Sara,

I read your essay quite a while ago. I found myself not able at first to respond particularly, because I have pondered much the same issue. My undergraduate specialization with physics was biophysics, and correspondingly I had biochemistry and molecular biology. I cloned genes and the whole thing. My doctoral work was with quantum fields and gravity though. This matter to me is huge open question, and frankly I have not the foggiest idea whether there something we might call the bio-state in the physical universe.

My sense of this issue is that it involves some extensive variables with a phase change. Extensive variables are not scale invariant. For instance pressure does not depend on scale, while the number of atoms or particles is dependent. In addition, if there is a bio-state it is not a phase of a system that exists in closed thermodynamics. It must necessarily be a property or phase that exists in open thermodynamic systems. These systems are similar to Prigogine's work. Further, a variable of importance is information. Information in biological systems has some parallels with algorithmic complexity. For instance the DNA --- > mRNA --- > polypeptide is a sort of Turing machine process. In fact the production of a polypeptide by reading the RNA is a sort of Chomsky lexical system. The polypeptide might then be a switching system, say a kinase that phosphorylates another polypeptide, which starts another process, which ... .

The complexity is that while maybe some local aspects of molecular biology are similar to information processing systems, these are all open and linked into huge webs of biochemical pathways. As such there is an extensive property to this information or complexity. Whether this can in some ways lead to a physical state or phase, the bio-state, is something that I think we have no idea about. It might be the case, and there is certainly a qualitative sense there is such a state, but as yet we have no theory or data.

Cheers LC

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    • Post #65

    Hi Sara. I should have elaborated a little more on my position. Gravity involves vision, touch, and feeling. BOTH gravity and electromagnetism enjoin and balance visible and invisible space. With direct bodily experience being fundamental to physics, what do you think of the following in relation to your position/essay please?

    Paul Davies says: "The ultimate source of biological information and order is gravitation." Now, what of this: Thought is integrated and interactive in and with the range of gravitational feeling that is experienced by the body, in comparison with the rest of this post, AND with this: BOTH gravity and electromagnetism enjoin and balance visible and invisible space. Do you see this as having bearing or relevancy in your work? I would add the following.

    Gravity, invisible and visible (seen and felt), is fundamental to distance in/of space. Vision begins invisibly inside the eye/body because the space is also invisible at the very top of the head while waking/standing.We always start with typical/ordinary experience (such as dreams and waking/standing PHYSICAL experience) when establishing physical fundamentals/truth(s). Gravity is in an even/incremental range of [gravitational] feeling as we experience it (my essay covers this fully) because it goes from visible space to invisible space (while waking/standing).

    Now, importantly, regarding gravity, we do consider touch, feeling, and vision together in relation thereto; especially because thought is integrated and interactive in and with the range of gravitational feeling that is experienced by the body -- a most important point. "The purpose of vision is to advise of the consequences of touch in time", per the philosopher Bishop Berekeley. This is important too.

    Modern physics is basically lost and in divided fragments because direct bodily experience -- typical/ordinary experience (dreams and waking) -- (seen, felt, and touched considered TOGETHER) is fundamental to thought/theory and to physics (fundamentally and generally).

    What do you think please Sara? Can you review and rate my essay please?

    Dear Sara Imari Walker,

    Big Bang nucleosynthesis is not expressional with this paradigm of Coherently-cyclic cluster-matter universe that describes the universe as eternal, in that the nucleus of a chemical element is described as a dense region of tetrahedral-branes within a domain that represents that element itself. In this paradigm, distribution of chemical elements in universe differs for the holarchial segments as per the gravitational potentials of these segments in that the nuclear transmutation and reverse transmutation of the elements are in correlation with the fluctuations of gravitational potentials of these holarchial segments.

    Excessive energy in a holarchial segment that is not proportional with the gravitational potential of that segment is causal for the evolution of life in that specific holarchial segment that has favourable conditions. Increase of chemical potential by the evolution of organic compounds, sustains the continuous evolution of complex organic compounds in that holarchial segment, that have life and continues with the evolution of higher order of species in that segment. Thus the homeomorphic segmental-fluctuation cycle of the universe is imperative for the evolution and extinction of life in a specific holarchial segment, in that the physical causality of homeomorphic segmental-fluctuation is the collective effect of the entirety of universe.

    With best wishes

    Jayakar

      Sarah

      Wonderfully written and fascinating essay on an important subject poorly covered here. I also agree it's not 'either/or' between top down and bottom up causation but both. In Architecture the design process is certainly mainly top down but component relations are bottom up. Construction can of course be both (the 'Shard' was both at once!).

      I find a multiple circle or dipole, commonly forming a torus, or when translating through space, interestingly not only derives the strong force (found in Vladimir Tamari's work) but also gives the form of DNA. Of course the spiral re-ionizing jets of quasars (from a toroid/AGN axis) does the same, and electron spin can be analogous. Quite a universal morphology perhaps? (literally - as CMB anisotropies match the pattern!)

      Would you agree the big question is not just about 'life' or 'not life' but whether one day intelligent life may evolve. Perhaps then we may understand universes, (or at least my essay!) And on to that. I think I find a massively important bottom up causality derived from to down analysis. Please do read it if you can and give me your views.

      Very best wishes

      Peter

        Dear Sara,

        Interesting point of view. To put it in your terms I would find much more remarkable if life actually can be reduced to chemistry and physics (or information) than requiring anything not known to science today. I enjoyed the way you explain that Darwinian evolution is actually more general than the processes involved only in life itself. Isn't the appearance of the field of complex systems (greatly also influencing other areas such as artificial life) the acknowledge of the notion that even if life is reducible one cannot study it but at a higher level of description? A level of description where interactions between the parts can be accounted for.

        The main downside of your approach is the overlooking (as various other essays do) the cutting-edge theories of complexity and information content, which is not Shannon's communication theory developed 60 years ago, but Algorithmic Information Theory (Kolmogorov complexity, variations of it and related measures). This would easily provide a possible explanation of the difference in genome length between a plant such as Paris Japonica compared to the relatively small human genome length by number of base pairs. From the Kolmogorov complexity perspective you would need to compare compressed genomes, from Bennett's logical depth you would need to compare uncompressing times from near compressed genomes, etc. to mention but 2 examples. This is a common straw man fallacy practice committed ignoring the current state of a field and substituting it with a misrepresented version of it (Shannon). In all other respects I think it is a well-written fine essay with very interesting suggestions.

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          • Post #70

          Dear Sara Imari Walker

          It seems to me that we have divided nature in two completely different worlds, the one that is made of carbon compounds, which consist mainly the annimate matter and the other with all the rest known elements, the inanimate matter.

          There is strong evidence that the behavior of inanimate and animated matter may have some common characteristics and that nature does not make any distinction between them. This common behavior is manifested better in huge agglomeration of matter, like galaxy clusters and equally well in the behavior of primitive life like bacteria, virus, prion.

          Maybe The Universe has been evolved as a self-organized system given the initial condition. It has the ability of reproduction and the power of multiplication.

          In that case life in our Univers is not an accidental phenomenon but it is closely related with the structure of the universe.

          But if the definition of life, is: a complex self-sustaining chemical network based on carbon biochemistry capable of undergoing Darwinian evolution, then what difference does it make from the definition of the inanimate matter.

          Best wishes

          B. Grispos

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            • Post #71

            I am thinking to an hypothetical measure of the life presence in a top-down approach.

            If an organic life exist in the space (on comets, or ice in the deep space), then I hypothesize that the metabolite molecules can be chiral; so that there is a difference in the absorption spectrum.

            If there is a percentage - in the deep space - of chirality spectrum in some luminous hot cloud, then I can suppose the presence of life.

            Saluti

            Domenico

              Dear Sara,

              Your submission is surely one of the best-written and deepest entries in the contest. Any one of a number of topics you discuss (self-reference, distributed causation, causal efficacy of information, evolving dynamical laws, etc.) is worthy of more comment and discussion than can be accomplished in a forum such as this; hence, I can only choose a few points to remark on.

              1. I am wondering if your rejection of the "fully reductionist picture" (page 2, last paragraph) really applies to the classical level, or only to the quantum level. I ask this for two reasons. The first reason is because digital computing (which is purely classical) has so far failed to produce many of the "lifelike" qualities repeatedly predicted by scientists in fields such as artificial intelligence, and it still seems reasonable (to me) to ask if life is intrinsically quantum-mechanical. The second reason is because classical holism in the strong sense seems to raise a host of problems (see subsequent points).

              3. I have severe difficulty with the subject of "top-down causation" in classical physics (quantum holism is a different story). I have thought about causal structures a great deal in the context of quantum gravity and the fundamental nature of "spacetime," and it seems to me that very radical conclusions arise when one attempts to make the notion of classical top-down causation precise. I can't explain all the details in a single post (if you are interested, you may see my essay here), but the main problem involves the nature of time.

              A short explanation is as follows: if causality is fundamental, then it seems reasonable to assume that the arrow of time aligns with the causal direction. This is already evident in special relativity, where causality can operate only over timelike intervals. Given an event E in spacetime, the set of all events that may be influenced by E is the "future light cone of E." Given a subset S of spacetime, the "future" of S is the union of all the future light cones of the events in S.

              Now, if one admits classical top-down causation, this picture becomes vastly more complicated, provided that one "really means it," and is not merely saying that it is useful to lump events together into systems and talk about aggregate effects on other systems. By "really means it," I mean that one assumes that subsets of spacetime exert influence on other subsets independent of the influences between their respective events. This replaces the connection between the "future" subset of spacetime and the scope of causal influence by something much more complex. One must construct a "space" with one point for every subspace of spacetime (the "power set," in mathematical terms). Cause and effect is now described in terms of relations between points in this huge new space, and if time aligns with the direction of cause and effect, time can only be understood in the ordinary way as a one-dimensional "direction" in the power set, not in the original spacetime.

              4. Regarding the causal efficacy of information, I have no doubt that something like this occurs in living organisms, but it seems more and more plausible to believe that all of physics works this way at a fundamental level, so it seems to me that it may ultimately be hard to distinguish life on this basis. Of course, this is too superficial an indictment of points you are making here, but something like it may still be relevant at some level.

              5. Alain Connes, simultaneously one of the world's greatest mathematicians and physicists, has written an interesting book called Triangle of Thoughts in which he discusses the way in which humans experience time and how it differs from the linear picture of standard physics. If one did adopt the most radical interpretations of the ideas you have presented here, something like Connes' ideas might be considered more than metaphorical.

              Congratulations on a splendid contribution! Take care,

              Ben Dribus

                Dear Juan, thank you very much for sharing the references!

                Best,

                Sara

                Dear Lawrence,

                It is interesting to think that there might be some extensive variables we could associate with a 'phase change' from non-life to life. The challenge is always to identify what precisely these might be. I like your notion of associating them with information/complexity in biochemical networks. This sounds very much in line with attempting to identify parameters associated with informational and causal architecture that I present in the essay. The difficulty is trying to identify the relevant parameters - is it information flow? network topology? algorithmic compressibility? I think this is the challenge to look to with moving forward trying to identify if a 'bio-state' exists. But, I agree - I don't think we know nearly enough at this stage to say whether this physical distinction between life and non-life actually exists or not - there is lots of work to be done!

                Thank you for sharing your thoughts.

                Best,

                Sara

                Dear Hoang Cao Hai,

                Thank you for your interest in my essay.

                Best,

                Sara

                Dear Jayakar,

                Thank you kindly for your well-wishes and interest in my essay.

                Best,

                Sara

                Dear Peter,

                I do very much agree that the big question here is not just about the emergence of life, but of intelligence as well. I am particularly interested in whether intelligent life will always (eventually) evolve given sufficient time (however long that actually may be!) once life has emerged, or if it is the case that the evolution of intelligence is exceedingly rare. I don't think we are in the position yet to answer this one way or the other, and I am very curious about whether similar physical mechanisms underly both processes (which I suspect is the case).

                I've found your essay and will plan to read it - excellent title!

                Best,

                Sara

                Dear Hector,

                Thank you for your thoughtful comments. I agree that the field of complex systems definitely suggests that higher-level descriptions are necessary in many areas of science!

                You bring up some interesting points on AIT complexity measures. Although I did not include a discussion of algorithmic information theory in my essay, I completely agree that it is central to the story and in retrospect it is a big omission in my discussion. It certainly provides a much better measure of genomic complexity than Shannon information as you point out. A challenge however is that not all the information is stored in the DNA. So even if we do calculate, for example, the kolmogorov complexity of two genomes from two distinct organisms, I am not convinced that this would provide a true comparison of their complexity (although it is a great place to start!). There seems to be a lot of algorithmic information content not stored directly in DNA, but instead stored in distributed biochemical networks (e.g. information that dictates self-assembly processes). I think AIT could still capture this, and is probably the most fruitful direction to take, but its not at all straightforward to determine where the algorithms are physically represented. In lieu of being able to precisely define these more distributed parts of biological information, I think exploring causality in biology is one interesting and possibly productive way of understanding how information operates in biology. I'd be very interesting to see development of connections between the two approaches.

                Thanks again for your insights!

                Best,

                Sara

                Dear B. Grispos,

                You have hit on one of the primary challenges in identifying any sort of rigorous definition for life - it is notoriously difficult to come up with a well-defined criteria that distinguishes living from nonliving. It certainly makes the task of identifying life's origins very difficult without a proper definition!

                I am not particularly satisfied with the definition of life as "a complex self-sustaining chemical network based on carbon biochemistry capable of undergoing Darwinian evolution" either. I don't think it makes a clear distinction between animate and inanimate matter. I discuss why Darwinian evolution may not be a sufficient (although it could certainly be necessary) condition in the essay, but what about for example that carbon is necessary? Carbon is certainly a very special element, but silicon is not completely ruled out as a possible alternative. And "complex self-sustaining chemical network" could describe just about any geochemical cycle. So I agree this definition is not adequate - it can certainly be used to describe a great number of systems, many of which we would not be willing to call alive and worse it may not include systems which are alive! This is why I think more fundamental distinctions may be necessary.

                Best,

                Sara

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                • Post #80

                Giovanni wrote:

                "In quantum-gravity research there is a long-standing effort

                of understanding how spacetime should be described when both

                Planck's constant ~ and Newton's constant GN are nonnegligible.

                We cannot claim much success addressing this issue."

                Giovanni,

                what mean "nonnegligible"?

                Give me please more detail...

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                • Post #81

                I am not sure if research has been done with phase structure in Progogine's open thermodynamics. Open thermodynamics is not on the same solid foundation thermodynamics of closed systems is on. There might be some research on this however which one could search out. If this has not been seriously looked at it could represent a considerable challenge.

                Cheers LC

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                • Post #82

                Sara Imari Walker,

                The human race may have been forced to become Reductionists simply to stay alive. One way to assure command over the elements that one must face for survival is to become a "Reductionist" and absorb all the physical knowledge required for assuring one's survival. A total "Holistic" approach to life may suffer extinction if the basic Reductionist manifestos "physically correlated event" concepts are not comprehended - like predicting the season for planting, etc, etc.... a club kills quicker then a stick, etc, etc. It therefore appears that human life is caught exactly in the middle of Reductionist & Holistic because for each Reductionist "learned action" we build a physical event string of correlation having Holistic value (i.e., a correlation between events, ie., comparison information). It seems like our thoughts may be caught in the very middle of building a physical Reductionist model (say the standard model of physics for instance) for the Holistic purposes of achievement, completion, curiosity, all Holistic.

                If you agree with the statement that Reductionism can feed a Holistic quality, and visa versa, then we may consider that we have a superposition of Holistic and Reductionist information going into "any" event (biological included) - our two brain hemispheres could accommodate the dissociation of Holistic and Reductionist information with our final physical actions that explore a common ground that is a balanced reaction to support the two extreme lines of thought, Reductionist and Holistic. It would be as if life has an "all from one" and "one from all" way of thinking and acting ... local, global... one physically affects all ..... all physically affect one ...

                Assume we can dissect information on BOTH Reductionist and Holistic grounds, can we find a model that allows us to combine the two seemingly extreme set's of information? To accommodate these extreme sets of information, we might want to look at the duals in string theory as providing a mathematical avenue to physically describe this information. "Astronomy" and "quantum physics" certainly fit into the Holistic and Reductionist information categories, respectively ... which brings us back to unification of measurable information. This is where ADS/CFT (super symmetry) tells us that that information regarding that which is extremely large (of cosmic size) can be exactly described by measuring information of that which is extremely small (sounds like a quantum worls to me)!! There appears to be a perfect reflection of information content (T dual) if one considers the conformal quantum field as the "information space" that can possibly be utilized to model BOTH the Holistic and Reductionist information. This implies that the quantum physicist and the astronomer will be capable of predicting each others information findings when they find the correct way to interpret the correlation of each bit of information whose common ground analysis provides the actions incurred by the masses ... whether they be atoms, cells, organs, humans, ecosystems, planet, galaxy, universe... The exact correlation of Holistic to Reductionist information (super symmetric string theory dual) may provide the proper boundary conditions for life to emerge and exist in a manner that maintains life by adhering to information gathered by the Reductionist (sustains physical life) but at a cost of losing sight of the Holistic contribution that actually provides half of the net information regarding any event (biological events included). This implies that by focusing on reductionism we may defocus on Holistic information and visa versa (possibly the result of information existing in a hyperbolic space, but, that's another story)... as if information used for physical reasoning has a Reductionist Holistic switch (the 2 sheets in the hyperbolic space) ... when the fact is that the switch has been set to 50% for everything that our senses that feed our conscious mind w/ information can measure (a Feynman/Wheeler emitter/absorber argument used for the 50% ... but... that's again another story).

                Anyway, I greatly enjoyed your article and appreciated your use of the word "information" extensively. I believe that we must define everything measurable simply as "information" (L. Suskind methodology) to build a model that allows this information to sustain life by merging both the Reductionist and Holistic information to drive all of life's measurable information (to which a physical action is the net result of the balance achieved between Reductionist and Holistic information that is reasoned out between the brains hemispheres). This top/down approach also appears to be on the minds of many more essay authors, including that by G. Ellis whose essay had many overtones of what you state you measure and observe. Maybe with information provided by J. Barbour's shape dynamics and G. Ellis's top/down approach you can model (via the string theory basis) the exact living biological shape and physical actions of a known life form that uses BOTH Holistic and Reductionist information to sustain life. You may then begin to predict your biological measures w/ functional stability?

                Best Regards,

                Anthony DiCarlo

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                  • Post #83

                  Hello Ms Walker and Mr Zenil,

                  I like these kind of discussions.Thanks for that :)

                  I beleive strongly that the evolution is a main part of the puzzle. The cybernetic seems very relevant when we consider the transfert of informations with the energy and its entropical arrow of times. The encoding is very complex, I return about the importance of the serie of spherical volumes considering the serie of uniqueness. The encodings can be synchronized.

                  The algorythms of evolution are so complex that it seems difficult to know the main code, the main central sphere of series of uniqueness.It is like trying to see our central universal sphere of our universal sphere.The walls are indeed far. We have our limits. All can be quantized if we begin with this serie of uniqueness , and the rotations and the volumes ....so it permit to imply the comportments and properties of spheres of light. The rotations of the light imply the mass, the energy , the light,the space. So with the volumes and the complexity of codings , it becomes very relevant when all is quantized in a pure road of evolution of mass. In a simple resume. The universal system can be computed with relevance with stil, I am insisting a lot :), the serie of uniqueness and its finite number, so we have quantum spheres, serie finite.....mcosV=constant. and E= mc² can be optimsed with the two others motions of the spheres of light so the spinal rotaion and the orbital rotation. The angles are relevant considering the informations of evolution. The electromagnetism seems very very complex and the volumes very small compared with the central spheres. So the informations are relevant there. The DNA and the RNA with their architecture of spheres (HCNOP) are relevant for the biological algorythmic building. The link OH ...O with the complementary polynucleotids and the serie of uniqueness are relevant for the tranfert of informations. The hydrogen bridge and the closed links of the adenin, guanin, thymin and cytosin more the P are intriguing when we fractalize the series of uniqueness.So we go towards the main central spheres, so the main codes. The road is very complex, and more we go towards these singularities, more the difficulties are important.And more the volumes of spheres also. The rotations of synchronizations, sortings of informations become very relevant when the oscillations are in harmony with the rotations, the rotations of volumes so are in synchronizations.It is the reason why probably all DNA is unique. We have all our velocities of rotations in fact. If the synchronizations of these rotations and if the increase of mass are correlated, more the variable volumes and the density.and if the serie of uniqueness of bosonic informations , so the light is inserted , it becomes relevant when the rotating spherical volumes are analyzed. The synchronizations of rotating spheres answer to a lot of things. The stability of the mass is seen with logic and the linearity of light also. So the synchro of volumes also, like the sortings.It is fascinating all this encoding of evolution.

                  Thanking you for these discussions. Good luck in this contest.

                  Regards

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                  • Post #84

                  Hi Sara. There is no true or ultimate difference between what is animate and inanimate because the self represents, forms, and experiences a comprehensive approximation of experience in general by combining conscious and unconscious experience. Accordingly, the fundamental and general unification of physics involves direct bodily experience (seen, felt, AND touched) -- as the ultimate understanding of physics combines, balances, and includes opposites in conjunction with our growth and becoming other than we are. DO YOU AGREE? What are your thoughts on this please?