Any non-biological complex systems?

[Marcus G. Daniels]

Eric writes:

"This creates difficulties like deciding when two things are the same molecule; when two molecules arrived at through different pathways are actually isomorphisms of the same label set, etc.  In random network-extension algorithms, this entails solving the graph-isomorphism problem a very very large number of times, and the underlying representational system must be provably well-defined."

Looks like MØD uses the Boost (C++) graph library in a deep way.  They must have thought about parallel approaches, but I suppose it is complicated enough already.

Eventually, the D-Wave or another annealer could be a useful tool here...

https://www.nature.com/articles/srep11168

"5. There has been some discussion of raising pattern-matching above the level of atoms or local clusters, to inductively-defined patterns like crystal faces, but no serious attempt to formulate that problem yet."

..and also for this and the stereochemistry matching. 

Anyway, thanks for all that.  It is really interesting..

Marcus

---

From: Friam <[hidden email]> on behalf of Eric Smith <[hidden email]>
Sent: Sunday, June 4, 2017 5:10:36 AM
To: The Friday Morning Applied Complexity Coffee Group
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Thanks for this Marcus,

> One could imagine coupling a physical simulation to a search procedure for functional behaviors like memories and doorways.   The detection combinatorics would be challenging, assuming the physical simulation were possible at sufficient fidelity, but perhaps could be constrained by virtue of spatial locality.  

Yes.  I can’t bring to mind anybody who seems to be doing important work in this entirely within simulation, but Leroy Cronin in Glasgow is trying to combine highly parallel robot-maintained reaction vessels with pattern-matching computation and feedback, so see if he can search for properties and then extract chemical mixtures that will instantiate them.
http://www.chem.gla.ac.uk/cronin/
Lee is a handful, and his group is the size of a small town (larger than some small towns in NM, I suspect), so one gets the sense of massive seiving for most-anything, with the hope that some fraction of that will remain of interest for longer than the time Lee is promoting it.  The project is really different, though, from anything I have seen before.  It begs to be integrated with modern AI, which has become quite flexible in what you are allowed to call salient, so one can search in very open-ended ways.

> I don't know much about coarse-graining organic chemistry simulators.  For comparison, with molecular dynamics a billion atoms is possible (on a budget of a few megawatts), but not for more than tens of nanoseconds.   I've found game physics engines like Bullet Physics are nice for coarse-grained models because they are fast (optimized to graphics processors) and easy to interleave control or detection logic.  However, they couldn't (without more work) decompose the space across memory domains of a cluster.

Interesting.  I don’t know much about molecular-dynamics simulations, which is deeply an expert’s game, though I guess most major universities have somebody in chemistry or biochem who specializes in it.  If one is willing to go one level out, and ask which questions are hard at the level of network synthesis and search, taking reaction primitives as input data, the graph-grammar methods are becoming pretty sophisticated.  The best I know of is the current state of the project that started with Peter Stadler but is now dispersed across German-speaking Europe and Scandinavia:
http://cheminf.imada.sdu.dk/mod/
Much of what makes this a hard and interesting computational project doesn’t show if one merely wants to do chemistry.  It comes up because they are trying to create a consistent representational system.  This creates difficulties like deciding when two things are the same molecule; when two molecules arrived at through different pathways are actually isomorphisms of the same label set, etc.  In random network-extension algorithms, this entails solving the graph-isomorphism problem a very very large number of times, and the underlying representational system must be provably well-defined.  It is in coming up with representations that are more well-defined than SMILES or INCHI, and implementing most-modern isomorphism searches, that these guys are the furthest along.  There is also a playground linked from their main page, though I am told they recognize their documentation may be a bit off-putting to people not used to wading into new systems. 

The current state of the graph-grammar project is several-fold:
1. Bond topology is present, and has been for some time.
2. Simple stereochemistry of carbon is now implemented, and less-simple stereochemistry that requires non-local propagation through a molecule to determine equivalence of representations is next to come.
3. Stereochemistry of metals, which will be the gateway to crucial mechanisms of metal catalysis, is planned.
4. There is a project, privately held, to port the entire Beilstein database of reaction mechanisms to graph-grammar representations, after which engines like this become an incredible tool.  RIght now the bottleneck is usually manual coding of the mechanisms of interest. 
5. There has been some discussion of raising pattern-matching above the level of atoms or local clusters, to inductively-defined patterns like crystal faces, but no serious attempt to formulate that problem yet.

Even with the limited state of what they can do, they have achieved some tolerable comparisons against messy chemical systems, like the formaldehyde-addition network known as the “formose network”, and the HCN polymerization and hydrolysis system.  Both are famously complicated, and both have long-standing interest to Origin of Life people, though their exact situation relative to planetary chemistry is easy to argue about.

All best,

Eric



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FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
to unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
FRIAM-COMIC http://friam-comic.blogspot.com/ by Dr. Strangelove

[gepr]

Excellent typology, Eric.

1) Memory, 2) doorways, 3) autonomous, 4) model, 5) control system, and 6) agency.

It seems 1-2 are about the boundary. 3 is the closure. 4-5 are proto-semantic, separating what a thing is from what it means. And 6 is the mechanism for ambiguity (symbols, switches, where a thing can mean more than one thing).

re: "a natural sense of a system's own delimitation."  I think you describe it well enough when talking about reflectivity. Such a natural boundary must be natural to a given sense/perspective. A pre-reflective system's boundary is determined in part by its context (since you cited Ashby, H_c >= H_s). But it's a much stronger statement to suggest that a boundary can be determined from/by the perspective of the bounded.


On June 3, 2017 8:53:18 AM PDT, Eric Smith <[hidden email]> wrote:

>1. Protected degrees of freedom are a precondition to even the
>possibility of MEMORY.  If you are a mere physical degree of freedom,
>and you are always coupled to your environment, you are nothing
>different than an instant-by-instant reflection of the immediate local
>state of your environment.  All of the later concepts in the list
>require various forms of internal state that have enough insulation to
>be protected from constant harassment.  So where in the physical world
>are suitably decoupled degrees of freedom available to be found?  (Much
>later, to be built, but not yet.)
>
>2. Some kind of dynamical variables need to be capable of being
>couplers that can become DOORWAYS, so that the other DOF are sometimes
>coupled and sometimes not.  A DOF that is always behind a wall (a
>chemical reaction behind such a high energy barrier that it is never
>achieved) can’t remember anything because, although it can certianly
>hold a state, it is never in contact with the environment that would
>imprint anything on that state.  This doesn’t yet talk about how the
>open/close states of the doorway happen, which will determine when and
>what it allows the environment to imprint on the memory variable, and
>for how long that imprint can be held.  Here one can be quite precese
>with examples without invoking biology.  Organic chemistry at low
>energy in water is largely non-active.  Metal centers, particular
>d-block elements, are the major doorways that govern the sectors of
>organic chemistry available to early ocean-rock worlds.  Many enzymes
>still use them in something not too far from a mineral or soluble
>metal-ligand complex state, with a little tuning.  In this case, the
>doorway works just through physical drift.  Molecules free in solution
>are inert; those that bump into a metal can potentially become active;
>when they dissolve and drift on, they become inert again.  This leads
>to a very different set of relations between thermal energy and
>information in reactions, than simple thermally-activated reactions
>among the same species.  Probably one can invoke many other examples.  
>
>3. Some of the internal variables need to be capable of carrying on an
>AUTONOMOUS dynamics or internal process.  I guess a memory variable can
>sit there passively and still, at some level, categorize the way a
>system (set of DOF) responds to an environmental event, but for most of
>the later levels, there needs to be actual internal dynamics.  This in
>itself is not so hard; the world is far from equilibrium in any number
>of dimensions, and for something to be moving in a direction is not
>rare.
>
>4. Internal dynamics can be autonomous, but it isn’t really “about”
>anything unless something about the configuration constitutes a MODEL
>in the sense of Conant and Ashby from old 1950s control theory.  How
>the model is registered, and how reflexive or self-referential the
>internal dynamics needs to be for a meaningful model to be imprinted,
>probably ramify to many differenent questions.  I would of course be
>happy to produce an interesting case of the emergence of any of them.
>
>5. At some stage, a protected internal process of which the state of
>the model is part needs to act back on the doorway, if we are to be
>justified in saying the basic relation of a CONTROL SYSTEM has come
>into existence.  Here again I intend a Conant and Ashby line of
>thought: that “Every good controller “contains? entails?” a model of
>the system controlled.  There has to be some internal state that is
>capable of being in different relations to the state of the world, and
>then the internal dynamics has to take an input from a comparison of
>those two states.  Only if the resulting action feeds back on the
>state, does the system start controlling its own interaction with the
>world (for instance, what gets remembered).
>
>6. The next one is hard for me to say, even at the very low standards
>of the previous five:  I can be a control system with a model of my
>world, even if I have only modest machinery.  A membrane-bound protein
>that lets in some molecules and ignores others, and which is preserved
>in a population through some kind of filtering, is a perfectly good
>control-theoretic model in the C&A sense.  But it only implicitly
>models its environment.  I have not yet added the assumption that there
>is some kind of REFLEXIVITY or REFLECTION (in the sense of Quines) so
>that the model includes representations of possible counterfactual
>states of the internal variables themselves.  If there is a physical
>process that drives a system’s parts into a configuration where that
>happens, then one of the things an internal process _could_ do is use
>the modeled futures to internally select among many responses to a
>situation of which it is capable.  Only at that stage would I feel
>compelled to introduce a concept of AGENCY, where for my practical
>purposes, I am happy to use the word as game theorists use it.  An
>agent is a kind of thing that fills one of the slots that games have
>for “players”, which must be provided for the mechanics of the game to
>execute, and where the agents have some way to convert specification of
>the game into a sequence of moves that are not individually dictated by
>the game itself.  I am sure there are lots of other notions of agency
>(ABM has a much more permissive notion, which can be as little as a
>dynamical Monte Carlo, or can be full-blown game-theoretic player), but
>for the purpose of trying to draw levels from the foregoing, this one
>seemed enough to me to propose a concrete problem.

...

>So I would argue that, with respect to the accumulation of hierarchy,
>there is a natural sense of a system’s own delimitation, to the extent
>that the parts that are sufficiently stable and sufficiently
>consequential to build something on top of by reinforcement become the
>foundation that holds other parts together.  


--
⛧glen⛧

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[Nick Thompson]

Dear Eric and Steve, and the gang,

 

When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest. 

 

Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.

 

So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.    

 

So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”

 

An object is any collection or entity designated for the purposes of conversation.

 

A system is a set of objects that interact more closely with one another than they do with entities outside the set.  

 

A system is complex if the objects that compose it are themselves systems.

 

Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”    

 

                Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system. 

 

Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  . 

 

One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not. 

 

I miss you all already.  If any of you have any inclination to envy a sojourn in the East, just be advised that the sun has barely been out since we got here, the temperature has NEVER been above 75, and… and … I can walk to my mailbox without touching the ground  on the backs of the deer ticks waiting in ambush outside my front door.  Why Roger has not died of exposure or rickets in Boston Harbor is a mystery to me.

 

All the best,

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of Eric Smith
Sent: Saturday, June 03, 2017 11:53 AM
To: Stephen Guerin <[hidden email]>
Cc: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Hi Steve and Nick,

 

Sorry to have dropped off.  I tried to read the very vigorous thread, to the extent I could, as it went by.  There is a lot there that seems to remain in the core of one thing that brings this crowd and several others together, and is conceptually far from finished business.  I can’t aim for Nick’s precision, or Steve’s coverage, unless there is some particular thing to solve, so my way of doing these things tends to be more limited than the main thread was.

 

On Russ’s question, I tried to give a lecture in an informal summer school a couple of years ago, to propose what sequence of changes in physical architecture would justify bringing in each of a series of new concepts.  I don’t have worked examples behind any of these cases (for a couple of them there are toy-model ideas), so this is the kind of work that is probably of little value and even less trustworthiness.  I don’t remember exactly the layout, but I think the sequence contained something like this (ALLCAPS are meant to be informal descriptors for concept keywords):

 

1. Protected degrees of freedom are a precondition to even the possibility of MEMORY.  If you are a mere physical degree of freedom, and you are always coupled to your environment, you are nothing different than an instant-by-instant reflection of the immediate local state of your environment.  All of the later concepts in the list require various forms of internal state that have enough insulation to be protected from constant harassment.  So where in the physical world are suitably decoupled degrees of freedom available to be found?  (Much later, to be built, but not yet.)

 

2. Some kind of dynamical variables need to be capable of being couplers that can become DOORWAYS, so that the other DOF are sometimes coupled and sometimes not.  A DOF that is always behind a wall (a chemical reaction behind such a high energy barrier that it is never achieved) can’t remember anything because, although it can certianly hold a state, it is never in contact with the environment that would imprint anything on that state.  This doesn’t yet talk about how the open/close states of the doorway happen, which will determine when and what it allows the environment to imprint on the memory variable, and for how long that imprint can be held.  Here one can be quite precese with examples without invoking biology.  Organic chemistry at low energy in water is largely non-active.  Metal centers, particular d-block elements, are the major doorways that govern the sectors of organic chemistry available to early ocean-rock worlds.  Many enzymes still use them in something not too far from a mineral or soluble metal-ligand complex state, with a little tuning.  In this case, the doorway works just through physical drift.  Molecules free in solution are inert; those that bump into a metal can potentially become active; when they dissolve and drift on, they become inert again.  This leads to a very different set of relations between thermal energy and information in reactions, than simple thermally-activated reactions among the same species.  Probably one can invoke many other examples. 

 

3. Some of the internal variables need to be capable of carrying on an AUTONOMOUS dynamics or internal process.  I guess a memory variable can sit there passively and still, at some level, categorize the way a system (set of DOF) responds to an environmental event, but for most of the later levels, there needs to be actual internal dynamics.  This in itself is not so hard; the world is far from equilibrium in any number of dimensions, and for something to be moving in a direction is not rare.

 

4. Internal dynamics can be autonomous, but it isn’t really “about” anything unless something about the configuration constitutes a MODEL in the sense of Conant and Ashby from old 1950s control theory.  How the model is registered, and how reflexive or self-referential the internal dynamics needs to be for a meaningful model to be imprinted, probably ramify to many differenent questions.  I would of course be happy to produce an interesting case of the emergence of any of them.

 

5. At some stage, a protected internal process of which the state of the model is part needs to act back on the doorway, if we are to be justified in saying the basic relation of a CONTROL SYSTEM has come into existence.  Here again I intend a Conant and Ashby line of thought: that “Every good controller “contains? entails?” a model of the system controlled.  There has to be some internal state that is capable of being in different relations to the state of the world, and then the internal dynamics has to take an input from a comparison of those two states.  Only if the resulting action feeds back on the state, does the system start controlling its own interaction with the world (for instance, what gets remembered).

 

6. The next one is hard for me to say, even at the very low standards of the previous five:  I can be a control system with a model of my world, even if I have only modest machinery.  A membrane-bound protein that lets in some molecules and ignores others, and which is preserved in a population through some kind of filtering, is a perfectly good control-theoretic model in the C&A sense.  But it only implicitly models its environment.  I have not yet added the assumption that there is some kind of REFLEXIVITY or REFLECTION (in the sense of Quines) so that the model includes representations of possible counterfactual states of the internal variables themselves.  If there is a physical process that drives a system’s parts into a configuration where that happens, then one of the things an internal process _could_ do is use the modeled futures to internally select among many responses to a situation of which it is capable.  Only at that stage would I feel compelled to introduce a concept of AGENCY, where for my practical purposes, I am happy to use the word as game theorists use it.  An agent is a kind of thing that fills one of the slots that games have for “players”, which must be provided for the mechanics of the game to execute, and where the agents have some way to convert specification of the game into a sequence of moves that are not individually dictated by the game itself.  I am sure there are lots of other notions of agency (ABM has a much more permissive notion, which can be as little as a dynamical Monte Carlo, or can be full-blown game-theoretic player), but for the purpose of trying to draw levels from the foregoing, this one seemed enough to me to propose a concrete problem.

 

I am sure there are more, but I think I stopped there, and this was about as far as Russ was asking, too, I think.

 

So the challenge (speaking only for myself, of course) is to find places in matter where the structure of the dynamics as one starts with it, drives the activity into regions of material architecture that take on first one, and then another, of the above new patterns.  I assume they have to occur in more or less this order, because it is hard for me to see how to build the later concepts without having the earlier ones as building blocks.  I like chemistry as a medium, because the state space itself supports a lot of complexity, and the temporal variability of reactions, plus the fact that catalytic relations exist, offer large separations of timescales that can be used to fill functional classes like memories.  Whether it becomes hard to build much hierarchy in any system that doesn’t benefit from the intensive way chemistry makes complexity easy, is a question I find interesting.  I don’t know how one answers it with better than musing.

 

This is all kind of armchair statements of the obvious, and I don’t mean to make it out as more.  I know there are people like Rosen who made long careers of trying to tease all this out at length, and have written a lot on it.  Maybe they include all this obvious stuff and also much more.

 

 

But branching, to Nick’s point about the extent to which “a system” “chooses” something about the relevant delimitations of itself.  I think this becomes an operationalizable question in the spirit of Leslie Valiant’s PAC learnability framework.  (Probably Approximately Correct).  Valiant’s wish was to show that the learnable tasks, like the computable functions, make a formally definable class.  I don’t think that discussion is anywhere near being closed one way or another, but the attempt to systematize what can be learned, how hard it is, and how much either of those depends on the embedding context, seems very helpful and clarifying to me.

 

The connection would be this:  Suppose you have some internal state, and some internal dynamics, and the state under the influence of the dynamics — or even intervals within the dynamics under the influence of their longer trajectory — can pass through many different patterns.  Suppose that somewhere there is a reinforcement learner working on those patterns in some systematic way.  It could be an environment selectively filtering many copies of you with slight variations, or it could be some other subroutine within your internal dynamics.  The kind of thing I have in mind is: suppose there is a synthetic organic chemistry generating small molecules, lots of copies of some of them, fewer copies of others, and as a by-product of that molecular pool, something like polymers large enough to be capable of function, but happening to have functions only at random, are one of the things that can arise.  Out of all this mess, focus on the PAC-learnability problem of evolving an enzyme.  The things that should determine whether a given selective protocol can find and then fix something should be:

1. how frequently is that substrate even encountered?  If not often, it is hard to maintain any memory about it.  It is easy for farmers to remember to water the crops during dry spring winds, because that happens every year.  It is harder for a culture to remember to run uphill when the tide goes way out for a very long time, since maybe that hasn happened where they live in the past 600 years.

2. how consequential is the particular molecule.  If very consequential, selection can be more severe, and leave a stronger signal, which maybe can be remembered a little longer. 

There is probably lots of other fine structure to learnability, such as whether the environment is effectively serving as a “teacher” with respect to that particular problem (Valiant’s term, used to illustrate concrete cases), but I won’t ramble more than this.

 

How does that relate to Nick’s point; one more indirection on the way to getting there:

Steve mentioned (in some thread, a few weeks ago) the concept of Order Parameter, which is a kind of predictive statistic that suddenly starts to have a lot more predictive content, and to be more stable, when a system goes into an ordered phase.  If you are going to try to use reinforcement learning to select higher-order structure on some low-order patterns that you are already producing, the order parameters are the things that take the most regular values, and they most robustly support induction, which is what all reinfocement learning is.  (A finite system cannot help but induct: in a world of potentially unlimited variability, it has only finitely many possible states, so perforce it will make infinite equivalence classes of environmental states, by responding to many situations that in detail are different, with the same response.  That doesn’t mean that “the problem of induction” “has” any solution.  It only means that every finite system is perforce a commitment to some inductive hypothesis.) 

 

So I would argue that, with respect to the accumulation of hierarchy, there is a natural sense of a system’s own delimitation, to the extent that the parts that are sufficiently stable and sufficiently consequential to build something on top of by reinforcement become the foundation that holds other parts together.  I agree with the purpose underlying Steve G’s point: that this can depend in part on what kind of environment there is, since this is part of the learning protocol.  But we also all recognize that — at least insofar as the statistical concepts found useful in equilibrium thermo and fundamental processes continue to be useful in more elaborate dynamical realms — the Order Parameter as a Minimum Sufficient Statistic for distributions over future states is an informationally special quantity.

 

Sorry for long harangue, and I don’t know whether this has anything new in it that the list hasn’t revisited many times.

 

All best,

 

Eric

 

 

 

 

> On May 29, 2017, at 8:29 PM, Stephen Guerin <[hidden email]> wrote:

>

>

>

> ______________________________________________________________________

> _

> [hidden email]

> CEO, Simtable  http://www.simtable.com

> 1600 Lena St #D1, Santa Fe, NM 87505

> office: [phone] mobile: [phone]

> twitter: @simtable

>

> On Mon, May 29, 2017 at 12:10 PM, Nick Thompson <[hidden email]> wrote:

> SG,

>

> 

>

> There are now THREE issues lurking here between us.

>

> 

>

> IS THE CRITERION FOR A SYSTEM ARBITRARY: You say yes; I say no.  We’ve already covered that ground.

>

>

> In my post, I said it is not arbitrary. It's a function of what the researcher is trying to use it for or explain.

> 

>

> 

>

> IS A HURRICANE A SYSTEM:  For me, that is the question of whether the collection of thunderstorms we call a hurricane interact with one another more than they interact with their collective surroundings.  Another way to put this question is in terms of redundancy.  If we were to go about describing the movements of the thunderstorms of a hurricane, would we get a simpler, less redundant description if we referred their movements to the center of the hurricane.  I think the answer to this question is clearly YES.

>

>

> Yes you could model the movement in a simpler way by modeling the movement of the center point. And that was my second model of a hurricane as a random walker biased by a global wind vector and Coriolis curve term. And I said that was not a complex system.

> 

>

> 

>

> IS A HURRICANE COMPLEX?  For me, complexity means “multi-layered” .  So, a complex system is one composed of other systems.  A hurricane is a system of thunderstorms which themselves are a system of thermals (handwaving, here).  Thus a hurricane is at least a three-level system.  So, yes.  It is complex.

>

>

> I agree about complex systems as having multiple layers - a macro

> scale and a micro scale. I would say there's one system. If I was

> trying to model a hurricane in my first example of an emergent vortex

> dissipating temperature and pressure gradients, I would model the air

> with a combination of air particles and patches of air - at LANL they

> would describe these as particle in a box models or hybrid lagrangian

> and eulerian models. I would not introduce thunderstorms at the micro

> level. But there's many ways to skin a hurricane :-)

>

> Some would say the micro level air particles and air cell components which I would model as finite state machines (agents with a lower case "a") are systems in their own right and have boundaries. I don't see the benefit of calling them systems as their aren't multiple interacting components within them. But don't feel like arguing too hard here.

> 

>

> Eric Smith?

>

>

>

>

> Yes, where are you Eric Smith?

 

 

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[gepr]

Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.  (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.  So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_.  Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.  And that means that your working definition is not naive.  It does rely on an intuition that many of us share.  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.



On 06/06/2017 07:20 AM, Nick Thompson wrote:

> Dear Eric and Steve, and the gang,
>
>  
>
> When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest.  
>
>  
>
> Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.
>
>  
>
> So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.    
>
>  
>
> So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”
>
>  
>
> An object is any collection or entity designated for the purposes of conversation.
>
>  
>
> A system is a set of objects that interact more closely with one another than they do with entities outside the set.  
>
>  
>
> A system is complex if the objects that compose it are themselves systems.
>
>  
>
> Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”    
>
>  
>
>                 Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system.  
>
>  
>
> Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  .  
>
>  
>
> One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not.  

--
␦glen?
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[glen ep ropella]

E.g. this seems like a coherent definition of coherence.  Is it lost in its technical detail?  Maybe.  Ontologies are rife with assumptions, like any other model.

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules
http://www.sciencedirect.com/science/article/pii/S0002929715004954

> Cluster biological coherence was calculated as follows. First, we retrieved the GO terms associated with the disease genes under- lying cluster syndromes. These GO terms were then pooled across all genes causing the same syndrome, resulting in a set of GO terms annotated to the syndrome. To incorporate ontological relation- ships between GO terms into the comparison, we added all term ancestors to the GO term set, excluding the root terms for the three GO categories. This approach has been shown to work as well as more complicated approaches.31 For each syndrome pair, we deter- mined the GO term overlap between the two syndromes:
>
>   S_p(i,j) = n(G_i ∩ G_j)/n(G_i ∪ G_j)              (1)
>
> where S_p(i,j) is the pairwise GO term overlap score for diseases i and j, n is the number of GO terms meeting the specified criteria, and G_i and G_j are the sets of GO terms associated with diseases i and j, respectively. For each cluster, the mean pairwise overlap was used as the biological coherence score for that cluster:
>
>           n
>    S_c =  Σ S_p(i,j)/n
>          i,j
>
> where S_c is the genetic cohesiveness score for cluster c, S_p(i,j) is the GO overlap score for diseases i and j, and n is the number of disease pairs in the cluster. The mean biological coherence score across all clusters was used as the overall cluster biological coherence score for the database:
>
>        n
>    S = Σ S_c/n
>        c
>
> where S is the overall genetic cohesiveness score for the phenotype data set, S_c is the genetic cohesiveness score for cluster c, and n is the number of clusters in the phenotype data set.

On 06/06/2017 08:33 AM, ┣glen┫ wrote:
> Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_.  Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.  And that means that your working definition is not naive.  It does rely on an intuition that many of us share.  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

--
glen ep ropella ⊥ 971-280-5699

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[Marcus G. Daniels]

If one had full genome sequences for a lot of people and used a supervised learning procedure to predict the intellectual disability, that would not be result in a coherent explanation?

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of glen ep ropella
Sent: Tuesday, June 06, 2017 4:00 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

E.g. this seems like a coherent definition of coherence.  Is it lost in its technical detail?  Maybe.  Ontologies are rife with assumptions, like any other model.

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules
http://www.sciencedirect.com/science/article/pii/S0002929715004954

> Cluster biological coherence was calculated as follows. First, we retrieved the GO terms associated with the disease genes under- lying cluster syndromes. These GO terms were then pooled across all genes causing the same syndrome, resulting in a set of GO terms annotated to the syndrome. To incorporate ontological relation- ships between GO terms into the comparison, we added all term ancestors to the GO term set, excluding the root terms for the three GO categories. This approach has been shown to work as well as more complicated approaches.31 For each syndrome pair, we deter- mined the GO term overlap between the two syndromes:
>
>   S_p(i,j) = n(G_i ∩ G_j)/n(G_i ∪ G_j)              (1)
>
> where S_p(i,j) is the pairwise GO term overlap score for diseases i and j, n is the number of GO terms meeting the specified criteria, and G_i and G_j are the sets of GO terms associated with diseases i and j, respectively. For each cluster, the mean pairwise overlap was used as the biological coherence score for that cluster:
>
>           n
>    S_c =  Σ S_p(i,j)/n
>          i,j
>
> where S_c is the genetic cohesiveness score for cluster c, S_p(i,j) is the GO overlap score for diseases i and j, and n is the number of disease pairs in the cluster. The mean biological coherence score across all clusters was used as the overall cluster biological coherence score for the database:
>
>        n
>    S = Σ S_c/n
>        c
>
> where S is the overall genetic cohesiveness score for the phenotype data set, S_c is the genetic cohesiveness score for cluster c, and n is the number of clusters in the phenotype data set.

On 06/06/2017 08:33 AM, ┣glen┫ wrote:
> Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_.  Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.  And that means that your working definition is not naive.  It does rely on an intuition that many of us share.  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

--
glen ep ropella ⊥ 971-280-5699

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[Marcus G. Daniels]

To clarify, one could contrast a procedure that resulted in the most reliable predictions but was not built on any ontology vs. one that could be communicated in a compact way and generalized to make other kinds of predictions but all of its predictions were not as reliable.

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of Marcus Daniels
Sent: Tuesday, June 06, 2017 4:16 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

If one had full genome sequences for a lot of people and used a supervised learning procedure to predict the intellectual disability, that would not be result in a coherent explanation?

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of glen ep ropella
Sent: Tuesday, June 06, 2017 4:00 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

E.g. this seems like a coherent definition of coherence.  Is it lost in its technical detail?  Maybe.  Ontologies are rife with assumptions, like any other model.

Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules
http://www.sciencedirect.com/science/article/pii/S0002929715004954

> Cluster biological coherence was calculated as follows. First, we retrieved the GO terms associated with the disease genes under- lying cluster syndromes. These GO terms were then pooled across all genes causing the same syndrome, resulting in a set of GO terms annotated to the syndrome. To incorporate ontological relation- ships between GO terms into the comparison, we added all term ancestors to the GO term set, excluding the root terms for the three GO categories. This approach has been shown to work as well as more complicated approaches.31 For each syndrome pair, we deter- mined the GO term overlap between the two syndromes:
>
>   S_p(i,j) = n(G_i ∩ G_j)/n(G_i ∪ G_j)              (1)
>
> where S_p(i,j) is the pairwise GO term overlap score for diseases i and j, n is the number of GO terms meeting the specified criteria, and G_i and G_j are the sets of GO terms associated with diseases i and j, respectively. For each cluster, the mean pairwise overlap was used as the biological coherence score for that cluster:
>
>           n
>    S_c =  Σ S_p(i,j)/n
>          i,j
>
> where S_c is the genetic cohesiveness score for cluster c, S_p(i,j) is the GO overlap score for diseases i and j, and n is the number of disease pairs in the cluster. The mean biological coherence score across all clusters was used as the overall cluster biological coherence score for the database:
>
>        n
>    S = Σ S_c/n
>        c
>
> where S is the overall genetic cohesiveness score for the phenotype data set, S_c is the genetic cohesiveness score for cluster c, and n is the number of clusters in the phenotype data set.

On 06/06/2017 08:33 AM, ┣glen┫ wrote:
> Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_.  Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.  And that means that your working definition is not naive.  It does rely on an intuition that many of us share.  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

--
glen ep ropella ⊥ 971-280-5699

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[Nick Thompson]

Thanks, Glen,

 

Larding below:

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of ?glen?
Sent: Tuesday, June 06, 2017 11:34 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.

[NST==>I missed this, and going back through the thread, I have not found it.  Can you reproduce it for me without too much strain?  <==nst]

 (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.

[NST==>I am not talking about tautology, here: x is x.  I am talking about circular explanation: x is the cause of x.  Surely you would agree that having defined X as whatever is caused by Y, I have not added much to our store of knowledge concerning what sorts of things Y causes.  But you are correct, not all circular explanations are entirely vicious/vacuous, of course. It depends on the assumptions the discussants bring to the table.  See, https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations<==nst]

 So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

[NST==>I would be grateful for a passage from any of these folks where strictly circular reasoning is used to good effect. <==nst]

 

Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_. 

[NST==>Well, if that is how one defines closure, then I am bound to agree.  Then, it’s not clear to me what the function of “nothing but” is, in your sentence.  But reading through your earlier posts (petri dish) suggests that for you closure is absolute; for me, systematicity is a variable and we would have to have some sort of a mutual understanding of where along that dimension we start calling something a system. <==nst]

Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.

[NST==>Yes, but coherence, for me, carries more richness than what I was grasping for.  For you, perhaps not.  I guess “coherence” is ok.  <==nst]

 And that means that your working definition is not naive.

[NST==>Huh?  You mean I don’t get to be in charge of whether I am naïve, or not?  Are you some kind of behaviorist?  <==nst]

 It does rely on an intuition that many of us share.

[NST==>Bollox!  It relies on the plain meaning of the word (he said grumpily).  <==nst]

  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

[NST==>This thread isn’t coherent for me.  Somebody asks if natural systems can be complex.  This is a lot of intricate talk which I frankly didn’t follow but which seemed to suggest that only symbol systems could be complex.  But I could detect no definition of complexity to warrant that restriction.  So I offered a definition of complexity (which may have been the same as yours – forgive me), offered an example of a natural complex system, a hurricane, and came to the conclusion that indeed, some natural systems are complex.  To my knowledge, nobody has addressed that claim.  But I have been traveling, my eye sight sucks, and I may have missed it.  If anybody has addressed this claim, could somebody direct me to a copy of their post.  I would be grateful. <==nst]

 

Perhaps Steve Smith, who has often rescued me when I have made these messes in the past, could gently point out to me my error. 

 

Top temperature today 49 degrees.  90’s predicted for next week. I am ready.

 

Best to you all,

 

Nick

 

 

 

 

 

On 06/06/2017 07:20 AM, Nick Thompson wrote:

> Dear Eric and Steve, and the gang,

>

> 

>

> When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest. 

>

> 

>

> Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.

>

> 

>

> So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.   

>

> 

>

> So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”

>

>  

>

> An object is any collection or entity designated for the purposes of conversation.

>

> 

>

> A system is a set of objects that interact more closely with one another than they do with entities outside the set. 

>

> 

>

> A system is complex if the objects that compose it are themselves systems.

>

> 

>

> Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”   

>

> 

>

>                 Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system. 

>

> 

>

> Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  . 

>

> 

>

> One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not. 

 

--

␦glen?

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[Russ Abbott]

Nick,

When you suggested a hurricane as an example of a complex system I replied that a hurricane is interesting because it's a non-biological system (and not a human artifact) that uses energy that it extracts from outside itself to maintain its structure. That's an interesting and important characteristic. Biological systems do that also, Maturana & Varela, but I don't see that as sufficient to grant it the quality of being a complex system.

-- Russ

On Tue, Jun 6, 2017 at 9:06 PM Nick Thompson <[hidden email]> wrote:

Thanks, Glen,

 

Larding below:

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of ?glen?
Sent: Tuesday, June 06, 2017 11:34 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.

[NST==>I missed this, and going back through the thread, I have not found it.  Can you reproduce it for me without too much strain?  <==nst]

 (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.

[NST==>I am not talking about tautology, here: x is x.  I am talking about circular explanation: x is the cause of x.  Surely you would agree that having defined X as whatever is caused by Y, I have not added much to our store of knowledge concerning what sorts of things Y causes.  But you are correct, not all circular explanations are entirely vicious/vacuous, of course. It depends on the assumptions the discussants bring to the table.  See, https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations<==nst]

 So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

[NST==>I would be grateful for a passage from any of these folks where strictly circular reasoning is used to good effect. <==nst]

 

Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_. 

[NST==>Well, if that is how one defines closure, then I am bound to agree.  Then, it’s not clear to me what the function of “nothing but” is, in your sentence.  But reading through your earlier posts (petri dish) suggests that for you closure is absolute; for me, systematicity is a variable and we would have to have some sort of a mutual understanding of where along that dimension we start calling something a system. <==nst]

Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.

[NST==>Yes, but coherence, for me, carries more richness than what I was grasping for.  For you, perhaps not.  I guess “coherence” is ok.  <==nst]

 And that means that your working definition is not naive.

[NST==>Huh?  You mean I don’t get to be in charge of whether I am naïve, or not?  Are you some kind of behaviorist?  <==nst]

 It does rely on an intuition that many of us share.

[NST==>Bollox!  It relies on the plain meaning of the word (he said grumpily).  <==nst]

  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

[NST==>This thread isn’t coherent for me.  Somebody asks if natural systems can be complex.  This is a lot of intricate talk which I frankly didn’t follow but which seemed to suggest that only symbol systems could be complex.  But I could detect no definition of complexity to warrant that restriction.  So I offered a definition of complexity (which may have been the same as yours – forgive me), offered an example of a natural complex system, a hurricane, and came to the conclusion that indeed, some natural systems are complex.  To my knowledge, nobody has addressed that claim.  But I have been traveling, my eye sight sucks, and I may have missed it.  If anybody has addressed this claim, could somebody direct me to a copy of their post.  I would be grateful. <==nst]

 

Perhaps Steve Smith, who has often rescued me when I have made these messes in the past, could gently point out to me my error. 

 

Top temperature today 49 degrees.  90’s predicted for next week. I am ready.

 

Best to you all,

 

Nick

 

 

 

 

 

On 06/06/2017 07:20 AM, Nick Thompson wrote:

> Dear Eric and Steve, and the gang,

>

> 

>

> When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest. 

>

> 

>

> Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.

>

> 

>

> So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.   

>

> 

>

> So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”

>

>  

>

> An object is any collection or entity designated for the purposes of conversation.

>

> 

>

> A system is a set of objects that interact more closely with one another than they do with entities outside the set. 

>

> 

>

> A system is complex if the objects that compose it are themselves systems.

>

> 

>

> Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”   

>

> 

>

>                 Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system. 

>

> 

>

> Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  . 

>

> 

>

> One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not. 

 

--

␦glen?

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[gepr]

Sorry.  I've abused the word coherent as a joke. I probably shouldn't be so flippant.  The defn of coherence they use does depend on an ontology.  But (I think) they use it as an immediate proxy for the real objects.  So, their defn of coherence wouldn't change.  My focus isn't so much on whether their calculation actually works as intended.  Just that it is a more formal concept than Nick's "objects that interact more with themselves than others".

On 06/06/2017 03:44 PM, Marcus Daniels wrote:
> To clarify, one could contrast a procedure that resulted in the most reliable predictions but was not built on any ontology vs. one that could be communicated in a compact way and generalized to make other kinds of predictions but all of its predictions were not as reliable.
>
> -----Original Message-----
> From: Friam [mailto:[hidden email]] On Behalf Of Marcus Daniels
> Sent: Tuesday, June 06, 2017 4:16 PM
> To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
> Subject: Re: [FRIAM] Any non-biological complex systems?
>
> If one had full genome sequences for a lot of people and used a supervised learning procedure to predict the intellectual disability, that would not be result in a coherent explanation?

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[Marcus G. Daniels]

"But (I think) they use it as an immediate proxy for the real objects.  So, their defn of coherence wouldn't change.  My focus isn't so much on whether their calculation actually works as intended.  Just that it is a more formal concept than Nick's "objects that interact more with themselves than others".

In this example, the discussion was more about the composition of functional relationships (ion transport, DNA repair) and their consequences than it is about objects.  

My concern isn't that a calculation work as intended, it is that the desire for formalism could be in opposition to quantitative prediction.   If your goal is to weed out intellectual disability, it might be better to use a statistical model method based on higher dimensional data (e.g. comparing raw sequences), than one that invokes biological concepts.

Marcus
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[gepr]

On 06/06/2017 09:05 PM, Nick Thompson wrote:
> [gepr] Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.
>
> [NST==>I missed this, and going back through the thread, I have not found it.  Can you reproduce it for me without too much strain?  <==nst]

Below is what I wrote in response to Stephen's suggestion that any physical system might qualify as complex.

On 05/26/2017 12:40 PM, glen ☣ wrote:
> Yeah, but you're relying on the ambiguity of the concept.  A system that is only complex for very short spans of time, or under very special conditions wouldn't fit with _most_ people's concept of "complex".  To boot, unadulterated oscillation wouldn't satisfy it either.  And, as has been said earlier in the thread, allowing any an all physical systems to be called "complex" when they're placed under special circumstances defeats the purpose of the concept.

>  (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.
>
> [NST==>I am not talking about tautology, here: x is x.  I am talking about circular explanation: x is the cause of x.  Surely you would agree that having defined X as whatever is caused by Y, I have not added much to our store of knowledge concerning what sorts of things Y causes.  But you are correct, not all circular explanations are entirely vicious/vacuous, of course. It depends on the assumptions the discussants bring to the table.  See, https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations <https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations%3c==nst> <==nst]


We've talked about your recursive filter explanation paper before.  I don't think you responded to what I said about it after EricC's explanation.  Here is my comment: http://redfish.com/pipermail/friam_redfish.com/2017-January/075190.html


>  So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.
>
> [NST==>I would be grateful for a passage from any of these folks where strictly circular reasoning is used to good effect. <==nst]



I will find some.  But a more fundamental read is this: http://math.stanford.edu/~feferman/papers/predicativity.pdf



> Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_.  
>
> [NST==>Well, if that is how one defines closure, then I am bound to agree.  Then, it’s not clear to me what the function of “nothing but” is, in your sentence.  But reading through your earlier posts (petri dish) suggests that for you closure is absolute; for me, systematicity is a variable and we would have to have some sort of a mutual understanding of where along that dimension we start calling something a system. <==nst]


Yes, I can see that.  I'm used to thinking in terms of things being closed to one operation and open to others.  I'm also used to using it as a verb, e.g. "closing a set" by, say, adding the limit point to it.  Or more appropriate to this context, closing a region by wrapping a boundary around to itself like you would by tying a string to itself to get a loop.  Further, a region of some "space" can be "partially closed" by being very convex ... like some champagne flutes, bulging in the middle with a small-ish opening at one end ... or maybe think of a pinhole camera or a black body radiation device.


> Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.
>
> [NST==>Yes, but coherence, for me, carries more richness than what I was grasping for.  For you, perhaps not.  I guess “coherence” is ok.  <==nst]


Coherence can be ambiguous, too.  But my main point is that much of what we've been arguing about in this thread is about closure, what it means, and whether it's necessary for something to be called a complex system.  Russ' claim includes some form of closure.  This is much stronger than Stephen's claim.  Yours falls somewhere between.  But we won't be able to get at your middle ground without more formality.


>  And that means that your working definition is not naive.
>
> [NST==>Huh?  You mean I don’t get to be in charge of whether I am naïve, or not?  Are you some kind of behaviorist?  <==nst]


8^)  Right.  You can't say you're being naive and then get all hyper-technical about whatever naive statement you made.



>   But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.
>
> [NST==>This thread isn’t coherent for me.  Somebody asks if natural systems can be complex.  This is a lot of intricate talk which I frankly didn’t follow but which seemed to suggest that only symbol systems could be complex.  But I could detect no definition of complexity to warrant that restriction.  So I offered a definition of complexity (which may have been the same as yours – forgive me), offered an example of a natural complex system, a hurricane, and came to the conclusion that indeed, some natural systems are complex.  To my knowledge, nobody has addressed that claim.  But I have been traveling, my eye sight sucks, and I may have missed it.  If anybody has addressed this claim, could somebody direct me to a copy of their post.  I would be grateful. <==nst]


Well, as I said above, we have 2 extremes.  Complex systems are everywhere, as long as you catch them at the precise time and in the precise conditions.  The other side is that complex systems rely on a cumulative hierarchy of some sort (Russ's is less fleshed out than EricS'), which means they might be relatively rare.  The discussion of hurricanes is a good one.  My focus here was to shunt your preamble about circularity and getting lost in technicalities.


--
␦glen?

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[gepr]

That's completely reasonable.  I suppose this was a bad example because it's difficult to decouple from its context.


On 06/07/2017 07:10 AM, Marcus Daniels wrote:
> In this example, the discussion was more about the composition of functional relationships (ion transport, DNA repair) and their consequences than it is about objects.  
>
> My concern isn't that a calculation work as intended, it is that the desire for formalism could be in opposition to quantitative prediction.   If your goal is to weed out intellectual disability, it might be better to use a statistical model method based on higher dimensional data (e.g. comparing raw sequences), than one that invokes biological concepts.


--
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[Nick Thompson]

Russ,

 

I seem to be missing some of the correspondence, and I apologize for that.  Thanks for updating me.

 

So, did you also, in your post, offer a definition of “complex system” that excludes hurricanes? 

 

I am, as you would predict, a little troubled by your locution, “that uses energy.”  Seems somehow to suggest that the hurricane, as a system, exists in advance of the energy flows that make it happen.  The “use” metaphor – I use a hammer to hit a nail – implies that both me and the hammer exist before the use takes place.  If we use the hurricane as a metaphor for nail use, the nail and the hammer construct me to use them, or something like that.  That formulation is weird, also, but sufficient to make my point.

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

From: Friam [mailto:[hidden email]] On Behalf Of Russ Abbott
Sent: Wednesday, June 07, 2017 12:46 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Nick,

 

When you suggested a hurricane as an example of a complex system I replied that a hurricane is interesting because it's a non-biological system (and not a human artifact) that uses energy that it extracts from outside itself to maintain its structure. That's an interesting and important characteristic. Biological systems do that also, Maturana & Varela, but I don't see that as sufficient to grant it the quality of being a complex system.

 

-- Russ

 

On Tue, Jun 6, 2017 at 9:06 PM Nick Thompson <[hidden email]> wrote:

Thanks, Glen,

 

Larding below:

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of ?glen?
Sent: Tuesday, June 06, 2017 11:34 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.

[NST==>I missed this, and going back through the thread, I have not found it.  Can you reproduce it for me without too much strain?  <==nst]

 (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.

[NST==>I am not talking about tautology, here: x is x.  I am talking about circular explanation: x is the cause of x.  Surely you would agree that having defined X as whatever is caused by Y, I have not added much to our store of knowledge concerning what sorts of things Y causes.  But you are correct, not all circular explanations are entirely vicious/vacuous, of course. It depends on the assumptions the discussants bring to the table.  See, https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations<==nst]

 So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

[NST==>I would be grateful for a passage from any of these folks where strictly circular reasoning is used to good effect. <==nst]

 

Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_. 

[NST==>Well, if that is how one defines closure, then I am bound to agree.  Then, it’s not clear to me what the function of “nothing but” is, in your sentence.  But reading through your earlier posts (petri dish) suggests that for you closure is absolute; for me, systematicity is a variable and we would have to have some sort of a mutual understanding of where along that dimension we start calling something a system. <==nst]

Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.

[NST==>Yes, but coherence, for me, carries more richness than what I was grasping for.  For you, perhaps not.  I guess “coherence” is ok.  <==nst]

 And that means that your working definition is not naive.

[NST==>Huh?  You mean I don’t get to be in charge of whether I am naïve, or not?  Are you some kind of behaviorist?  <==nst]

 It does rely on an intuition that many of us share.

[NST==>Bollox!  It relies on the plain meaning of the word (he said grumpily).  <==nst]

  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

[NST==>This thread isn’t coherent for me.  Somebody asks if natural systems can be complex.  This is a lot of intricate talk which I frankly didn’t follow but which seemed to suggest that only symbol systems could be complex.  But I could detect no definition of complexity to warrant that restriction.  So I offered a definition of complexity (which may have been the same as yours – forgive me), offered an example of a natural complex system, a hurricane, and came to the conclusion that indeed, some natural systems are complex.  To my knowledge, nobody has addressed that claim.  But I have been traveling, my eye sight sucks, and I may have missed it.  If anybody has addressed this claim, could somebody direct me to a copy of their post.  I would be grateful. <==nst]

 

Perhaps Steve Smith, who has often rescued me when I have made these messes in the past, could gently point out to me my error. 

 

Top temperature today 49 degrees.  90’s predicted for next week. I am ready.

 

Best to you all,

 

Nick

 

 

 

 

 

On 06/06/2017 07:20 AM, Nick Thompson wrote:

> Dear Eric and Steve, and the gang,

>

> 

>

> When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest. 

>

> 

>

> Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.

>

> 

>

> So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.   

>

> 

>

> So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”

>

>  

>

> An object is any collection or entity designated for the purposes of conversation.

>

> 

>

> A system is a set of objects that interact more closely with one another than they do with entities outside the set. 

>

> 

>

> A system is complex if the objects that compose it are themselves systems.

>

> 

>

> Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”   

>

> 

>

>                 Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system. 

>

> 

>

> Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  . 

>

> 

>

> One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not. 

 

--

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[Russ Abbott]

I didn't define complex system. (Actually, this thread is so long I may have offered one. I don't remember.)  

I take a complex system to be a system (do we need to define that? Presumably some collection of interacting entities around which one can draw a boundary that distinguishes the collection from its environment.) that has the following characteristics/capabilities.

• It can acquire and store free energy, e.g., as fat biologically or stress geologically. The free energy is acquired from outside the system.
  
• It does that in multiple (more or less) independent ways, (E.g., lots of "agents.")
• Those reservoirs of free energy can be released by triggers. (E.g., there are switches that open and close the flow of energy from these reservoirs.)
• The released energy flows in some cases act as triggers, i.e., they flip switches, to release other energy flows. 

I think that's the core of it. (I haven't attempted to develop a complete definition. I'm not sure it's worth doing.)

I would like an additional feature, although I'm unsure to what extent I would consider it necessary.

• The system operates in part on the basis of symbols, i.e., information. (I'm not sure things other than biological systems and human artifacts do that, which is what probably prompted my question in the first place.)
  

On Wed, Jun 7, 2017 at 9:05 AM Nick Thompson <[hidden email]> wrote:

Russ,

 

I seem to be missing some of the correspondence, and I apologize for that.  Thanks for updating me.

 

So, did you also, in your post, offer a definition of “complex system” that excludes hurricanes? 

 

I am, as you would predict, a little troubled by your locution, “that uses energy.”  Seems somehow to suggest that the hurricane, as a system, exists in advance of the energy flows that make it happen.  The “use” metaphor – I use a hammer to hit a nail – implies that both me and the hammer exist before the use takes place.  If we use the hurricane as a metaphor for nail use, the nail and the hammer construct me to use them, or something like that.  That formulation is weird, also, but sufficient to make my point.

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

From: Friam [mailto:[hidden email]] On Behalf Of Russ Abbott
Sent: Wednesday, June 07, 2017 12:46 AM

To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Nick,

 

When you suggested a hurricane as an example of a complex system I replied that a hurricane is interesting because it's a non-biological system (and not a human artifact) that uses energy that it extracts from outside itself to maintain its structure. That's an interesting and important characteristic. Biological systems do that also, Maturana & Varela, but I don't see that as sufficient to grant it the quality of being a complex system.

 

-- Russ

 

On Tue, Jun 6, 2017 at 9:06 PM Nick Thompson <[hidden email]> wrote:

Thanks, Glen,

 

Larding below:

 

Nick

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of ?glen?
Sent: Tuesday, June 06, 2017 11:34 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.

[NST==>I missed this, and going back through the thread, I have not found it.  Can you reproduce it for me without too much strain?  <==nst]

 (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.

[NST==>I am not talking about tautology, here: x is x.  I am talking about circular explanation: x is the cause of x.  Surely you would agree that having defined X as whatever is caused by Y, I have not added much to our store of knowledge concerning what sorts of things Y causes.  But you are correct, not all circular explanations are entirely vicious/vacuous, of course. It depends on the assumptions the discussants bring to the table.  See, https://www.researchgate.net/publication/281410347_Comparative_psychology_and_the_recursive_structure_of_filter_explanations<==nst]

 So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

[NST==>I would be grateful for a passage from any of these folks where strictly circular reasoning is used to good effect. <==nst]

 

Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_. 

[NST==>Well, if that is how one defines closure, then I am bound to agree.  Then, it’s not clear to me what the function of “nothing but” is, in your sentence.  But reading through your earlier posts (petri dish) suggests that for you closure is absolute; for me, systematicity is a variable and we would have to have some sort of a mutual understanding of where along that dimension we start calling something a system. <==nst]

Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.

[NST==>Yes, but coherence, for me, carries more richness than what I was grasping for.  For you, perhaps not.  I guess “coherence” is ok.  <==nst]

 And that means that your working definition is not naive.

[NST==>Huh?  You mean I don’t get to be in charge of whether I am naïve, or not?  Are you some kind of behaviorist?  <==nst]

 It does rely on an intuition that many of us share.

[NST==>Bollox!  It relies on the plain meaning of the word (he said grumpily).  <==nst]

  But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

[NST==>This thread isn’t coherent for me.  Somebody asks if natural systems can be complex.  This is a lot of intricate talk which I frankly didn’t follow but which seemed to suggest that only symbol systems could be complex.  But I could detect no definition of complexity to warrant that restriction.  So I offered a definition of complexity (which may have been the same as yours – forgive me), offered an example of a natural complex system, a hurricane, and came to the conclusion that indeed, some natural systems are complex.  To my knowledge, nobody has addressed that claim.  But I have been traveling, my eye sight sucks, and I may have missed it.  If anybody has addressed this claim, could somebody direct me to a copy of their post.  I would be grateful. <==nst]

 

Perhaps Steve Smith, who has often rescued me when I have made these messes in the past, could gently point out to me my error. 

 

Top temperature today 49 degrees.  90’s predicted for next week. I am ready.

 

Best to you all,

 

Nick

 

 

 

 

 

On 06/06/2017 07:20 AM, Nick Thompson wrote:

> Dear Eric and Steve, and the gang,

>

> 

>

> When I first moved to Santa Fe on Sabbatical 12 years ago, I was merely 67, and there was a chance, just a chance, that I might become expert enough in complexity science and model programming  to deal with you guys on a somewhat equal footing.  But that never happened, and, now, it is too late.  I am amazed by the intricacy of your discussion and the broad reach of your thought.  There is really little more than I can do then wish you all well, and back out of the conversation with my head bowed and my hat clasped to my chest. 

>

> 

>

> Before I leave this conversation, I would like to offer the dubious benefits of what expertise I do have, which concerns the perils of circular reasoning.  I come by that expertise honestly, through years of struggling with the odd paradox of evolutionary biology and psychology, that neither field seems every to quite get on with the business of explaining the design of things.  When George Williams famously defined adaptation as whatever natural selection produces he forever foreclosed to himself and his legions of followers, the possibility of saying what sort of a world an adapted world is, what the products of natural selection are like.  One of you has pointed out that this is an old hobby horse with me, and suggested, perhaps, that it's time to drag the old nag to the glue factory.  But I intend to give it one last outing.

>

> 

>

> So, I have a question for you all:  Do you guys know what you are talking about?!  Now I DON’T mean that how it sounds.  I don’t mean to question your deep knowledge of the technology and theory of complexity.  Hardly.  What I do mean to ask is if,  perhaps, you may sometimes lose sight of the phenomenon you are trying to explain, the mystery you hope to solve.  Natural selection theory became so sophisticated, well-developed and intricate that its practitioners lost track of the phenomenon they were trying to account for, the mystery they were trying to solve.  We never developed a descriptive mathematics of design to complement our elaborate explanatory mathematics of natural selection.  Until we have such a descriptive system, natural selection theory is just a series of ad hoc inventions, not a theory subject to falsification but  “a metaphysical research program” as Popper once famously said, which can always be rejiggered to be correct.   Is there a risk of an analogous problem in complexity science?  You will have to say.   

>

> 

>

> So, I will ask the question again:  Do you guys know what you are talking about?!  What is complexity??  If the answer you give is in terms of the deeply technical, causal language of your field, there is a danger that you have lost sight of what it is you are trying to account for.  And here a little bit of naivety could be very helpful. Naivety is all I have to offer, I will offer it.  Whatever complexity might be, it is the opposite of simplicity, no?  It is in that spirit that I propose a working definition of complexity with which to explore this thread’s question:  “Are any non-biological systems complex?”

>

>  

>

> An object is any collection or entity designated for the purposes of conversation.

>

> 

>

> A system is a set of objects that interact more closely with one another than they do with entities outside the set. 

>

> 

>

> A system is complex if the objects that compose it are themselves systems.

>

> 

>

> Only when complex systems have been clearly defined, is it rational to ask the question, “Are any natural systems complex?”  Now you may not like my definition, but I think you will agree that once it is accepted, the answer to the question is clearly, “Yes!”   

>

> 

>

>                 Take hurricanes.  Is a hurricane composed of thunderstorms?  Clearly, Yes.  Are thunderstorms themselves systems. This is a bit less clear, because the boundaries among thunderstorms in a hurricane may be a bit hazy, but if one thinks of a thunderstorm as a convective cell -- a column of rising air and its related low level inflow and high level outflow – then a thunderstorm is definitely a system, and a hurricanes are made up of them.  Hurricanes may also display an intermediate system-level, a spiral band, which consists of a system of thunderstorms spiraling in toward the hurricane’s center.  Thus, a hurricane could easily be shown to be a three-level complex system. 

>

> 

>

> Notice that this way preceding saves all the intricate explanatory apparatus of complexity theory for the job of accounting for how hurricanes come about. Now we can ask the question, What kinds of energy flows (insert correct terminology, here) occur in all complex systems?   Notice also, that this procedure prevents any of us from importing his favorite explanation for complex systems into their definition, guaranteeing the truth of the explanation no matter what the facts might be, and rendering the theory vacuous.  . 

>

> 

>

> One last comment.  When I wrote that perhaps we might inquire of the system whether it is complex or not, I left myself wide open to be misunderstood.  I meant only to say, that it is the properties of the system, itself, not its causes, that should determine the answer to the question.  Remember that, in all matters, I am a behaviorist.  If I would distrust your answer concerning whether you are hungry or not, I certainly would not trust a systems answer concerning whether it is complex or not. 

 

--

␦glen?

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FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
to unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
FRIAM-COMIC http://friam-comic.blogspot.com/ by Dr. Strangelove

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FRIAM Applied Complexity Group listserv
Meets Fridays 9a-11:30 at cafe at St. John's College
to unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
FRIAM-COMIC http://friam-comic.blogspot.com/ by Dr. Strangelove

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Meets Fridays 9a-11:30 at cafe at St. John's College
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[Nick Thompson]

Hi, glen,

 

Thanks.  No wonder you're annoyed at me.  See larding below.

 

Nicholas S. Thompson

Emeritus Professor of Psychology and Biology

Clark University

http://home.earthlink.net/~nickthompson/naturaldesigns/

 

 

-----Original Message-----
From: Friam [mailto:[hidden email]] On Behalf Of ?glen?
Sent: Wednesday, June 07, 2017 10:31 AM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Any non-biological complex systems?

 

 

 

On 06/06/2017 09:05 PM, Nick Thompson wrote:

> [gepr] Although you're repeating what I'd said earlier about relying on a more vernacular sense of "complex", we have to admit something you've yet to acknowledge.

>

> [NST==>I missed this, and going back through the thread, I have not

> found it.  Can you reproduce it for me without too much strain? 

> <==nst]

 

Below is what I wrote in response to Stephen's suggestion that any physical system might qualify as complex.

 

On 05/26/2017 12:40 PM, glen ☣ wrote:

> Yeah, but you're relying on the ambiguity of the concept.  A system that is only complex for very short spans of time, or under very special conditions wouldn't fit with _most_ people's concept of "complex".  To boot, unadulterated oscillation wouldn't satisfy it either.  And, as has been said earlier in the thread, allowing any an all physical systems to be called "complex" when they're placed under special circumstances defeats the purpose of the concept.

[NST==>I am keen to know what is meant by “the purpose of the concept”.  Peirce says the meaning of a concept is the difference in the observations (experiments) that it leads us to make.  What difference does calling something complex make for you.  Forgive me please if this requires you to direct my attention to earlier posts.  <==nst]

 

>  (I realize that the things I've said in this thread have been mostly ignorable.  So, it's reasonable that they've been missed.)  First, circular reasoning is used all the time in math.

>

> [NST==>I am not talking about tautology, here: x is x.  I am talking

> about circular explanation: x is the cause of x.  Surely you would

> agree that having defined X as whatever is caused by Y, I have not

> added much to our store of knowledge concerning what sorts of things Y

> causes.  But you are correct, not all circular explanations are

> entirely vicious/vacuous, of course. It depends on the assumptions the

> discussants bring to the table.  See,

> https://www.researchgate.net/publication/281410347_Comparative_psychol

> ogy_and_the_recursive_structure_of_filter_explanations

> <https://www.researchgate.net/publication/281410347_Comparative_psycho

> logy_and_the_recursive_structure_of_filter_explanations%3c==nst>

> <==nst]

 

 

We've talked about your recursive filter explanation paper before.  I don't think you responded to what I said about it after EricC's explanation.  Here is my comment: http://redfish.com/pipermail/friam_redfish.com/2017-January/075190.html

 

[NST==>For whatever reason, server feckless or my own, I don’t remember ever seeing this before.  It looks like the most through going attempt to confront the ideas in that paper that anybody has ever provided, and deserved (and deserves) to be read carefully and discussed.  Please forgive my failure to do so.  I will get on it.  <==nst]

 

 

>  So, it is not the bug-a-boo logicians claim it to be.  Again, Maturana & Varela, Rosen, Kaufmann, et al have all used it to valid and sound effect.

>

> [NST==>I would be grateful for a passage from any of these folks where

> strictly circular reasoning is used to good effect. <==nst]

 

 

 

I will find some.  But a more fundamental read is this: http://math.stanford.edu/~feferman/papers/predicativity.pdf

[NST==>Don’t do any more work for me until I have read this.  You are giving me guilt feelings<==nst]

 

 

 

> Second, your "interact more closely with one another than they do with entities outside the set" is nothing but _closure_. 

>

> [NST==>Well, if that is how one defines closure, then I am bound to

> agree.  Then, it’s not clear to me what the function of “nothing but”

> is, in your sentence.  But reading through your earlier posts (petri

> dish) suggests that for you closure is absolute; for me, systematicity

> is a variable and we would have to have some sort of a mutual

> understanding of where along that dimension we start calling something

> a system. <==nst]

 

 

Yes, I can see that.  I'm used to thinking in terms of things being closed to one operation and open to others.  I'm also used to using it as a verb, e.g. "closing a set" by, say, adding the limit point to it.  Or more appropriate to this context, closing a region by wrapping a boundary around to itself like you would by tying a string to itself to get a loop.  Further, a region of some "space" can be "partially closed" by being very convex ... like some champagne flutes, bulging in the middle with a small-ish opening at one end ... or maybe think of a pinhole camera or a black body radiation device.

[NST==>But doesn’t this bring us back to the question that I got into a tangle with Steve about: Whether a system can close it self?  Or whether closure has to be be provided “from the outside” (=petri dish).  <==nst]

 

 

> Or if I can infer from the lack of response to my broaching the term, we could use "coherence" or some other word.

>

> [NST==>Yes, but coherence, for me, carries more richness than what I

> was grasping for.  For you, perhaps not.  I guess “coherence” is ok. 

> <==nst]

 

 

Coherence can be ambiguous, too.  But my main point is that much of what we've been arguing about in this thread is about closure, what it means, and whether it's necessary for something to be called a complex system.  Russ' claim includes some form of closure.  This is much stronger than Stephen's claim.  Yours falls somewhere between.  But we won't be able to get at your middle ground without more formality.

 

 

>  And that means that your working definition is not naive.

>

> [NST==>Huh?  You mean I don’t get to be in charge of whether I am

> naïve, or not?  Are you some kind of behaviorist?  <==nst]

 

 

8^)  Right.  You can't sa[NST==><==nst] by you're being naive and then get all hyper-technical about whatever naive statement you made.

[NST==>Naïve in the sense of standing apart from the technical details.  Would “phenomological” be better?  I am a great believer in the importance of outsiders to the health of science – the Emperor’s New Clothes metaphor. Outsiders can be really annoying and slow things up, but they also have an essential role to play.  Hard to know when one is playing that role, or merely being annoying. <==nst]

 

 

 

>   But in order for you to know what you're talking about, you have to apply a bit more formality to that concept.

>

> [NST==>This thread isn’t coherent for me.  Somebody asks if natural

> systems can be complex.  This is a lot of intricate talk which I

> frankly didn’t follow but which seemed to suggest that only symbol

> systems could be complex.  But I could detect no definition of

> complexity to warrant that restriction.  So I offered a definition of

> complexity (which may have been the same as yours – forgive me),

> offered an example of a natural complex system, a hurricane, and came

> to the conclusion that indeed, some natural systems are complex.  To

> my knowledge, nobody has addressed that claim.  But I have been

> traveling, my eye sight sucks, and I may have missed it.  If anybody

> has addressed this claim, could somebody direct me to a copy of their

> post.  I would be grateful. <==nst]

 

 

Well, as I said above, we have 2 extremes.  Complex systems are everywhere, as long as you catch them at the precise time and in the precise conditions.  The other side is that complex systems rely on a cumulative hierarchy of some sort (Russ's is less fleshed out than EricS'), which means they might be relatively rare.  The discussion of hurricanes is a good one.  My focus here was to shunt your preamble about circularity and getting lost in technicalities.

 

 

--

␦glen?

 

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[gepr]

I don't want to distract from the new thread, which I think is more important than this part of this thread.  So, feel free to ignore this one.  But I'll answer now because I have the time now.  FWIW, I'm not annoyed.  But I'd like to see us (everyone) make some progress, even if it's not toward a paper or other artifact.  (To answer Owen, I am willing to help organize the content.)  Anyway, the rest below:

On 06/07/2017 09:31 AM, Nick Thompson wrote:
> [gepr] Below is what I wrote in response to Stephen's suggestion that any physical system might qualify as complex.
>
> On 05/26/2017 12:40 PM, glen ☣ wrote:
>
>> [gepr] Yeah, but you're relying on the ambiguity of the concept.  A system that is only complex for very short spans of time, or under very special conditions wouldn't fit with _most_ people's concept of "complex".  To boot, unadulterated oscillation wouldn't satisfy it either.  And, as has been said earlier in the thread, allowing any an all physical systems to be called "complex" when they're placed under special circumstances defeats the purpose of the concept.
>
> [NST==>I am keen to know what is meant by “the purpose of the concept”.  Peirce says the meaning of a concept is the difference in the observations (experiments) that it leads us to make.  What difference does calling something complex make for you.  Forgive me please if this requires you to direct my attention to earlier posts.  <==nst]



It means nothing to _me_.  Whenever someone says it, I a) abandon the conversation, b) ask them what they think it means, or c) impute what I think they mean.  But I can tell you what I think it means to most.  "Complex" is like "obscenity".  And this is why the discussion of the "order parameter" is important (and why so many ABMs are qualitiative and not quantitative).  When other people use the term, I think they mean "I can't tease out the causes of the phenomenon I'm looking at."  Sometimes they might (also) mean "It would take me a lot of effort to discuss what we're looking at."  Hence, the purpose of the concept of complexity (better termed "plectics") is to identify that "interesting region" of the phenotype ... or perhaps to distinguish one phenotype from another.

So, Stephen's suggestion that complexity is common defeats that purpose.  It's like when someone asks me if I believe in extraterrestrial life.  I say yes.  But if someone asks if I believe in extraterrestrial intelligence, I say no.  Further, to say that a system is complex, when only tiny regions of its behavior space exhibit complexity is equally useless.  It's like saying that all the air molecules in a room _could_ condense up into the corner, "in principle".  Sure, to people who think hard about theories and ideas, that helps explain what the theory means.  But to most people, it's either misleading or useless.



> [gepr] I'm used to thinking in terms of things being closed to one operation and open to others.  I'm also used to using it as a verb, e.g. "closing a set" by, say, adding the limit point to it.  Or more appropriate to this context, closing a region by wrapping a boundary around to itself like you would by tying a string to itself to get a loop.  Further, a region of some "space" can be "partially closed" by being very convex ... like some champagne flutes, bulging in the middle with a small-ish opening at one end ... or maybe think of a pinhole camera or a black body radiation device.
>
> [NST==>But doesn’t this bring us back to the question that I got into a tangle with Steve about: Whether a system can close it self?  Or whether closure has to be be provided “from the outside” (=petri dish).  <==nst]


Yes, but we don't _have_ to go there.  Closure can be done by an outside actor (lab grad student setting up a BZ reaction in a dish).  Russ states it well: "around which one can draw a boundary".  That is a type of closure.  A hollow sphere or a shallow dish or whatever.  We can even attribute/draw a boundary around a hurricane.  But where and how we "close" the collection of thermals/molecules/trees/trucks/etc matters.  It's a study of how things are closed or open.

A self-referencing closure, a boundary defined by the bounded, is a fantastic sophisma, well beaten but not dead by Rosen et al.  But you don't have to leap all the way from ordinary closures to "teleological" or anticipatory closures.




>> [NST==>Huh?  You mean I don’t get to be in charge of whether I am
>
>> naïve, or not?  Are you some kind of behaviorist?  <==nst]
>
>  
>
> 8^)  Right.  You can't sa[NST==><==nst] by you're being naive and then get all hyper-technical about whatever naive statement you made.
>
> [NST==>Naïve in the sense of standing apart from the technical details.  Would “phenomological” be better?  I am a great believer in the importance of outsiders to the health of science – the Emperor’s New Clothes metaphor. Outsiders can be really annoying and slow things up, but they also have an essential role to play.  Hard to know when one is playing that role, or merely being annoying. <==nst]


Aha!  Yes, phenomenological would be better.  I agree about outsiders and (as Marcus pointed out) using language with wiggle room so that even if you can object to any given argument, perhaps you can still grok the gist.  But we still have to "listen with empathy".  And to do that, we have to model the other discussants and try to talk about what they're talking about, regardless of the language used.  So, a sophist[†] feigning naivete is annoying, whereas _actual_ naivete is essential.


[†] You may have also missed that I don't use "sophist" in a derogatory sense.  It is the identifier for those of _us_ who like to use paradoxical or koan-like issues to spark discussion and disambiguate perspectives.  Sophistry is that practice.  It's fun and useful (e.g. the claim that all the air molecules could condense into the corner of a room).


--
☣ glen

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