This is a reply to Plamen’s comment about autopoeisis. In their paper Maturana,Uribe and Varela give a working model (computer model) for autopoeisis. It is very simple, consisting of a subtrate of nodal elements that tend to bond when in proximity, and a collection of catalytic nodal elements that promote bonding in their vicinity. The result of this dynamics is that carapaces of linked nodal elements form around the catalytic elements and these photo-cells tend to keep surviving the perturbations built into the system. This model shows that cells can arise from a very simple dynmamic geometric/topological substrate long before anything as sophisticated as DNA has happened.
> On Mar 29, 2016, at 2:54 PM, Stanley N Salthe <ssal...@binghamton.edu> wrote: > > Plamen wrote: > > I begin to believe that the transition from abiotic to biotic structures, > incl. Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying > matrix/”skeleton”/”programme” which has nothing in common with the nature of > DNA, and that DNA and RNA as we know them today may have emerged as secondary > or even tertiary “memory” of something underlying deeper below the > microbiological surface. It is at least worth thinking in this direction. I > do not mean necessarily the role of the number concept and Platonic origin of > the universe, but something probably much more “physical” > > > > > > S: An interesting recently published effort along these lines is: > > Alvaro Moreno and Matteo Mossio: Biological Autonomy: A Philosophical and > Theoretical Enquiry (History, Philosophy and Theory of the Life Sciences 12) > Springer > > They seek a materialist understanding of biology as a system, attempting to > refer to the genetic system as little as possible. > > I have until very recently attempted to evade/avoid mechanistic thinking in > regard to biology, but, on considering the origin of life generally while > keeping Howard Pattee's thinking in mind, I have been struck by the notion > that the origin of life (that is: WITH the genetic system) was the origin of > mechanism in the universe. Before that coding system, everything was mass > action. I think we still do not understand how this mechanism evolved. > > STAN > > > On Tue, Mar 29, 2016 at 7:40 AM, Dr. Plamen L. Simeonov > <plamen.l.simeo...@gmail.com <mailto:plamen.l.simeo...@gmail.com>> wrote: > > Dear Lou, Pedro and All, > > > I am going to present a few opportunistic ideas related to what was said > before in this session. Coming back to Pivar’s speculative > mechano-topological model of life excluding genetics I wish to turn your > attention to another author with a similar idea but on a sound mathematical > base, Davide Ambrosi with his resume at > https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf > > <https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf>: > > “Davide Ambrosi: > > A role for mechanics in the growth, remodelling and morphogenesis of living > systems In the XX Century the interactions between mechanics in biology were > much biased by a bioengineering attitude: people were mainly interested in > evaluating the state of stress that bones and tissues undergo in order to > properly design prosthesis and devices. However in the last decades a new > vision is emerging. "Mechano-biology" is changing the point of view, with > respect to "Bio-mechanics", emphasizing the biological feedback. Cells, > tissues and organs do not only deform when loaded: they reorganize, they > duplicate, they actively produce dynamic patterns that apparently have > multiple biological aims. > In this talk I will concentrate on two paradigmatic systems where the > interplay between mechanics and biology is, in my opinion, particularly > challenging: the homeostatic stress as a driver for remodeling of soft tissue > and the tension as a mechanism to transmit information about the size of > organs during morphogenesis. In both cases it seems that mechanics plays a > role which at least accompanies and enforces the biochemical signaling.” > > > Some more details about this approach can be found here: > http://rsta.royalsocietypublishing.org/content/367/1902/3335 > <http://rsta.royalsocietypublishing.org/content/367/1902/3335> > http://biomechanics.stanford.edu/paper/MFOreport.pdf > <http://biomechanics.stanford.edu/paper/MFOreport.pdf> > In other words, for the core information theorists in FIS, the question is: > is there really only (epi)genetic evolution communication in living > organisms. Stan Salthe and Lou Kauffman already provided some answers. I > begin to believe that the transition from abiotic to biotic structures, incl. > Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying > matrix/”skeleton”/”programme” which has nothing in common with the nature of > DNA, and that DNA and RNA as we know them today > > http://www.sciencedirect.com/science/article/pii/S0022519314006778 > <http://www.sciencedirect.com/science/article/pii/S0022519314006778> > http://www.sciencedirect.com/science/article/pii/S0022519316001260 > <http://www.sciencedirect.com/science/article/pii/S0022519316001260> > https://www.sciencedaily.com/releases/2015/01/150107101405.htm > <https://www.sciencedaily.com/releases/2015/01/150107101405.htm> > may have emerged as secondary or even tertiary “memory” of something > underlying deeper below the microbiological surface. It is at least worth > thinking in this direction. I do not mean necessarily the role of the number > concept and Platonic origin of the universe, but something probably much more > “physical” or at least staying at the edge between physical/material and > immaterial such as David Deutsch’s constructor theory > (http://constructortheory.org/ <http://constructortheory.org/>) and Brian > Josephson’s “structural/circular theory” > (http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf > <http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf>; > http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf > <http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf>; > http://arxiv.org/pdf/1108.4860.pdf <http://arxiv.org/pdf/1108.4860.pdf>) > searching for the theories underpinning the foundations of the physical laws > (and following Wheeler’s definition for a “Law without Law”. > > Some of you may say that QT and Gravitation Theory are responsible for such > kind of strange effects, but I would rather leave the brackets open, because > the recent discussion about potentialities and actualities in QM brings up > the idea that there are still different ways of looking at those concepts > (although they are strictly defined in their core domains). This was actually > also the lesson from the last special issue on integral biomathics (2015) > dedicated to phenomenology, with the different opinions of scientists and > philosophers on obviously clear matters in their domains. This is why also > the question of what we define as science needs to be probably revised in > future to include also such issues that are “felt” rather than “reasoned”, > even if we do not have the “proofs” yet, because the proofs also emerge as > subjective (or perhaps “suggested”! – ask the psychologists for that aspect) > thoughts in the minds of the mathematicians. I am really glad that we began > such a phenomenological discussion on this aspect such as Hipolito’s paper > (http://www.sciencedirect.com/science/article/pii/S0079610715000899 > <http://www.sciencedirect.com/science/article/pii/S0079610715000899>) that > was widely commented in the reviewer’s circle. In many cases when we have a > “fuzzy” intuition about a certain relationship or analogy we miss the correct > definitions and concepts, and so in a creative act to hold down the flying > thought we move to using examples, metaphors, pictures. Pedro correctly > addressed the explanatory problem of science which presupposes a certain > causative and predicative “workflow” to derive a conclusion from the facts, > and this is the way in which also proofs are (selectively) made. As a young > scholar I often wondered how artificially people like Gauss, Cauchy and > Weierstrass design their proofs, but then I got used to that style. I am > thankful to Lou for his response on my question about using adequate > “resonant” methods to model developmental biology, because this is also an > important aspect of the biology (and physics as well) including the > phenomenological/first-person view of an “observer-participant” (to use > Vrobel’s term) which is crucial for understanding the process of > self-reflection/recursion/cycle in science, which is usually led by what?: > the intuition, also well recognized by such giants like Poincare and > Einstein. Isn’t not “resonance” in the core of detecting such vibration > between the observer and the observed? Because logic, back trace, prove come > later. > > And finally, when looking at the clear simple mathematical abstractions of > numbers, vectors, directions, sets, algebras, geometries, etc. used by many > without scrutinizing when developing system (biological) models of yet > another kind of mechanics/automation/machinery of the physical reality, I am > asking myself which are the premises for using such tools to describe a > model: the parameters, or the idea behind? It is probably not a commonly > known fact (even for those who are engaged with such exciting disciplines as > algebraic geometry and geometrical algebra, now considered to be very close > to what we wish to express in biology) that William Hamilton, the inventor of > the quaternions did not simply use the already known concept of “vector” in > his method. Instead he used “step” with “direction” to express a duration of > time (or “duree” as Husserl called it from the other side of the > phenomenological divide) and action (to move from A to B): two very > biology-related concepts at that time (although they may be considered as > physical or computational today). He actually stated that if there is > geometry as a pure science of space, then algebra must be the pure science of > time [1]. What did we actually gain for biology from merging space and time > in physics? > > Reference: > > [1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic > Couples; with a Preliminary or Elementary Essay on Algebra as the Science of > Pure Time. Trans. Royal Irish Acad., Vol. XVII, Part II. 292-422. > > > Best, > > > Plamen > > > I have a few provoking notes related to what was said before in this session. > Coming back to Pivar’s speculative mechano-topological model of life > excluding genetics I wish to turn your attention to another author with a > similar idea but on a sound mathematical base, Davide Ambrosi with his resume > at > https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf > > <https://www.uni-muenster.de/imperia/md/content/cim/events/cim-mathmod-workshop-2015_abstracts.pdf>: > > “Davide Ambrosi: > > A role for mechanics in the growth, remodelling and morphogenesis of living > systems In the XX Century the interactions between mechanics in biology were > much biased by a bioengineering attitude: people were mainly interested in > evaluating the state of stress that bones and tissues undergo in order to > properly design prosthesis and devices. However in the last decades a new > vision is emerging. "Mechano-biology" is changing the point of view, with > respect to "Bio-mechanics", emphasizing the biological feedback. Cells, > tissues and organs do not only deform when loaded: they reorganize, they > duplicate, they actively produce dynamic patterns that apparently have > multiple biological aims. > In this talk I will concentrate on two paradigmatic systems where the > interplay between mechanics and biology is, in my opinion, particularly > challenging: the homeostatic stress as a driver for remodeling of soft tissue > and the tension as a mechanism to transmit information about the size of > organs during morphogenesis. In both cases it seems that mechanics plays a > role which at least accompanies and enforces the biochemical signaling.” > > > Some more details about this approach can be found here: > http://rsta.royalsocietypublishing.org/content/367/1902/3335 > <http://rsta.royalsocietypublishing.org/content/367/1902/3335> > http://biomechanics.stanford.edu/paper/MFOreport.pdf > <http://biomechanics.stanford.edu/paper/MFOreport.pdf> > In other words, for the core information theorists in FIS, the question is: > is there really only (epi)genetic evolution communication in living > organisms. Stan Salthe and Lou Kauffman already provided some answers. I > begin to believe that the transition from abiotic to biotic structures, incl. > Maturana-Varela.-Uribe’s autopoiesis may, really have some underlying > matrix/”skeleton”/”programme” which has nothing in common with the nature of > DNA, and that DNA and RNA as we know them today > > http://www.sciencedirect.com/science/article/pii/S0022519314006778 > <http://www.sciencedirect.com/science/article/pii/S0022519314006778> > http://www.sciencedirect.com/science/article/pii/S0022519316001260 > <http://www.sciencedirect.com/science/article/pii/S0022519316001260> > https://www.sciencedaily.com/releases/2015/01/150107101405.htm > <https://www.sciencedaily.com/releases/2015/01/150107101405.htm> > may have emerged as secondary or even tertiary “memory” of something > underlying deeper below the microbiological surface. It is at least worth > thinking in this direction. I do not mean necessarily the role of the number > concept and Platonic origin of the universe, but something probably much more > “physical” or at least staying at the edge between physical/material and > immaterial such as David Deutsch’s constructor theory > (http://constructortheory.org/ <http://constructortheory.org/>) and Brian > Josephson’s “structural/circular theory” > (http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf > <http://arxiv.org/ftp/arxiv/papers/1502/1502.02429.pdf>; > http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf > <http://arxiv.org/ftp/arxiv/papers/1506/1506.06774.pdf>; > http://arxiv.org/pdf/1108.4860.pdf <http://arxiv.org/pdf/1108.4860.pdf>) > searching for the theories underpinning the foundations of the physical laws > (and following Wheeler’s definition for a “Law without Law”. > > Some of you may say that QT and Gravitation Theory are responsible for such > kind of strange effects, but I would rather leave the brackets open, because > the recent discussion about potentialities and actualities in QM brings up > the idea that there are still different ways of looking at those concepts > (although they are strictly defined in their core domains). This was actually > also the lesson from the last special issue on integral biomathics (2015) > dedicated to phenomenology, with the different opinions of scientists and > philosophers on obviously clear matters in their domains. This is why also > the question of what we define as science needs to be probably revised in > future to include also such issues that are “felt” rather than “reasoned”, > even if we do not have the “proofs” yet, because the proofs also emerge as > subjective (or perhaps “suggested”! – ask the psychologists for that aspect) > thoughts in the minds of the mathematicians. I am really glad that we began > such a phenomenological discussion on this aspect such as Hipolito’s paper > (http://www.sciencedirect.com/science/article/pii/S0079610715000899 > <http://www.sciencedirect.com/science/article/pii/S0079610715000899>) that > was widely commented in the reviewer’s circle. In many cases when we have a > “fuzzy” intuition about a certain relationship or analogy we miss the correct > definitions and concepts, and so in a creative act to hold down the flying > thought we move to using examples, metaphors, pictures. Pedro correctly > addressed the explanatory problem of science which presupposes a certain > causative and predicative “workflow” to derive a conclusion from the facts, > and this is the way in which also proofs are (selectively) made. As a young > scholar I often wondered how artificially people like Gauss, Cauchy and > Weierstrass design their proofs, but then I got used to that style. It was a > question of overall convention. I am thankful to Lou for his response on my > question about using adequate “resonant” methods to model developmental > biology, because this is also an important aspect of the biology (and physics > as well) including the phenomenological/first-person view of an > “observer-participant” (to use Vrobel’s term) which is crucial for > understanding the process of self-reflection/recursion/cycle in science, > which is usually led by what?: the intuition, also well recognized by such > giants like Poincare and Einstein. Isn’t not “resonance” in the core of > detecting such vibration between the observer and the observed? Because > logic, backtracing and proof come later. > > > > And finally, when looking at the clear simple mathematical abstractions of > numbers, vectors, directions, sets, algebras, geometries, etc. used by many > without scrutinizing when developing system (biological) models of yet > another kind of mechanics/automation/machinery of the physical reality, I am > asking myself which are the premises for using such tools to describe a > model: the parameters, or the idea behind? It is probably not a commonly > known fact (even for those who are engaged with such exciting disciplines as > algebraic geometry and geometrical algebra, now considered to be very close > to what we wish to express in biology) that William Hamilton, the inventor of > the quaternions did not simply use the already known concept of “vector” in > his method. Instead he used “step” with “direction” to express a duration of > time (or “duree” as Husserl called it from the other side of the > phenomenological divide) and action (to move from A to B): two very > biology-related concepts at that time (although they may be considered as > physical or computational today). He actually stated that if there is > geometry as a pure science of space, then algebra must be the pure science of > time [1]. What did we actually gain for biology from merging space and time > in physics? And if we apply a specific mathematical-computational technique > what is the key idea/intuition behind it?. Because, as a colleague > pathologist told me this morning about the model correctness when predicting > the development of tumors: the model can be assumed for being correct based > on the interpretation of some (limited) set of data, but Ptolemy's system was > also considered to be correct in its rather complex way of predicting the > movement of the celestial bodies. Where is the difference? I am curious about > your opinion. > > > > Reference: > > [1] W. R. Hamilton, 1835. Theory of Conjugate Functions, or Algebraic > Couples; with a Preliminary or Elementary Essay on Algebra as the Science of > Pure Time. Trans. Royal Irish Acad., Vol. XVII, Part II. 292-422. > > > Best, > > > Plamen > > ______________________ > > 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics > and Phenomenological Philosophy > <http://www.sciencedirect.com/science/journal/00796107/119/3> > (note: free access to all articles until July 19th, 2016) > > > _______________________________________________ > Fis mailing list > Fis@listas.unizar.es <mailto:Fis@listas.unizar.es> > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis > <http://listas.unizar.es/cgi-bin/mailman/listinfo/fis> > > > _______________________________________________ > Fis mailing list > Fis@listas.unizar.es > http://listas.unizar.es/cgi-bin/mailman/listinfo/fis
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