A reaction to not so thoughtful comments of a young otherwise friendly fellow in FB inspired me to ask why the young people who have got through the the basic courses are not only ignorant but sometimes also - well - arrogant. Why they are ignorant is easy to understand but arrogance remains a mystery for me. Personally I was also extremely ignorant as also the my fellow students but quite too shy to be arrogant: could I have been as arrogant as other if I had not been so hopelessly shy? This fellow had not understood much of what I had written - something completely acceptable, understandable, and predictable since something completely new is in question and text book wisdom or what professor said is simply not enough.
So he concluded that I am writing only weird fairy tales and that it seems that I have never heard about mathematics, electrodynamics, or thermodynamics. According to him these fields of science allow to understand biology more or less completely: I do not know whether this wisdom originated form from a text book or whether a professor told it. My FB friend also wanted to know whether I have read any book about biology during my lifetime.
I responded that I have not only heard the word "biology" but have even written a book about quantum consciousness and quantum biology (1000+ something pages). I forgot to mention that I have also written two published books about TGD and there are 17 online books at my homepage (9 of them about quantum biology) plus numerous articles both published articles and at homepage. I told that I have also recently published a long article in a book published by Springer about adelic physics: the goal of adelic physics is to describe the correlates of cognition and consciousness in terms of number theory and whose most important applications are to biology.
I also informed that I have also heard the word "thermodynamics" and even developed what I call p-adic thermodynamics providing a first principle approach to particle massivation replacing Higgs mechanism. I forgot to mention that quantum TGD can be seen formally as a complex square root of thermodynamics replacing Boltzman weights with the complex square roots defining vacuum functionals and that the generalization of so called microcanonical leads to extremely predictive view about scattering amplitudes serving as the building bricks of zero energy states.
1. Importance of philosophical thinking
This discussion once again made manifest both the extreme importance and regrettable lack of philosophical thinking - not only biology but in natural sciences in general. I do not mean with philosophical thinking academic philosophy, which I have found mostly deadly boring. Rather, for me good philosophical thinking means posing critical questions - rather than personal insults.
What we really know and what we do not know? What do we believe and what part of this is just beliefs? Are there facts challenging these beliefs? What is consciousness: is it really a property of something as "-ness" suggests? What is free will? How it manifests itself? Is it an essential aspect of consciousness so that AI hype could be forgotten? Are free will and non-determinism really in conflict with physics as physicalist has decided to believe? Concerning consciousness, what guidelines come from modern, physics, biology, and neuroscience?
In physics critical thinking would have allowed to avoid the numerous fads and fashions that have plagued us during last 4 decades: GUTs that led to the wrong track, inflation theory, various ad hoc models of dark matter postulating some exotic strong AI, supersymmetry in its GUT form, superstring models, loop gravity,...
Critical thinking would have challenged various "interpretations" of quantum theory and we could have continued immediately the work of the fathers of quantum theory rather than waiting for almost a century. Critical thinking would have also inspired the question whether the non-determinism of state function reduction has something to do with free will and how one should generalize the ontology of physics (Copenhagen ontology gives is it up altogether) to build a logically consistent framework.
Unfortunately critical thinking tends to lengthen the time spent in academic assembly line so that it is strongly discouraged. Thinkers tend also to become isolated from their social groups since everyone of us wants desperately to belong to some group and this requires sharing of its beliefs. It is easier to believe what professor and text book tell and get the research position and funding.
People are also very lazy. AI scientist decides that consciousness is running computer program or a property of the network structure or something equally ad hoc: no need to learn huge amount of physics, biology, neuroscience. Biologist decides that biology is nothing but Schrödinger equation and electromagnetism (or mere chemistry as in the older variant of the belief still prevailing). Neuroscientist desides that physicalism is correct and brain is the seat of the consciousness module. Brain as a computer paradigm makes the situation even easier. Physicist decides to believe in physicalism stating in its modern version that all physics reduces to Planck length scale: one can safely forget all other branches of sciences as a kind of taxonomy and specialize to apply one particular algorith to build CV.
2. Basic dogmatics
The key dogmas common to all branches of natural science are physicalism and reductionism. Physicalism states that matter is all that matters and consciousness is mere epiphenomenon and that world is deterministic - in the quantum version of the dogma it obeys statistical determinism. Reductionist sees natural sciences are a victorious march towards shorter and shorter space and time scales. Science is an imperium that grows conquest by conquest.
We are told that super string theorists have taken the last step to Planck scale by building the only possible theory of everything. This step is really gigantic: from electroweak length scale there are 16 orders of magnitude to Planck length scale. Before this every order of magnitude has contained a lot of su4prises but now the situation would be different as already GUT theorists revealed to us.
The surprise was however that the theory in Planck length scale does not allow to predict anything in long length scales: situation is like trying to predict the behavior of initial value sensitive system. The question of philosopher would be obvious: could something have gone wrong? This question has been made by some theoreticians. The decision of elite however seems to be that physics has reached its end. Nothing can be predicted and we should be happy about this marvellous feature of the only possible theory.
This series of conquests is marked by transitions. From biology to biochemistry, from biochemistry in vivo to organic chemistry in vitro, from chemistry to molecular physics, from molecular physics to atomic physics. Then follows a transition from atomic physics to nuclear physics: the assumption is that these two physics have practically nothing to do with each other. There are numerous experimental anomalies found during the last century challenging this belief. "Cold fusion" people were labelled next to criminals for their scandalous claims. Luckily the situation has now changed. But people talking about water memory belong still to the pariah of science.
After this jump we jump from nuclear physics to hadron physics to physics at quark-gluon level and then comes the really really big Planck jump. So simple.
There is however a little problem. Every successful conqueror must build a lot of bridges, without them the maintenance fails. Reductionistic conquerors were so hasty that they did not have time to to build the bridges between these different physics. We do not understand how nuclear physics emerges from hadron physics emerges from quark physics. We do not understand how biochemistry emerges from organic chemistry emerges from molecular physics emerges from atomic physics. But we can decide that this is only a technical difficulty: if we had enough computational power we could fill these gaps.
Actually, I know a couple of finnish fellows who tried to fill a gap. The first one has read from text book that the notion of chemical bond emerges from atomic physics. He wrote a lot of computer programs and did not find a slightest indication for this. Second fellow had learned that cell membrane emerges and started to study a model in which one has just molecules and molecular dynamics simplifying the situation. Not a slightest indication.
3. Restricting the attention to biology and neuroscience
In the following the attention is restricted mostly to the philosophical problems of biology and neuroscience. It however turns that these problems are actually also problems of physics.
3.1 Biology as nothing but biochemistry and electromagnetism
The basic dogmatics says that life is nothing but chemistry plus a little bit of electromagnetism needed to model cell membrane and neuronal membrane. There is also EEG but this is taken as noise due to neural circuits so that there is no need to waste time with it. Luckily, not all experimentalists know or care about dogmatics and have found correlations of EEG with behavior and physiology and they are used as a diagnostic tool. Most of them however refuse to consider seriously the possibility that EEG might possibly communicate something from brain somewhere. Where would this somewhere could reside: outside brain?
No! Philosopher must be producing totally weird fairy tale now! Says the mainstreamer inside me with such a friendly ut delicate tone that it becomes clear that he regards the poor philosopher as a screwball.
But philosopher continues asking. Didn't Libet discover that our sensory data is fraction of second old? Could it take fraction of second of this data to propagate as EEG signals from brain to this something. As a matter fact, Libet discovered also that the conscious decision to raise finger is preceded by neural activity starting for a fraction of second earlier. One cannot understand this unless one decides that it supports the absence of free will.
Philosopher asks also whether our decision that experienced time and the time of physicist are one and the same thing is be wrong. They are indeed different in many respects as any first year physics student understands. Should we trust facts instead of textbook wisdom? And what about Libet's second finding: could we give up our firm decision that signals propagate in only single direction of geometric time?
There is also a second strange electromagnetic phenomenon in biology: bio-photons. Already discovered almost century ago, they are still taken as pseudoscience by many biologists. They appear in visible and UV range but it seems that they are not produced in molecular reactions (this would mean peaks in the distribution). What is their origin?
3.1 Why vivo-vitro difference?
Even the basic dogmatist must admit that one must speak about organic chemistry in vivo and in vitro. In vitro one can build models for reactions, deduce estimates for the excitation energies of molecules, construct thermodynamical models for reactions in terms of thermodynamics involving parameters like activation energies and chemical potentials, one can develop complex networks of reaction pathways.
The typical assumption of these models is that everything is homogenous and isotropic: one has spatially constant concentrations of various reactions obeying differential equations determined by the kinetics. One can however construct more complex structure by allowing diffusion making possible spatial gradients.
The problem is that this dynamics has very little to do with what happens in living cell. The in vitro estimates for the rates of reactions are many many orders of magnitudes too low as compared to those in living matter. We do not understand anything about bio-catalysis. We know that enzymes and ribozymes somehow make the miracle but that's all. We do not have slightest clue about how reactants manage to find each other in the molecular soup full of different molecules. We have no idea wherefrom the reactants get the energy to jump over potential wall making the reaction quite too slow.
Philosopher would say that here is an excellent opportunity for new physics to enter in biology. How can reactants find each other? Could they possibly be connected by something, which shortens as the reactants meet? Could the notion of tensor network involving quantum entanglement be essential element of biology and entire physics. Particles would not be lonely riders but could be connected by something at least temporarily. Could this something liberate energy quanta allowing to get over the potential wall making reaction so slow? Could these networks have dynamical topology and make living systems what they are.
Unfortunately, standard space-time picture does not allow this something. Also Planck constant is quite too small. Should we conclude that the philosopher is weirdly fairytaling again?
3.2 What selected the biomolecules?
Now philosopher is asking why only very few candidates for relevant biomolecules are actually selected. Who/what selected and how? This leads to very unpleasant questions circumvented by deciding that the emergence of life was nothing but a thermodynamical fluctuation. It has however become clear that complex organic molecules are present even in interstellar and intergalactic space. The miraculous thermodynamical fluctuation explaining evolution without real evolution would have been really huge.
Philosopher tends to conclude that we simply have no clue about what selection at the bio-molecular level really is and continue that some new physics is involved so that it is time to think giving up the reductionistic narrative.
The selection problem appears also at the level of biochemical reaction pathways. One can imagine endless variety of "reaction vertices". If one assumes that only very few basic "reaction vertices" are allowed but the rest not, one can construct a limited number of reaction pathways. But this is an ad hoc assumption: this selection of allowed reaction pathways certainly occurs but we do not have a slightest idea about the physics behind it.
There is also an analogy with computer science. One can construct endless variety of linguistically correct computer programs: why only very few of them would be selected. And with neuroscience: from a huge array of behavioral patters only some are selected.
Here one can of course try a loophole: Darwinian selection. But there is no selection in the Universe of physicalist. This would require free will and intentionality. The trick does not work.
But what about this network in which biomolecules are connected by this something already mentioned?, asks philosopher. Could this something connect only biomolecules if they are in the same relationship as sender and receiver of radio signal. Could these somethings connect stably only systems possessing common resonance frequencies? Could this criterion could select both the preferred biomolecules and the "reaction vertices" and thus also reaction pathways?
Easy to guess the reaction of me the mainstreamer: fairy-taling again.
3.3 Where does the coherence come from?
A further mystery is how the biochemical reactions can occur coherently in length scales longer than atomic scale. Without this coherence I could not write this, play piano, or even raise my hand. If we were just sacks of water containing some chemicals we would be doing science and arts. We would be indeed just sacks of water containing some chemicals in chemical and thermodynamical equilibrium and microscopic sample from this water would characterize us completely.
Mysteriously the coherence of biodynamics in scales up to the size of the organism emerges somehow. The required coherence need not be quantum coherence - and probably it is not - but it could be induced by quantum coherence. Quantum coherence of what? There is also the problem due to quite too small value of Planck constant. We have learned about the effects supporting the vision about quantum biology. It is now however becoming clear that these effects would however require large value of Planck constant.
Here the philosopher remembers the findings of Blackman and other pioneers of bio-electromagnetism. They found that the irradiation of vertebrate brain by ELF radiation at EEG frequencies scale had effects on both behavior and physiology and these effects look quantal occurring at harmonics of endogenous magnetic field of .2 Gauss. E=h× f makes these effects extremely small and totally masked by thermal noise. What if the value of Planck constant were so large that the energies were above thermal energy?
Now the mainstream physicist inside us is getting really angry: is this recklessly speculating philosopher really suggesting that our cherished quantum theory might not be the final word of science?
The problem of structure formation in biology - morphogenesis - was put under the rug by most biologists after the emergence of genetics. Sheldrake is one of those who have taken it seriously and has been labelled as a crackpot by mainstreamers. One just assumes that the structures are there and performs chemistry around these structures. This approach is very practical and has given an enormous amount of data but practically no understanding.
In standard physics the description of spatial structure would be in terms of enhanced densities of biomolecules or of their gradients in some space-time region. This is the only possibility because the space-time of standard physics is topologically and geometrically utterly trivial. Empty Minkowski space is an excellent approximation for it.
What philosopher has to say about this? If space-time topology were topologically non-trivial, situation would change dramatically. Already Wheeler saw this possibility and in the biology inspired by TGD (for which Wheeler suggested its name) all structures correspond to structures of topologically non-trivial space-time identified as surface in certain 8-D space-time: space-time sheets, magnetic flux tubes, etc... The entire TGD inspired quantum biology relies on this vision. The structures that we see around us would represent the non-trivial topology of space-time surface.
All structures - including bio-molecules, membrane like structures, organelles, organs, ... - would be 4-D space-time surfaces. Again philosopher gets excited since this would reduce the notion of shape in biology to a precisely defined and testable geometrodynamics coupling to em fields.
3.4.1. The dynamics of space-time surfaces
This dynamics predicts two kinds of space-time regions (see this.
These observations lead to a rather general view about morphogenesis.
Metabolism is one of the key aspects of biology. We must eat and plants must busily photosynthesize in order to survive. But why metabolic energy feed is needed? Again a mystery.
Non-equilibrium thermodynamics is one attempt to answer this question. Thermodynamical equilibrium is completely uninteresting, entropy is maximal and in the case of local dynamics the state of system is completely determined by a small sample of it. However, if one has energy feed, situation changes since equilibrium becomes flow equilibrium. The energy feed guarantees that there is macroscopic dynamics rather than mere thermal motion at microscopic level.
Also in this case one has essentially the same situation everywhere unless one introduces macroscopic parameters - also energy flow - depending on time and position to get something more interesting. Simple reaction kinematics determined by differential equations can be replaced with that determined by partial differential equations obtained by allowing diffusion. Also temperature, pressure and other thermodynamical parameters can be allowed to depend on position and time. Turing proposed a model for the coloring of Zebra as outcome of this kind of dynamics. The model for neuronal membrane and nerve pulse generation is also a rough model trying to reproduce basic facts about nerve pulse generation using thermodynamics for neuronal membrane regarded as a capacitor. This is of course a mere parametrization of the situation involving a lot of parameters. TGD leads to a quantum model for the situtation. Also the interpretation about the role of nerve pulse patterns at neuronal level changes dramatically.
In non-equilibrium thermodynamics one speaks of self-organization. One can generalize this notion to quantum self-organization and the crucial criticality associated to the transitions between different self-organization patterns generalizes to quantum criticality. Could these transitions correspond to spatio-temporal self organization patterns, behaviors, functions, programs. This in turn leads to deep connections with conformal symmetry (even its generalization in TGD), fractality, and universality of the dynamics. It is a pity that biologists do not seem to know much about these possibilities.
Now the philosopher starts to talk about ontology. Try to be patient. In standard physics the 3-D time= constant snapshot defines the state. This belief has led to weird proposals: in quantized general relativity one ends up with a proposal that there is no time.
Could it be that 4-D deterministic time evolution between initial and final states could be more fundamental than the 3-D snapshot? Could superpositions of these 4-D evolutions define quantum states. If so, the state function reductions would occur between these superpositions and their non-determinism would be consistent with the determinism of field equations. Free will would not break laws of physics. It would be like starting new deterministic computer program. Our philosopher calls this ontology Zero Energy Ontology and claims that it leads to a theory of consciousness as a generalization of quantum measurement theory. Irritating.
3.6 Does metabolic energy feed generate conscious information?
The basic question about the role of metabolic energy remains, says the philosopher. What is its real role? Energy feed generates structures and structural complexity means information. It seems that metabolic energy feed involves also a feed of information or generation of information. And because living systems are in question, philosopher cannot avoid the question whether this information is actually conscious information. Is there any other kind of information than conscious information?
To this question standard physics has no answer: it can only describe entropy mathematically and identification of information as lack of entropy is the easy answer suggested in lack of anything better. The question about a possible measure for conscious information analogous to Shannon entropy is one manner to end up with p-adic physics as a correlate of cognition and the necessary fusion of real and various p-adic physics leads to adelic physics. Adelic physics in turn predicts - surprise- surprise - a hierarchy of phases of matter labelled by the value of Planck constant. These phases residing at these somethings defining the networks - magnetic flux tubes - make possible macroscopic quantum coherence inducing the coherence of living matter.
3.7 Genetic code
Genetic code definitely represents information. Is it really an outcome of thermodynamical fluctuation? Is there some deep mathematics associated with the genetic code?, asks the philosopher now. Be patient!
Genome contains also intronic portion: most of it consists of introns and the intronic portion is the larger the higher the evolutionary level is. The prevailing interpretation has been as "junk". Is it really junk?, wonders philosopher. Luckily, the attitude that trash bin represents the highest level of evolution has begun to slowly change to more rational one.
Could there be a beautiful mathematics behind genetic code? Could it be something similar to codes in computer science and have not only one representation - the chemical one - but numerous representations? If computer science would have developed before genetics - this question would have been completely natural and we would probably know a lot about these representations. Could this dark matter with large Planck constant at these mysterious somethings identified by our philosopher tentatively as magnetic flux tubes realize the really fundamental representation of the genetic code and also of of DNA, RNA, tRNA, and amino-acids in information theoretic sense? And could also radiation provide realization of genetic code necessary for communications?
3.8 The mystery of replication
Replication is one of the deepest mysteries of biology. It is really something totally counterintuitive if cell is seen as a sack of water plus some chemicals. We have a lot facts about what happens in the replication at DNA level but how this miracle happens is a mystery. At cell level the situation gets even more complex.
Philospher thinks that behind the chemistry there might lurk a much simpler quantum dynamics and that chemistry only makes its best to mimic this deeper dynamics. Is biochemistry controlled by something? Does this something provide a template for the dynamics at chemical level? The idea about the presence of this something popped up already in the mystery of EEG. What could this something perhaps receiving sensory information from vertebrate brain and maybe providing feedback as control signals affecting also chemistry?
Now our brave philosopher attacks the length scale reductionism again. Isn't it quite too much to require that all these replications in different length scales would result as accidental "emergences" due to thermodynamical fluctuations? Could the dynamics be fractal with same patterns - for instance replication - occurring in different scales. Could this dynamics be induced what happens on this something.
Philosopher also suggests a concrete model for the controlling level: dark matter with large value of Planck constant heff/h0=n at magnetic flux tubes and asks whether the conjectured dark realization of DNA in various scales performs the fundamental replication inducing in turn the biological replication in various scales as a mimicry? Morphogenesis controlled by the hierarchy of dark realizations of genetic code would be the basic vision. This would simplify the situation enormously but in totally different manner than length scale reductionism.
3. 9 Evolution
I forgot perhaps the most important piece from the original text. Philosopher cannot avoid the question "What is evolution?"
In standard biology evolution is mystery. If one believes on standard thermodynamics, evolution is impossible by second law and the eventual heat death is unavoidable. Evolution means generation of structures and second law indeed states that all gradients die so that the finals state is totally uninteresting homogenous stuff.
I already mentioned the weird proposal that biology is just an enormous thermodynamical fluctuation. Boltzmann brain was indeed a kind of fad of pop physicists for some years ago. The idea - if you want to call it such - was that Boltzmann brains - and also ours - popped up from the multiverse by a complete accident. One could even argue that this occurred only at planet Earth to make the claim more plausible. This is however not science anymore, this is just pure plain idiocy.
Philosopher asks questions and now the most obvious questions are following. Is evolution something much more general than biological evolution? Is evolution a basic aspect of physics as already cosmological evolution suggests? Is evolution "must", something completely unavoidable? What could force it?
The Universe governed by second law certainly does not allow evolution: just the contrary. Could the increase of entropy and increase of conscious information and development of cognition relate somehow? It has been argued by that biological evolution involves increase of the rate of entropy production as any-one can see by just looking around. These two things are not the same but are they somehow related.
Philosopher gets now childishly excited. We must just tolerate. Our philosopher already mentioned that p-adic physics as physics of cognition not only leads to a measure for conscious information - something very non-trivial - but to adelic physics fusing physics in various number fields. Adeles form a hierarchy labelled by the dimension of the extension of rationals inducing the extension of p-adic number fields labelled by primes. This dimension corresponds to the effective value of Planck constant and the larger it is, the larger the scale of quantum coherence is.
This has been already said but now comes the basic point and philosopher gets really excited. Since the number of extensions of rationals with dimension larger than given integer n is finite and the number of those with dimension larger than n is infinite, this dimension is bound to increase in statistical sense in the sequence of state function reductions recreating the quantum Universe again and again. Evolution is unavoidable! This is like random work from origin upwards. The height from the origin unavoidably increases.
Even more, the total negentropy coming from various p-adic sectors turns out to be larger than the entropy coming from the real sector. The bad news - not actually a news - is that increase of this negentropy is accompanied by the increase of entropy: civilizations indeed have the bad habit of polluting their environments. The good news is that negentropy increases faster than entropy: for a trivial extension of rationals from which everything would have started, negentropy equals to entropy. But for more complex extensions it is larger.
See the chapter Getting philosophical: some comments about the problems of physics, neuroscience, and biology or the article with the same title.