β and IL-6 and NF-κB.

PD Necroptosis_Pathway_DiagramNegative Feedback: In different mechanisms, NLR provide negative feedback to inhibit TLR responses. These mechanisms involve elaborate cascades using ubiquitin tags and enzymes. These can work through influencing the inflammasomes that are built to promote inflammation. One of these mechanisms is critical in the creation of rheumatoid arthritis. They involve two complex processes called pyroptosis (a special form of programmed cell death with caspace enzymes that, also, increases inflammation cytokines) and necroptosis (another type of cell death that doesn’t use caspace that causes more cytokines.)

Very Complex Regulation of Pattern Receptors

Nucleosomes With Dna ModelRegulation involves a very large number of factors and processes. These include genetic stimulation and inhibition, epigenetic tags, alteration of proteins, control of metabolism, building of nano machines and responding to the environment. There are many factors that increase and many that inhibit processes. The risks in either direction is great—super-infection or chronic autoimmune diseases.

Many of these processes converge on triggering genes of specific cytokines such as interferons and nuclear factor-κB (NF-κB). There are special regulatory factors that create many different effects at the same genes. Also, the regulation occurs differently in each different tissue of the body, and with the various kinds of immune cells involved with particular unique microbes.

From EldritchKnot

From EldritchKnot

Somehow, the receptors alter pathways and cascades in many different cells. These altered pathways create signals such as specific cytokines that communicate between cells and alter the processes in the other cells. These factors can be separated in the different organelles, so that these organelles are also important in the regulation. Metabolic cycles are altered that influence the rapid increase of certain types of immune cells for the job at hand.

As well as affecting genes, epigenetic tags are, also critical in these processes, making it much more complex. How do these receptors trigger these epigenetic behaviors? When specific factors alter genes, they also trigger combined use of very particular enzymes through other processes. Unique types of programmed cell death are part of these methods.

Diseases Related to Pattern Receptors

Increasingly, the processes mentioned here are found to be extremely relevant in important diseases. A short list includes diseases of the gut (inflammatory bowel disease, food allergies and damage to the gut), liver disease (viral hepatitis, metabolic cirrhosis, fibrosis, and alcoholic cirrhosis), heart disease (atherosclerosis, carditis), metabolic (diabetes, obesity) and brain (neuro inflammation, stroke, Alzheimer’s, lupus, MS, chronic pain).

Vast Complexity of Immune Pattern Recognition Receptors

B0004153 White blood cell - polymorphonuclear leucocyteFor many years, the vast array of immune responses seemed unfathomable. Discovery of complex effects of pattern receptors has greatly advanced understanding of the extremely varied responses to microbes with different kinds of inflammation. Regulation of these many different responses is just being discovered. It involves a large number of different receptors, factors and cells, including metabolic cycles.

Where is the regulation for all of this? How can the wireless brain of the immune system coordinate such an immense regulatory network in many different cells at once and on many different orders of magnitude? Is this not an example of extraordinary cellular intelligence and inter cellular intelligence? Where does this intelligence come from?

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  • IntelligentAnimation

    “When it is determined that an even greater response is necessary these multiple pathways increase the force of the inflammation.”
    Determined by whom? The wireless brain of the immune system, I suppose.
    When I was younger and bought into materialism and Darwinian foolishness, I assumed that functional biological activities were standard chemistry and that the specific chemicals were merely forcing a particular predictable chemical outcome that could not be avoided.
    However, now that I realize that multiple different paths are taken to the same functional outcome, I know that my original ideas can not be correct. Lieff spells out 5 different ways that the pattern recognition receptors of our immune system are regulated. He also correctly notes similar and related processes in epigenetics.
    It can not be an unavoidable chemical pathway if it takes multiple varied pathways using various chemicals and with various interactions – all leading to the same outcome of life saving function. The clear consistency is the GOAL is achieved and the inconsistency is in how we get to the goal. Life is ubiquitously goal-directed.
    All of the questions in the last paragraph of the post are rhetorical, thus they answer themselves. Can I focus on the word “wireless”? Yes, the brain has wiring, but the wiring is changing through Hebbian neuroplasticity, hence the changes to the wiring are also quite wireless. Axons are “wires” but they extend and enhance without wires, without an electrician intelligently running the wires. It is still an immaterial intelligent process, that uses the materials at hand as a tool, not an originator.
    The immune system, however has even less indication of a physical tightly controlled communication network, but the highways of the immune system are blood vessels. There are forces at hand controlling the blood, such as the heart and arteriole muscles, but these are rather uniform in transporting all contents in the same circulatory routes.
    The immune system works rather independently of the larger picture. It uses PRR’s and tags and, well… “determining” need. It also moves toward addressing the need and meeting goals, not simply going with the flow of standard physic-chemical forces.

    • the_professeur

      “When it is determined that an even greater response is necessary these
      multiple pathways increase the force of the inflammation.”
      Determined by whom?

      An interesting question. The answers you get are determined by the questions you ask. While I may ask a quite different question, we both may not ask a question that sheds light on a final answer.

      One thing that stood out to me while reading this article is the incredible complexity involved in the processes and the multiple feedback loops in the signalling, etc.

      This gives me a greater appreciation for biological processes and how holographic they seem to be set up.

      When I closely examine a human-designed machine, it can seem complex at first and then be revealed as much simpler the more I look. Biological processes only turn out to be more complex on closer examination.

      • Roy Niles

        As long as you’re convinced that immaterial information exists, then there’s no point in arguing with you further.
        If you believe in immaterial power, you’re in line with the believers of an immterial god.

    • Roy Niles

      “It is still an immaterial intelligent process, that uses the materials at hand as a tool, not an originator.”
      The process cannot use a tool without having a powered force to use it. All such forces must be used for intelligent purposes, but that intelligence can’t operate without a physical component available to add power to its forcefulness.
      Electricity is a good example, as even without a conducting channel, it supplies its own materials to consrtuct its force fields.

      • IntelligentAnimation

        Yes, there are a lot of mysteries in the understanding of intelligence, consciousness and related mental states.

        “All such forces must be used for intelligent purposes, but that intelligence can’t operate without a physical component available to add power to its forcefulness.”

        I’m not entirely sure what you are saying here, but it sounds like you are saying intelligence needs a physical component. I don’t think we can accurately say that intelligence even HAS a physical component, let alone that it needs one.

        As microtubules are assembling a scaffolding for axon formation or dendritic spines, or as a neurotransmitter is released into a synapse, intelligence is already there, leading the way. The physical aspects follow, if the thought is repetitive or intense, but the intelligence spanned that gap first or at the very least it was aware of the proper location for the physical things to go. And the thoughts ALWAYS come first.
        So it CAN operate independently of the physical.

        I would say it is true to say that physical things enhance the abilities of intelligence, but only because they are intelligently arranged. The brain, like the genome, is a read-write data storage tool, most likely to be used when the information is important enough to focus on. There is no where near enough data in either notepad – the brain or the genome – to be comprehensive information needed for the task at hand. Most of the work is still done by the immaterial teleological forces.
        I would also say one of the best ways of identifying immaterial intelligence is observing its effect on materials, but if wind is blowing a flag, we don’t claim the flag to be a “component” of the wind.
        This is all besides the reality that cells with no brains have high intelligence and even besides Dr Lieff’s wireless mind of the immune system and other evidences of intelligent agency having little need for physical items, yet having a profound impact on the physical.
        There is no PHYSICAL difference between a brain in a dead man and a brain in a live one, but the behavior of the two could not be more different. If there was even a single physical thing found missing in the brains of corpses, then that might be the missing physical component, but until we find it, I see no reason to even suspect such a thing as a physical component of immaterial thought.

        • Roy Niles

          You wrote “I don’t think we can accurately say that intelligence even HAS a physical component, let alone that it needs one.”
          If intelligence didn’t need a physical component, there would seemingy have been no physical systems in the universe that have either used it or been used by it to evolve.
          There would, for example, be no such thing as a wave function, which a physicist might tell you is energy convertible to physical mass, and that in theory, no wave function, anywhere, then no big bang — and more importantly no forces that have been able to intelligently construct our various physical systems without having the physical powers of intelligence to construct those systems that have learned to serve a variety of intelligent purposes.
          But if you still insist that immaterial intelligence exerts some form of non-physicsl working forces within our cells, please explain how such forceful powers can exist at all in within a universe where intelligence seems to you to have somehow emerged on earth without a physical presence.

          • Roy Niles

            IntelligentAnimation, I should also add this comment that you wrote: “There is no PHYSICAL difference between a brain in a dead man and a brain in a live one, but the behavior of the two could not be more different. If there was even a single physical thing found missing in the brains of corpses, then that might be the missing physical component, but until we find it, I see no reason to even suspect such a thing as a physical component of immaterial thought.”
            The difference is that there is NO behavior in the dead brain, and there is powered behavior in the live one.
            And the powered behavior is obvious;y being made to move. And to argue that the movement is being caused by immaterial forces is bereft of supporting evidence.

          • IntelligentAnimation

            So unless we insert an undetermined piece of material into thought for no apparent reason, quantum waveforms will cease to exist and even the Big Bang will collapse? Care to explain any of these claims and how you derived them?

            Ironically, you bring up two scientific facts that are highly damaging to materialistic religious beliefs. In particular, we DO know that information WILL collapse a waveform… and information is quite immaterial. Oh sure, it is measured and documented data, but it has to be available to a conscious entity to collapse a wave. Something as immaterial as potential knowledge is what causes specific attributes to particles.

            I am having a hard time following your point, but let me be clear about mine: Intelligent agency has an EFFECT ON matter, but it isn’t composed of matter. If a boy throws a ball, both the ball and the arm are made of matter, but the action only took place because of the will of the boy, and will is NOT made of matter. The arm is no more a “component” of the boy’s free will than the ball is.

            RN: “If intelligence didn’t need a physical component, there would seemingy have been no physical systems in the universe that have either used it or been used by it to evolve.”

            Huh? Matter can be “used by” intelligence, so yes, intelligence CAN use matter, but there is no reason to believe that it NEEDS to. Also, even if it does use matter as a tool, that doesn’t mean that the matter is a “component” of intelligence. If I use a water hose, is the water hose a part of me?

            RN: “intelligence seems to you to have somehow emerged on earth without a physical presence.”
            Of course there is matter “present”, but that does not mean it is a “component” of intelligence. I also would avoid the word “emerged” if you are trying to say that at one point it didn’t exist and then “poof”, it did. The only “emerging” involved in intelligence is in the fact that it learns, remembers, problem solves and communicates with others over time.
            Yes the BEHAVIOR of a living brain is much different than a dead one, but behavior is not a material. I’m not sure what you mean by “powered” behavior. The dead brain has all of the electrolytes, all of the ATP and all of the materials present in the live one. It just acts completely different. It acts like it is alive and intelligent, because it is.
            Can you clarify: Are you saying that you think intelligence is part material and part immaterial? If so, can you elaborate on which of these two alleged components are the one causing functional, relevant and coherent thought?

          • Roy Niles

            As long as you’re convinced that immaterial information exists, then there’s no point in arguing with you further.
            If you believe in immaterial power, you’re in line with the believers of an immaterial god.

          • IntelligentAnimation

            I’m not sure why you are bringing religious concepts into a scientific discussion, but I have no concerns whatsoever if what the facts tell me is closer to – or further from – a religious belief. I suggest you take the same unbiased approach.
            Calling intelligence a form of energy, or perhaps a force of nature, makes more sense than calling it matter or insisting it is made of materials. However, science has found that it becomes rather problematic when trying to measure it, predict it, or when applying the law of conservation of energy, or any laws of thermodynamics.
            I should add that not all forms of energy are material or physical. Gravitational energy, potential kinetic energy and others are not really a physical thing. They AFFECT the physical, and are mathematically consistent as well. While there are physical things involved, reduced to the phenomenons themselves. gravity and PKE are not physical. Just because the materialist religion accepts gravity and PKE does not make those things material.
            But is intelligence like gravity or PKE? Not so much.
            Not only can we not see it, weigh it or touch it, but it can self-restrain and worse, self-expand. All intelligence in the entire biosphere came from one intelligent cell or perhaps protocell. We gain intelligence within our lifetimes as well, not physically, but as we gain information and even general insights, intuitions or feelings.
            Of course, intelligence is far harder than that to categorize and quantify mathematically. It remembers, problem solves, decides and even subjectively experiences. Trying to reconcile it with other energy forms is like wrestling a greased pig.
            You didn’t answer any of my other questions, but I’ll keep asking: Do you think that all energy thinks and subjectively experiences, but they just have no free will or self-improvement skills?
            If it is an energy, then it is an energy that can intentionally use other forms of energy. This reality brings us back to the realization that intelligent agency is a phenomenon capable of manipulating matter and energy, which means it doesn’t need to BE an energy or have energy as a component.
            We have a long way to go on understanding intelligent agency. Materialists have been trying to deny it, twist it and censor science for too long. We need to keep our minds open and research this. Intelligence clearly DOES exist and I would argue it is the most certain of all facts. We do not know if it has a physical component or if it merely affects physical things.
            If we reduce it down, at some point it is an unavoidable reality that something non-physical is subjectively experiencing, deciding by free will and affecting matter and energy to cause functional order. Call it what you want, but lets research it, not pretend it doesn’t exist or insist that it NEEDS a physical component.

          • Roy Niles

            To me this is more of a philosophical discussion where we bring logic to bear on scientific misunderstandings. You can’t “research” intelligence by putting it in a test tube full of chemicals and/or zapping it with a photon gun. You will need to try to determine why it exists and what its purposes have evolved to be before you can begin to understand its nature.
            It’s logical to assume intelligence is NOT a godlike substance because, when you assume it has no material essence, that’s what you are presuming that it is, a supernaturally eternal component of nature. And I can agree that, logically, it must have had and will continue to have an eternal existence, but scientifically, we have no answer as to how something that has no beginning has yet begun. That’s the “unbiased” way to approach a philosophical problem, i.e., to use logic as a scientific tool.
            And logic tells us that to purposefully use force we need energy and if, as you seem to believe, energy has no material component, what does it use to “force’ material to move? And if energy has no intelligent component, how does your version of intelligence, that’s devoid of either energy or material, force anything to react to it’s “will” at all?
            And if you pooh pooh that as a religious question, you fail to understand that all religions are based on the intelligent misunderstandings of philosophy and the logical versions of it that we now call science.
            And a science that somehow you have found to run on mathematics rather than logic, assuming that mathematics can determine why we have intelligence where logic can’t. Or, as you’ve brought into the conversation, that math can tell us something about determination and free will.
            or about the intelligence that is, philosophically speaking, the determiner of everything that in a deterministic universe would have been illogically or non-logically determined in the past by an immaterial godlike creator.
            Intelligence, in my philosophical view, is a strategic system, that absolutely needs a physical component to have the power to constructively determine anything, and to build, intelligently, whatever our randomly changing nature requires it to do.
            A randomness that may, itself, have been intelligently devised for evolution to exist at all.
            And you can tell us, intelligently, that strategies do not exist for such a purpose, but in doing so, you haven’t used the logic that intelligence has, in all mathematical probability, created for that very purpose.
            And when you deny that energy needs both intelligence and matter to do its operative duties, using what you consider to be different varieties of itself, which thus must have produced its evolutionary results by willful accidents, is, to me, illogical and intelligently powerless.
            Okay I’m starting to have a little too much fun here, so it’s time to stop. But when you’ve said things like “at some point it is an unavoidable reality that something non-physical is subjectively experiencing, deciding by free will and affecting matter and energy to cause functional order,” I can’t help but chuckle, unavoidably, at the lack of logic. The point being, unavoidably, that intelligence invented logic but hasn’t yet evolved the biological beings that can use it with immaterial perfection.

          • IntelligentAnimation

            For someone who uses the word “logic” so much it seems you think you own the word, your message is an illogical mess. You are clearly obsessed with religion even though nobody else is discussing anything religious, and you misrepresent my standpoint far too much.

            I did not call intelligence a “god-like substance”. “God” is not a scientific word and I specifically stated that we see no sign of any substance at all. Lacking a physical material does not mean “perfection” or “supernatural” or “god-like”.

            That we can’t put intelligence in a test tube is MY point. If it was physical, we could, but it is not physical. That’s the point being made.

            You chastise me for supposedly saying intelligence is eternal, which I never mentioned, then in the next breath you state that it IS eternal. “logically, it must have had and will continue to have an eternal existence.”
            While I would certainly agree that intelligence can not be the result of random chemicals and that some form of intelligence had to have always existed, I would steer clear of the word “eternal” because it brings in concepts such as infinity and our understanding of a zero-time existence that may be factual but hard to fathom.

            You accuse me of “assuming that mathematics can determine why we have intelligence where logic can’t.” I never said that either. Mathematics can determine that intelligence is at work, but not “why” it works. You do a lousy job of re-phrasing my words.

            RN: “And when you deny that energy needs both intelligence and its material component to do its operative duties, using what you consider to be different varieties of itself, which thus must have produced its evolutionary results by willful yet powerless accidents, this denial is, to me, illogical and intelligently useless.”

            Wow. I never said evolution is an accident. It is an intelligent process without doubt. You are the one bringing up “randomness” and determinism. There is no such thing as a “willful accident” as that would be a paradox.

            Energy has “duties”? I’m trying to decipher this one-sentence paragraph. Are you saying that energy needs both intelligence and a material? I would like to know what I am supposedly denying, please.

            For the record, I have said that there could be some justification for considering intelligence an energy, but I think it is an awkward categorization that does not encapsulate all of what intelligence does and is. I accept the term “teleological forces” that I have heard used elsewhere, at least as a working model.

            You still haven’t explained why the entire Big Bang collapses unless we can find a material component to intelligence and I am still left wondering why you use the word “component” unless you consider intelligence partly immaterial. Do you think that intelligence is PARTLY immaterial? If so, maybe we are basically saying the same thing.
            I suggest you calm down, keep religious bias out of this and set aside the histrionics for rational conversation on a challenging topic.

          • Roy Niles

            I suggest that YOU calm down as I’m not the one that’s getting angry here. To remind you of what I actually wrote about religion – that you now claim I’m obsessed with, it’s this:
            “It’s logical to assume intelligence is NOT a godlike substance because, when you assume it has no material essence, that’s what you are presuming that it is, a supernaturally eternal component of nature.”
            To translate that, I was hoping to make it clear that it’s you who are presuming that there is such a thing as an immaterial substance in the universe and especially in the biological systems of the earth that exerts power without an iota of a material component. And the dictionary definition of component is “a part or element of a larger whole.” And no, energy has no immaterial component, but yet it seems to use a different strategic (as in intellligent) component in whatever duties that we ask it to perform for us, and evidently in the duties that it has performed in nature for (and again I’ll use the word that you seem to hate) “eternity.” Which is defined as “infinite or unending time.”

            And I note you are having trouble with the word teleological as in the teleological argument that only you’ve made mention of (why, I’m not sure), which is defined as “the argument for the existence of God from the evidence of order, and hence design, in nature.” And of course I’m arguing that you don’t need some immaterial element such as something godlike to explain intelligent designing as a naturally intelligent force that’s been able to intelligently evolve to logically design and redesign itself. (Using your referenced mathematics and not being logically used by it of course.)
            Logic being another word that seems to bother you, as either it’s myself who, as you claim, uses it too much, or you, as I claim, doesn’t use it quite enough.
            But then again, you keep saying you want a rational conversation, and then again, and yet again, get angry when I insist that a rational analysis requires the use of logic as evidence, and that your immaterial forces are, by logical argument alone, not logical.
            So we’ve reached an impasse, since I can’t seem to do anything but try to use what I call logic, and you can’t seem to do anything other than pooh pooh what you see as a defective version of it.

          • IntelligentAnimation

            I can assure you that I have no anger, trouble or hatred for you or any word that has been said and I apologize if I mistakenly figured that something was bothering you. I would like to get some clarity as to what you are actually saying.

            I asked if you think that intelligence is PARTLY material or FULLY material. You answered that “energy has no immaterial component” but that was not what I asked (nor is it true). I will assume this was a mistake on your part, but this is now at least the third time I am asking this: Do you think that intelligence is partly made of materials or fully made of materials?

            The definition of teleology is “a reason or explanation for something in function of its end, purpose, or goal.” “Telos” means “purpose” or “goal” and “logos” means “reason” or “explanation”. Once again you are jumping to religious ideas that are not being said by anyone but yourself.
            You seem to think (correct me if I misunderstand) that intelligence is either made of physical stuff or it is a god, which you seem to see as a concern. Why could it not just be neither a god nor a material? I can’t put the number 3 into a test tube either because it is not a physical thing, but numeric values are not gods either.
            Are you really just trying to prop up atheist beliefs or something? If so, I have no interest in your personal beliefs. I am interested in science and what the evidence shows us. We need to get all religious and atheist bias out of this and any scientific discussion.
            If intelligence is physical, then why can we not weigh it, see it or hold it? If it is eternal, then how did it exist before matter and energy existed? Why do you insist that thinking, remembering, free will, learning and subjectively experiencing are made up of physical stuff?
            We are not at an impasse. I have not figured out what you are trying to say and you obviously don’t know what I am saying either. Could you answer some of these questions?

          • Roy Niles

            I’m using religion as an example of where your arguments would lead us, but otherwise I’m neither for or against it, or any other workable phenomena of our varied cultures.
            Intelligence is a component of every particle in the universe, and thus it’s not immaterial in my view at all.
            So if you want to use the word physical to describe energy, then yes as a component of energy, intelligence is a physical component.
            But if you want call a natural force of nature immaterial, then it’s OK by me if you see intelligence as immaterial. But I cannot.
            As far as being interested in what the scientific evidence shows us, that’s all very fine, but if you want to ignore the philosophical side of scientific research, which involves the study of our elemental purposes, you’ll have a hard time discovering what intelligence is or does.
            As it is, you don’t seem to want to use logical hypotheses as a form of evidence, and I can’t persuade you otherwise.
            And I don’t feel at this point that I have to.
            We don’t think alike, and that’s where the impasse lies. So I agree to disagree here even if you don’t.

          • IntelligentAnimation

            I would love a little bit of logic, Roy, but this is what I am hearing:
            A is a component of B.
            B is a component of A.
            How is this even logically possible, and why don’t you have any evidence for any of this?
            You say intelligence IS energy, then that it is a “component” of energy.
            Yet intelligence HAS a physical component, you say, and that component is energy.
            So energy is a component of intelligence and intelligence is a component of energy. Pull yourself in the air by your bootstraps much?
            Intelligence is also in every particle in the universe, according to your assessment. I presume this includes elementary particles that are calculated to have no spatial dimensions or zero size. Where in this point mass is the “physical” intelligence and how big is it? Can this physical component fall off the particle in a supercollider or during particle annihilation?
            How many bits of information can be stored in say, a lepton, versus a hadron versus a neutrino?
            All matter is quantized, IOW digital, not analog. Is there intelligence in the space between particles and, if not, can the intelligent agency on one particle communicate across the space to another particle?
            How do you know this physical intelligence is there, again?

          • Roy Niles

            Actually I never said or had to that A is a component of B and that B is a component of A, because it’s a rather obvious fact that if one thing is a component of another, they are likely to both be components of each other. In any case if that’s the best argument you can make in support if your immaterial non-component alternatives, good luck.

            Let’s see now, you ask, “Is there intelligence in the space between particles and, if not, can the intelligent agency on one particle communicate across the space to another particle?”
            There is no necessity to add “agency” where it’s more accurate to refer to an intelligent entity. (Unless you are admitting that the agency itself must be intelligent.)
            As to the space between particles, did you ever ask yourself what sort of force it is that holds those particle together within that space – a space that you seem to consider must hold nothing – nothing being as impossible to exist as your immaterially!

            And again you turn to math as an explanation that if a particle has zero size, it’s immaterial as a particle. And your apparent argument is that if you have a particle that is no particle it can’t be an intelligent particle. But as I’ve noted before, your use of logic as a form of evidence is a bit bizarre.

            Actually I should not have bothered to answer this rather sardonic attempt of yours at a response, but at least it’s more amusing than your angry diatribes were.

            In any case, you’ve asked again at the end of this silliness that, how do I know this physical intelligence is there, and my answer is, as in the punchline of the old joke, everything intelligent gotta be hanging around in the closet somewhere.

          • IntelligentAnimation

            I was beginning to wonder if this was all your unique pipe dream or if you were getting all of this from some source. You seem to be advocating a strange mix of materialism and intelligent entities literally everywhere.
            I wish you would give a straight answer a bit more often. You really didn’t answer my question as to whether or not intelligence exists between particles or only on particles. I am well aware that there is force between particles, but I asked about intelligence.
            No, it is not true that two things can be components of each other in both directions. Hydrogen is a component of water, but water is not a component of hydrogen. Quarks are a component of bosons, but bosons are not a component of quarks. Hair s a component of mammals but mammals are not a component of hair. You are apparently just blabbering because you don’t know any answers that make sense.
            You claim that there is a physical chunk of intelligence attached to every particle in the universe. What holds them together? The color force? Are you really saying that, no matter what, they can NOT separate? Does one cause the other? If not, how did they disperse so evenly? There are 1 x 10 to the 90th particles in the universe. Does that mean there are that many pieces of intelligence?
            What are the physical properties of physical intelligence? Does it decay? Does it have an electric charge? Polarization or spin? Any mass? Is it water soluble? What does it look like?
            If intelligence must stay with a particle, then why does it appear that conscious intelligence leaves an organism when it dies? Does evidence have any relevance to you at all?
            I would certainly agree that evolution is an intelligent response to a stimulus, but is a drought or an ice age an “intelligent” stimulus?
            I think the extent of your “science” is when you insisted that it is impossible for something to exist without being made of materials, as if matter is the be-all, end-all. That is not a philosophy. That is a religious belief that has no supporting evidence.
            I am quite open minded on this. All you need to do is show me this “physical intelligence” or demonstrate that it exists somehow.
            Otherwise, all I have is your petty beliefs.

          • Roy Niles

            Are you really so bent on winning an argument that you don’t recognize that we were talking about system components? And so bent on pretending that I said several other different things that I did not say to boot? Such as having me making a claim that there’s a physical chunk of intelligence attached to every particle in the universe. Every particle in the universe has been intelligently constructed, or otherwise no particles could consistently react with other particles as predicted by what you don’t seem to understand are the intelligently operative laws of physics.
            And yes, if an entity is intelligently constructed, it’s for the purpose of constantly reacting to nature’s forces by using that intelligence for the purposes it was meant to serve. Yes, I know this is so far over your head that you can’t deal with it logically, and thus your usual recource is to lie about what you otherwise would have to admit is not only your philosophical ignorance but your lack of scientific understanding to boot.
            I’m not going to bother going down the list of all the ridiculous contentions that you pretend are somehow consequential to what you are pretending I have actually been contending.
            (I would have used the phrase “logically consequential” but you are so consistently.and abjectly illogical that I couldn’t.)
            Asking “is a drought or an ice age an “intelligent” stimulus?” makes no sense at all. Intelligence is a trial and error system which you apparently have never been taught to understand. And it operates in an indeterminate universe, which again you seem to have no idea as to how such a universal system has evolved. So instead you blabber on with one of the stupidest questions that someone who claims to be scientist would ever think made sense. Although what seems to be a belief of yours that there is a vacuum of empty space between all particles is even stupider. And yet you then have the gall to claim you have an open mind. If so, it’s one with nothing there that’s in any danger of falling out.
            And my so called petty beliefs are not just mine, but those of several others who have written books about the nature of intelligence. Including the one I cited that was co-authored by Dorion Sagan, who also did some editing of a book of mine.
            So whoever you are, your lack of understanding of either science or philosophy points to the probability that you’re a fraud. Good luck with that.

          • IntelligentAnimation

            I’m not “bent on” anything. I’m really just trying to get a handle on what the hell you are trying to say. If you didn’t feel the need to litter your messages with personal insults you might actually have time to explain yourself a bit.
            You said intelligence is on every particle in the universe and that it is a physical thing. This brings up questions such as whether or not the two can be separated, which is a legitimate question.
            You said evolution is an intelligent response to an intelligent stimulus. If ice ages or droughts are not the type of stimuli you were meaning, can you give an example of an “intelligent stimulus”? Yes, the question seems nonsensical for me to ask, but only because your claim was nonsensical and I am asking you about it. Was it a typo?
            If you didn’t really intend to say that intelligence is a component of energy AND energy is a component of intelligence, which is paradoxically impossible, you could simply correct yourself and let us know which half of those statements are your true position. You were doing better when you said intelligence is “probably” an energy, but then you got caught up in claiming all sorts of cross-referenced “components”.
            We simply don’t agree about your claim that intelligence is physical. I note that we have never seen any physical thing called intelligence that can be weighed, seen or touched. It is also highly nuanced in ways other phenomena are not.
            If it is an energy, it is the only energy which can choose whether or not to exert itself by free will, which would seem like a violation of the law of conservation of energy, and we have no evidence that any other energy subjectively experiences in a self-aware manner.
            You make a lot of claims here that I supposedly don’t understand concepts that were not even a part of the discussion. I’m probably much closer to agreeing with you than you understand, but your words in this discussion have been a complete mess of confusion.

          • Roy Niles

            “Yes, the question seems nonsensical for me to ask, but only because your claim was nonsensical and I am asking you about it. Was it a typo?”

            Somehow you consider insults like that to pass as being legitimately argumentative, and I consider them to be another sign that, first, there’s no way I can give an answer to someone who can’t ask a proper question, and second, there’s no way now that you can convince me you’re not a fraud..

          • Roy Niles

            To those who have been following me on disqus, etc., I feel obliged, in fairness, to state this:
            Further consideration prompts me to reconsider the conviction that this guy (or gal) could have the highly clever characteristics of a professional fraud.
            For example, this questionable statement in particular was a rather illogical one for even the average fraudster to argumentatively present:

            “If you didn’t really intend to say that intelligence is a component of energy AND energy is a component of intelligence, which is paradoxically impossible, you could simply correct yourself and let us know which half of those statements are your true position.”

            But if I didn’t intend to say what I did, I would not have said it, nor had a different “true position,” and this person’s sarcasm as a substitute for a valid argument becomes obvious.
            And the logical facts are, as I’ve posited, that if energy cannot be operative without intelligence and intelligence cannot exist without energy, they certainly will have to be components of the same systematic physical function that we’ve defined as energy. I.e., the strength and vitality required for sustained physical or mental activity.
            And since a paradox is defined as self contradictory or senseless, I’d argue that the paradoxical impossibility lies with the claim of the arguer that he has posed anything that resembles a logical argument.
            I expect that he won’t be able to resist some sort of insult in response, but again, I’ll have to leave it without a direct reply. Argument by insult is not my style, even though this person has seemed to consider arguments that logically counter his to be insulting.

          • IntelligentAnimation

            So both Intelligence (I) and Energy (E) are components of Energy? You have also stated that I is a form of E. So both E and E are components of E.

            Either you are saying E is a component of itself, which is not particularly enlightening or possible, or else you are saying that different forms of energy are a component of some other type of energy. If so, then what is the component form and what is the composite form? Or are you making up new forms of E as we go along?

            All this calling everything a component of itself while also a component of something that is also a component of a component is not helpful. The word “component” has a clear meaning, which is that it is part of the make-up of a composite unit, yet you are being very unclear about it.

            And you wonder why I keep having to ask further questions? It seems like every post confuses things more, and you are an author. I don’t even know if I agree or disagree with you, since you aren’t able to explain anything. I am not the one slinging out insults. You keep calling me “fraud”, an odd insult and I don’t know what you mean by that either, nor do I care.

            RN: “energy cannot be operative without intelligence.”

            Dare I even ask how you come to this conclusion? So sunlight can not create heat without intelligence? Does this mean that E can exist without I, but it can not actually “operate” or “serve its duties” as you put it? What does intelligence do to make E operative and how does it do it?

            If Intelligence can not exist without E and yet I is eternal, then E must also be eternal.

            What does the E do to cause abstract thinking or self-awareness? Is it various vibrations of this energy or is it digital bits of information? (If so, what caused the vibrations or bits?) Or is it a physical thing with a non-physical quality? Is intelligence digital or analog?
            Can you narrow this down a little bit as to what you think is actually taking place in intelligent thought?

          • Roy Niles

            The usual bullshit reply that doesn’t deserve a response. Intelligence is the component of energy that has allowed it to serve its purposes. It’s necessary companion is the mass that would not exist to serve any purposes without intelligence.
            We have tradionally called the mass energy

          • Roy Niles

            To other readers, I’m sure you can see that it’s obvious that my erstwhile opponent is up to his old tricks of pretending that he misunderstands my message, He has no other way to rebut it except to lie. He would have energy as operating with intelligent consistency with nothing but some weird concept of mechanical efficiency.
            Yes, I called the mass that energy consists of as energy, since there hasn’t been any other name for its functional system except that one.
            But its definition has been as follows: “the strength and vitality required for sustained physical or mental activity.” No mention there of intelligence, unfortunately. No mention of a mass either.
            So what do I do? I add intelligence as a component of energy, and voila, we have an intelligently operated mass. Which is still what everyone else will continue to call energy, except when they can manufacture a series of lies by calling it something else.
            Like the “open minded” lie when he pretends that intelligence can’t make E (as in energy) operative, yet has no other explanation as to why it does. (Or just accepts that it operates with magical machinations, I presume.)
            Oh, and he seems to think that sunlight creates heat accidentally, and there’s no logically predictable function involved. Yet even real scientists, who don’t believe that accidents happen for a purpose, have conceded that the sun’s activities are logically consistent and predictable.

          • IntelligentAnimation

            You highlighted this quote from a book: “evolution is an intelligent response to an intelligent stimulus.”
            Can you give an example of an intelligent stimulus?

          • Roy Niles

            Read the book.

          • Roy Niles

            Read the book.

          • Roy Niles

            Actually I never said or had to that A is a component of B and that B is a component of A, because it’s a rather obvious fact that if one thing is a component of another, they are likely to both be components of each other. In any case if that’s the best argument you can make in support if your immaterial non-component alternatives, good luck.

            Let’s see now, you ask, “Is there intelligence in the space between particles and, if not, can the intelligent agency on one particle communicate across the space to another particle?”
            There is no necessity to add “agency” where it’s more accurate to refer to an intelligent entity. (Unless you are admitting that the agency itself must be intelligent.)
            As to the space between particles, did you ever ask yourself what sort of force it is that holds those particle together within that space – a space that you seem to consider must hold nothing – nothing being as impossible to exist as your immaterially!

            And again you turn to math as an explanation that if a particle has zero size, it’s immaterial as a particle. And your apparent argument is that if you have a particle that is no particle it can’t be an intelligent particle. But as I’ve noted before, your use of logic as a form of evidence is a bit bizarre.

            Actually I should not have bothered to answer this rather sardonic attempt of yours at a response, but at least it’s more amusing than your angry diatribes were.

            In any case, you’ve asked again at the end of this silliness that, how do I know this physical intelligence is there, and my answer is, as in the punchline of the old joke, everything intelligent gotta be hanging around in the closet somewhere.

          • IntelligentAnimation

            So unless we insert an undetermined piece of material into thought for no apparent reason, quantum waveforms will cease to exist and even the Big Bang will collapse? Care to explain any of these claims and how you derived them?

            Ironically, you bring up two scientific facts that are highly damaging to materialistic religious beliefs. In particular, we DO know that information WILL collapse a waveform… and information is quite immaterial. Oh sure, it is measured and documented data, but it has to be available to a conscious entity to collapse a wave. Something as immaterial as potential knowledge is what causes specific attributes to particles.

            I am having a hard time following your point, but let me be clear about mine: Intelligent agency has an EFFECT ON matter, but it isn’t composed of matter. If a boy throws a ball, both the ball and the arm are made of matter, but the action only took place because of the will of the boy, and will is NOT made of matter. The arm is no more a “component” of the boy’s free will than the ball is.

            RN: “If intelligence didn’t need a physical component, there would seemingy have been no physical systems in the universe that have either used it or been used by it to evolve.”

            Huh? Matter can be “used by” intelligence, so yes, intelligence CAN use matter, but there is no reason to believe that it NEEDS to. Also, even if it does use matter as a tool, that doesn’t mean that the matter is a “component” of intelligence. If I use a water hose, is the water hose a part of me?

            RN: “intelligence seems to you to have somehow emerged on earth without a physical presence.”
            Of course there is matter “present”, but that does not mean it is a “component” of intelligence. I also would avoid the word “emerged” if you are trying to say that at one point it didn’t exist and then “poof”, it did. The only “emerging” involved in intelligence is in the fact that it learns, remembers, problem solves and communicates with others over time.
            Yes the BEHAVIOR of a living brain is much different than a dead one, but behavior is not a material. I’m not sure what you mean by “powered” behavior. The dead brain has all of the electrolytes, all of the ATP and all of the materials present in the live one. It just acts completely different. It acts like it is alive and intelligent, because it is.
            Can you clarify: Are you saying that you think intelligence is part material and part immaterial? If so, can you elaborate on which of these two alleged components are the one causing functional, relevant and coherent thought?