Talk:Introduction to Non-Genetic Darwinism

Terminology
Graeme, very nice work and absolutely spectacular given the background and resources you have. You seem to be intuitively good at identifying major scientific questions and bringing disparate fields together. Scientific criticism can be a rough-and-tumble process, but I strongly feel this course merits it. IMO it's already one of Wikiversity's most interesting, unique and well-thought-through courses, and with some refining, it might even become an original contribution to science.

Right now, my main criticism is with the terminology you use. Unless I am wrong, your primary thesis seems to be that self-organization explains many phenomena in the universe, from biological evolution (the traditional focus of a term such as Darwinism) to the organization of neurons in development to the self-ordering of inanimate objects such as crystals. If so, I would like to criticize your use of terms such as "Darwinism" and "non-genetic Darwinism" to describe this larger concept. I don't think these terms are appropriate. As you have brought up in your course, "Darwinism" is used for a broad spectrum of concepts that are not necessarily connected to one another. Most are directly or indirectly associated with biological evolution, and not all are scientific. Despite Dr. Edelman's use of the term "Darwinism", which seems to have influenced your thinking, perhaps a more pinpointed term that lacks a specifically biological connotation would be more appropriate for what you seem to be describing.

"Non-genetic" you seem to use to mean "non-biological." However, to a biologist "non-genetic Darwinism" implies physical characteristics, behavior etc. all within biology. Darwin himself thought in "non-genetic" terms because genetics were not known in his time, and even today there is somewhat of a conceptual rift in biology between genetics on one side, and physiology/behavior/ecology etc. on the other. To me, "non-genetic Darwinism" suggests that you are studying biology and focusing on the latter, which obviously does not describe what you are doing. So I would suggest using another term to communicate clearly.

The term for the phenomenon you describe sort of exists already, unless I have the wrong impression, and is called "self-organization." Perhaps call the phenomenon over a temporal scale "self-organizing selection"? What are your thoughts? --AFriedman 16:22, 23 February 2009 (UTC)


 * I think you are slightly mistaken. Self-Organization is the generic term, no doubt, but what I am trying to suggest, is that Darwinism describes how the Self-Organization is created. That the process of self-organization is a form of Darwinism just as much as genetics is. Not because of what Dr. Edelman suggests, but because it is so similar an algorythm. Furthermore I include Dr. Edelmans work because it is a Biological but not genetic form of Darwinism. I think you are stuck on Biological Darwinism and that is why you are having trouble accepting this interpretation. What do you want me to do, come up with a new term for a system that is common to both Biological and NonBiological systems just because common usage is for biological systems? Darwin himself considered Natural Selection to extend beyond the biological even to social dynamics, so why are you so narrowly focused? We could call it Natural Selection in Self-Organization I suppose, but wouldn't that have the same sort of criticisms?--Graeme E. Smith 18:16, 23 February 2009 (UTC)

When you refer to biological Darwinism, do you mean natural selection in particular or evolution as a whole? Either one, IMO, would work. Just be specific which one it is. Social systems are potentially a subcategory of hereditary Darwinism, because social behavior can affect differential reproduction.

By the way, the possibility that self-organization explains many or all aspects of evolution has been discussed in the recent literature. I think you should read Professor Massimo Pigliucci's article, "Do we need an extended evolutionary synthesis"? A section of it discusses ideas similar to yours, but I also recommend that you read the whole thing. You would be able to read it because there's a link to it on the "Papers" section of his lab web page. This is an active and interdisciplinary field and IMO, one that needs people who can think about it in new ways. I am talking mostly from a biological perspective because that is my background, but I am referring to the broader field as well. --AFriedman 18:36, 23 February 2009 (UTC)


 * Well I read the article, it was informative, although as you say there was only one really small part of it that was trying to deal with the Complexity Theory aspect. I was much more interested in the article on the Evolution of Evolvability. The idea of Evolutionary Capacitance, was also interesting. By the way, take a look back at the Forum, I have sequestered much of the history of the course in an archive in order to make it less unwieldy to read.--Graeme E. Smith 23:51, 23 February 2009 (UTC)

I saw your Archive and unless you mind, we can discuss things here for now. Re: Dr. Edelman's work, I think your use of the term "non-genetic" misses the fundamental difference between his work and the previous concept of "Darwinism." With the possible exception of Edelman, biological Darwinism generally refers to the mechanisms of inheritance across generations, which is perhaps what you are referring to as "genetics." Even evolutionary biologists understand that inheritance across generations is not restricted to the gene, or even the nucleic acid sequence. The phenotype is also inherited and understanding the mechanisms of phenotypic inheritance is considered one of the most important fields of modern day biology. This is my problem with your use of the term "genetics."

Dr. Edelman, in contrast, seems to use "Darwinism" to refer to the pattern of placement of neurons and neuronal connections during the development of a single individual. This is not the same as studying the heritability of these patterns across generations of dividing cells or reproducing individuals, or the presumed effects of these patterns on differential reproduction. Am I on the same page as what you were thinking? --AFriedman 04:38, 24 February 2009 (UTC)

Neural Selection, Signal Generation Model

 * Obviously we are not talking about patterns of differential reproduction across generation of individuals. However if you consider what makes up a generation of signals, there might be an analog. Since the signals by the nature of neurons, drive the growth of connections, connections are the Phenotypes of the signals. Thus we see the heritability of certain patterns of connections develop over generations of signals. The most interesting thing about this, is that without obvious consistency at the raw connections level, we gain consistency to the point where at the gyrus and sulcys level, we actually can map across individuals general functions. In other words, there is consistency in the phenotypes that increases with Layers of inheritance. Thus just like the Galapogus Lizards the phenotypes become similar when they fit the same niche. I think that it is the simularities in the high level connection phenotypes that make human language possible.--Graeme E. Smith 07:44, 24 February 2009 (UTC)

In other words, neurons with similar patterns of connections beget neurons with other similar patterns of connections as the brain develops, leading to a modular structure at higher levels? I still don't think I understand, and the Wikipedia page about Edelman's theory needs to have the writing cleaned up so it's clearer.

I saw your "Artificial Consciousness" pages and they look very nice. IMO this course still needs a lot of work to reach the level I think it should be, and I see you are putting in the time. I would like to focus on this course and not go off into other places.

At this point, I would like to tell you what I have in mind. I think this is a very interesting review of the literature with some quite original insights. If the overall thesis were carefully thought through and the writing of the individual sections were refined, perhaps (given a LOT of work) some form of this could become an essay type piece submitted to a professional journal. It is far from that level right now, but if you agree I would be happy to discuss the steps with you.

Since you've done a lot of reading, your next step is to synthesize the ideas you've written down and come up with a thesis statement, for writing an abstract. Then the rest of the writing could be reformulated around your argument.

I think the core of your argument is in your section "Darwinism as a description of the principle by which order emerges and is conserved," towards the end of the lesson called "Physics of self-organization." Life forms (as in Darwin's theory of natural selection), can be seen as assortments of molecules which have entered a looping algorithm. The loop continues when new molecules are co-opted to form a new organism, and it breaks when the life forms fail to reproduce and die. The fact that all the entities you have discussed enter looping algorithms that enable self-replication of some type, is what these entities seem to me to have in common. Parts of life forms (as in Edelman's theory of neural Darwinism) and non-living entities (as in molecules undergoing a phase transition) have fundamentally entered a self-replicating, looping algorithm.

Perhaps the main thrust of the thesis is that self-organization occurs when entities have entered a looping algorithm, and emergence is one property of the large-scale entities that appear during such an algorithm. Life forms are a particular kind of looping algorithm: they are large assortments of molecules that can co-opt energy and other molecules from the surrounding environment to create essentially similar copies of themselves. This is different from the phase transition in a crystal, for example--although the molecules themselves enter a looping algorithm to form the crystal, one larger crystal does not create another larger crystal, whereas one organism does create another organism. Edelman's neural Darwinism is perhaps only one of many components of the looping algorithm--an algorithm within an algorithm, if you will. What do you think? Then we can go back to discussing the name of the learning material, because I still don't think "Darwinism" is the right word for communicating what this is.

--AFriedman 20:38, 1 March 2009 (UTC)


 * Ok, I think you are right, in the sense that all these systems are iterative, (They Loop), but what is more important, is that they all have what I call the "Rachet Function" in that they protect their gains, as well.

Biological systems do and do not protect their gains. For example, many acquired characteristics that affect fitness (e.g., increased muscle strength gained from exercise) are not inherited. See Lamarckism. Even when traits that increase fitness are inherited, changes to organisms are only increases in fitness in the context of a very specific environment. Yes there are mechanisms in cells that prevent mutations from occurring, immune defenses against pathogens, etc. but I think your use of the word "protect" smacks of a deliberateness and purposefulness that is not there. --AFriedman 16:12, 4 March 2009 (UTC)


 * Hmmm... I can see that you misinterpreted the level at which that comment was meant to be read.
 * I am thinking in a much more abstract manner than you seem to be, so my statements come out sounding more specific than they should.... When I was talking about protecting gains, I was not talking at the individual level, but at the population level. The Population moves up the gradient, and protects its gains. The individual, does not. Thus Lamarckism has nothing to do with my statement. On the other hand the deliberateness or purposefulness that you attribute to my choice of words lies in your own interpretation of them, not in any implication that I made. I was in fact talking about the role of the ratchet mechanism, which is to lock in the gains. Admittedly a strong interpretation for a stochiastic system, but it was meant to be an analogy, not a judgment.


 * If my characterization of the Energy/Entropy balance as being a cycle itself, is true, then quite often, the energy entropy balance will work against proliferation of order. It is in these times that the BioDiversity, or population size, is the saving grace for the gaining of order, since if fewer of the population gain in order, at least they will still allow more population in the next generation, that has gone through the harrowing, and thus is more adaptive to whatever the increased entropic state has to offer. As long as some population survives we can hold onto the current level of order, until the environment becomes less selective.


 * I never said that Synthetic Annealing was a good model of Darwinism, merely that there were simularities in the algorythms between Evolution and Simulated Annealing. The main difference is that Evolution as suggested in your references is a hill climbing algorythm, and Simulated Annealing is a Gradient Descent algorythm. They both navigate on a gradient. I think that the difference is instructive, in that hill climbing involves an increase in order, while Gradient Descent involves a decrease in Chaos. It is important to note that the results are not synonymous as they would be in a system that followed the unmodified second law.


 * You keep trying to trivialize the role of Natural Selection, in my theory. I don't know if this is because you dislike Darwinisim for some reason, I can understand you reluctance to use the word Darwinism, or if you have a basic abhorrence to the base concept that natural selection works outside the boundaries of Biology just as well as within them. This has always been the basis of my thesis. --Graeme E. Smith 00:24, 2 March 2009 (UTC)

I am not a creationist or a proponent of "intelligent design," in case you were wondering. And I think your idea that natural selection occurs outside biological systems is very interesting. But if natural selection operates on entities other than living systems, in your formulation of the theory, what would be selected for and what would be selected against?

Also, I don't think you understand what I am trying to say about natural selection. As a biologist by training, I know that many people who don't completely understand evolution but believe in it, overemphasize natural selection at the expense of other factors such as chance. So my lesson about Darwin, for example, tried to emphasize the fact that natural selection was not the only cause of evolution. It is an important cause of evolution, though. --AFriedman 19:28, 3 March 2009 (UTC)


 * First of all, you ask what would be selected for, and what selected against. That depends entirely on what the selection test selects. In the pure energy configuration argument, what is selected against is chaos, and what is selected for, is order, at least up to a point that protects the variation of the system. In a Genetic Programming environment what is selected against is programs that do not meet the specifications, and what is selected for, is the programs that meet the specifications. In the connections as phenotypes of signals, what is selected for, is the connection that parallels the signals, essentially stabilizing connections so that they can be expressed as physical processes that connect neurons.


 * Ok, Natural Selection is the heart of Darwinism, it isn't the only factor, but it is the factor that Darwin discussed in his book. You talk about chance, I talk about uncertainty, they are both names for changes that happen in the system that are not predictable except statistically. Since they are not predictable their impact is difficult to assess. You also mentioned drift, and so on, I have accepted this. They are factors in genetic Darwinism. However they are not part of my thesis, which is that Natural Selection has impacts on non-genetic systems including some that are non-biological as well. The way I have presented the physics of self-organization is Quantum safe because it depends on uncertainty, this means that it is probably also chance safe as well. The main requirement is that entropy increase as a result of the process, equilibrium in this case is not a balancing of forces, but a balance between energy and entropy. Recently I came across a reference to the "Edge of Chaos" a contention that Evolutionary Systems tend to find a dynamic midpoint between chaos and order, that might suggest that they actually tend to balance on the Equilibrium point between energy and entropy. This is an interesting concept because the power curve I suggest oscillates between energy and entropy, probably in an attempt to reach the same equilibrium point despite changes in energy as entropy falls behind, and then catches up to it again.--Graeme E. Smith 20:35, 3 March 2009 (UTC)

Just to make sure I understand your definition of natural selection, would you consider that one ramification of natural selection in inanimate objects is that nature is filled with stable isotopes, yet unstable isotopes are rare?


 * Actually that is a function of Equilibrium

In other words, stable isotopes are more viable over a long period of time, and so they are maintained in nature whereas unstable isotopes disappear.


 * However, you are close, because unstable isotopes are responding to a gradient.

I perhaps disagree with your semantics here, because I would think that self-replication is a fundamental characteristic of natural selection. self-replication certainly does not occur in the situation I just described--self perpetuation, perhaps, but molecules don't co-opt resources from the environment to make copies of themselves. --AFriedman 16:12, 4 March 2009 (UTC)


 * I see the problem, beyond the fact that you are thinking in an individual oriented manner still, and haven't begun to think in terms of populations rather than individuals. There is the assumption in biological terms that what the new generation is doing is self-replicating the previous generation. That is of course simply biological chauvinism. What is important is the new generation, not how they were formed. How they were formed, (Self-replication) sets the rules for how one generation resembles another, and how it is perturbed from the previous generation, but what is really important is the fact that a new generation is formed that is similar enough to the previous generation that it retains the characteristics necessary for survival, and yet carries enough variation to allow the population to shift if the survival test requires it.


 * if you look at atomic elements from that point of view, then each new element can be seen to be a generation that was formed in a slightly different environment, thus limiting the survival to those that had the right energy/entropy balance for that particular environment. Because elements are mostly stable the previous generation did not die off, as in a biological system so we have the periodic table of elements. However unstable isotopes did die off, leaving only the atoms that were mostly stable as the greater population. The lighter isotopes tend to be more stable because they have a shorter half-life and therefore of the population of atoms left over after time, the lighter radioactive isotopes tended to decay faster, which is why the periodic table has more heavy radioactive isotopes than lighter ones.


 * Where the power curve fits in, is that it describes why each generation formed at a different energy/entropy balance point, and so why the characteristics of each generation (element) are so different. An interesting aside is that the number of atoms of an element in the Universe are determined partly by the amount of energy that was absorbed in making each atom. As a result the heavier elements are significantly rarer than hydrogen even though their formation probably took longer.

Uncertainty in Signal Pattern Phenotypes

 * I thought I should add something here, that is related but not to the point you are trying to make, but to the explanation I am making, and that is, that because of the opportunistic nature of the way connections are made, The system absorbs a certain amount of Uncertainty, essentially the low level connections are chaotic, and while the high level phenotypes are similar to each other, not all the uncertainty is taken out of them, which is why we cannot map to a lower level, than the gyrus and sulcys using standard mapping techniques. However because of the way that the Attention system works, we do not need commonality to the mapping level, as long as the order in the system is up to the tasks we require, in essence the locations of the Neural Groups are arbitrary, but the content is not. That is why Self-Ordering Maps like those produced by Teuvo Kohonen, can be used to recover the content of the high level connection phenotypes even though individualization makes mapping at the neural group level impossible except for maps of each individual.--Graeme E. Smith 20:47, 26 February 2009 (UTC)

Some references about Edelman, What is Life, etc.
--AFriedman 20:51, 1 March 2009 (UTC)
 * Review of Edelman's book bringing up the quite complicated question of whether Edelman's theory should be called "Darwinism"
 * Another review of an Edelman book that contains the clearest explanation of neural Darwinism I've seen
 * What is Life?--about Schrodinger's view of this question
 * PLoS ONE Article about a possible mechanism for how neuronal networks could be copied

Ok, I am amused at these references, they are good references don't get me wrong, I was for instance unaware of Schodingers contribution, and the last article was while technically over my head, informative about how scientists today are thrashing in an attempt to understand induction. But they seem to indicate that you are unaware that while I am willing to accept Dr. Edelman's basic Tennets about Neural Darwinism in a model of the Cerebral Cortex, I tend to violently disagree with where he thinks he is taking his theory of Consciousness. Just because he is a Nobel Prize winner and understands Non-Genetic Darwinism better than I do, doesn't mean that he is right to make some of the claims he is making about where Reentry applies, or to extend his TNGS theory so radically without adequate support for his contentions. What I am trying to do with this course, is lay a ground work for understanding the earlier theories that are well grounded in science. I will personally ignore his later work, mostly because it is too speculative and vague to work from. Don't get me wrong, I have learned from it, but have gone on to augment it with information about the current scientific thought, which is by no means as supportive of his contentions as he might like. The main problem I have, is that if you want to develop a hybrid consciousness theory that contains both phenomenal elements like Dr. Edelman's work, and Functional Elements like Bernard J. Baars work, You had better understand the concepts behind Dr. Edelman's work so that you can include phenomenal components. Non-Genetic Darwinism is hard to understand so I needed this course to explain it. I may have taken the physics of Self-organization too far but it helps capture my understanding of how Darwinism and Commplexity are linked, and I think that might be important.--Graeme E. Smith 00:24, 2 March 2009 (UTC)

Religious Exceptions
I am beginning to wonder if your objections to my thesis, in this topic, lie more in the religious vein, rather than in any Lack of acceptance of the concept. If so, I can understand why you would not want to accept my thesis. Creation, and the God that it requires, is mostly a judeau-christian concept based partially on the Creation Mythos that christians find in their bible within the first few pages. Since the bible was a rewrite of essential judaic writings there is bound to be some overlap in thought. One of the problems I have with this creation mythos, is that it seems to require a micro-managing deity, giving them on one hand the capability to design great things, and then taking away that power in order to make the things they do more understandable to humans.

Quite aside of the Lazy God Hypothesis, I put into my assignments, I believe that much of the discussion around creationism lies in the Dogma associated with how god created the earth. The assumptions that God Micro-manages creation is part of the rationalization for why Judaic people and by extension Christians are somehow special "In the eyes of the Lord". One of the reasons why this micro-managing is therefore so important to judeau-christian religions, is simply, it is needed to explain the favoritism. Fundamentalists in these religions depend on the favoritism of their god, in order to explain why they can demand favoritism in other things, and so they defend the creation mythos with great vigor.

Evolution, and by extension Non-Genetic Darwinism is seen as an attack on the creation mythos, because it indicates that God might use methods other than "Logical Design" to achieve his goals. Really what Evolution does, is show how dependent the creation mythos is, on the concept of a Micro-managing God figure. One of the reasons that Darwinism might be seen to be dangerous to religion, is that it is so simple a system, that it might actually apply earlier than speciation. If this is seen as an attack on religion, then of course it will be dogmatically resisted as a thesis. As a former christian, who gave up his religion when he realized that he believed in something else, I can sympathize with those who do not want to change religions just to understand a concept like this, and I want to emphasize that it is not an attack on religion, so much as an alternative view of something that some religions do not want to look at too closely for their own reasons that have nothing to do with the validity of the viewpoint--Graeme E. Smith 18:24, 2 March 2009 (UTC)

= Maybe a longer course, or split this course? =


 * I can see from the amount of discussion, that either the course does not explain my thesis well, or that it needs to be organized differently. Possibly because it is really covering two theses. I am thinking of extending the course somewhat or splitting it into two separate courses one on the Physics of Darwinism, and one on non-genetic Darwinsim, maybe make the Physics of Darwinism a pre-requisite for the Non-Genetic Darwinism course?--Graeme E. Smith 20:32, 5 March 2009 (UTC)

Perhaps the lesson about "Physics of self-organization" could be split and clarified. It is by far the longest lesson in the course and it seems to be the heart of the course, even more so than the sections about biology. By the way, what are the 2 theses? I don't see 2 so please explain. I'm not sure that you need to create another course. --AFriedman 22:35, 5 March 2009 (UTC)

I thought maybe the sub-thesis that we needed to re-examine the Second Law of Thermodynamics might be taking away from the argument that we can draw an analog to natural selection at different levels of self-organization.--Graeme E. Smith 00:14, 6 March 2009 (UTC)
 * I agree and the latter thesis is the one I would recommend focusing on, for a lot of reasons. Your issues with Thermodynamics are not particularly relevant to that thesis.  I see the thesis about the analog to natural selection at different levels of self-organization, as a possible partial answer to the question about complexity proposed in the Pigliucci paper we read.  Nice work so far, and nice thoughts about revising.  --AFriedman 13:42, 6 March 2009 (UTC)