Name It / Claim It: Epigenetics Now Just Another Evolutionary Mechanism

_{Cornelius Hunter

April 19, 2016

Epigenetics, Intelligent Design}

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It is often said that all truth passes through three stages. First, it is ridiculed. Second, it is violently opposed. Third, it is accepted as being self-evident. And so it is with epigenetics which evolutionists opposed and blackballed for a century before finally appropriating it as just another mode of evolutionary change. (see here, here, andhere for more discussion of this history of misdirections regarding Lamarckism and epigenetics). Here is an example of evolutionists, after a century of denial and rejection, claiming epigenetics as their own. Read more

Comments

mike1962: You can’t or won’t provide any source code of your implementation for analysis. No sense reinventing the wheel. Reynolds already did it for you, along with countless others since. mike1962: I asked for source code from you, using any algorithm you like We provided evidence how a basic algorithm based on simple interactions between neighboring birds results in flocking behavior. This evidence is easily available to you. We can point it out to you, but we can't make you look. Not sure what you are trying to accomplish.Zachriel_{May 2, 2016
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Zachriel, I asked for source code from you, using any algorithm you like, so we can analyze how "simple" your implementation is. I can see why you would want to wave your hand to someone else's algorithm without actually implementing it, but that's not what I asked for. You can't or won't provide any source code of your implementation for analysis. So your real answer is: I can't do it, or I won't do it. Okie dokie.mike1962_{May 2, 2016
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mike1962: Where’s your source code? An algorithm was provided in Reynolds, Flocks, herds and schools: A distributed behavioral model, Computer Graphics 1987. Because it is an algorithm, it is independent of the implementation.Zachriel_{May 2, 2016
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Zachriel, Where's your source code?mike1962_{May 2, 2016
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gpuccio: Still waiting for the video. We provided evidence. You can ignore it, or grapple with it. The choice is yours.Zachriel_{May 2, 2016
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Zachriel: And the source code, obviously, behind the video.gpuccio_{May 1, 2016
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Zachriel: Still waiting for the video.gpuccio_{May 1, 2016
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mike1962: Not. Holding. Breath. Asked and answered.Zachriel_{May 1, 2016
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Not. Holding. Breath.mike1962_{May 1, 2016
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mike1962: You already said that. And you already asked that.Zachriel_{May 1, 2016
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Zachriel, You already said that. Apparently, you are having trouble following.mike1962_{May 1, 2016
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mike1962: If you want to lift someone else’s algorithms and source code that implements what you described as “flock and swarm behavior [that] is simple to simulate”, what gpuccio specified and what I asked for, I’m OK with that. The algorithm was provided in Reynolds, Flocks, herds and schools: A distributed behavioral model, Computer Graphics 1987.Zachriel_{May 1, 2016
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Zachriel: You are beyond hope. I am waiting for a video of your experiment with model airplanes. The pattern is encoded by the encoding of the individual behaviours and complex rules which will generate it. The foundation for the "inherited behaviors" is not understood. They are certainly not simple, and only when we know how they are written and inherited will you be able to exercise your imagination to try to explain how RV and NS generated the necessary biological information. Good luck!gpuccio_{April 30, 2016
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Zachriel: The vee-formation is a modification wherein the rule is to minimize energy by flying in the wake of the bird before it. I asked you for an "implementation" that is a "simple" (your word.) Can you do it or not? If you want to lift someone else's algorithms and source code that implements what you described as "flock and swarm behavior [that] is simple to simulate", what gpuccio specified and what I asked for, I'm OK with that. When will you be providing your source code for us to scrutinize for "simplicity"? (Not. Holding. Breath.)mike1962_{April 30, 2016
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gpuccio: And how are those “simple” rules implemented biologically? By utilizing already well-developed adaptations for the senses and for flight. gpuccio: because it understands that such a behaviour will give it advantages, or because something in its genome/epigenome forces it to do so? My point is that the second explanation is obviously correct. That's right. As with most complex vertebrates, they inherit some instinctual behaviors, then refine them through learning. gpuccio: I quoted “complex flight dynamics” and “complex sensory feedback” from the abstract of the Nature paper. Those tools are described there as necessary to accomplish the flight in formation. So is a respiratory system, mating habits, mitochondrial activity, etc. However, we're discussing how the pattern of the flock forms. The pattern self-organizes from a few basic rules of individual behavior. gpuccio: The “simple” rules you quoted are obviously aimed at achieving the flocking pattern. So, if they are encoded, their necessary outcome, the flocking pattern, is encoded too as an aimed result. No. The pattern is not encoded. The pattern is the result of the individual behaviors. However, the pattern is subject to natural selection, which means the inherited behaviors are subject to change over generations. mike1962: I would be interested in seeing Zachriel pull off an implementation of this “simply.” The seminal experiment is Reynolds, Flocks, herds and schools: A distributed behavioral model, Computer Graphics 1987. The vee-formation is a modification wherein the rule is to minimize energy by flying in the wake of the bird before it.Zachriel_{April 30, 2016
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gpuccio: a) Take a couple dozen model airplanes, b) Encode those three simple rules in some software in them, so that c) As soon as you start them flying, unguided, they can easily and effectively fly in a V formation equivalent to what we observe in birds. Then, and only then, we can measure how “simple” your rules are. I would be interested in seeing Zachriel pull off an implementation of this "simply." The ball's in your court, Zachriel (Not. Holding. Breath.)mike1962_{April 30, 2016
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Zachriel: "Separation – avoid crowding neighbors (short range repulsion) Alignment – steer towards average heading of neighbors Cohesion – steer towards average position of neighbors (long range attraction)" And how are those "simple" rules implemented biologically? You have not really answered my main question: "Why do individuals follow those rules? Where are they written?" You say: "Because flocking has a number of advantages, both as predator and as prey, and because the rules are simple and directly related to other behaviors, there is a clear evolutionary pathway" What do you mean? Are the rules, however simple or complex they are, written in the genome/epigenome or not? Does each bird: "avoid crowding neighbors" "steer towards average heading of neighbors" " steer towards average position of neighbors" because it understands that such a behaviour will give it advantages, or because something in its genome/epigenome forces it to do so? My point is that the second explanation is obviously correct. Evolutionary pathways, true or imagined, are not the issue here. We are not, at present, discussing how the pertinent information was generated. We are discussing the existence of such pertinent information in the genome/epigenome, which you seem so eager to deny or minimize, and how it is written there. You say: "You are confused. Flight precedes flocking." No, you are confused. I quoted “complex flight dynamics” and “complex sensory feedback” from the abstract of the Nature paper. Those tools are described there as necessary to accomplish the flight in formation. Here is, again, the pertinent part:
Here we show that individuals of northern bald ibises (Geronticus eremita) flying in a V flock position themselves in aerodynamically optimum positions, in that they agree with theoretical aerodynamic predictions. Furthermore, we demonstrate that birds show wingtip path coherence when flying in V positions, flapping spatially in phase and thus enabling upwash capture to be maximized throughout the entire flap cycle. In contrast, when birds fly immediately behind another bird—in a streamwise position—there is no wingtip path coherence; the wing-beats are in spatial anti-phase. This could potentially reduce the adverse effects of downwash for the following bird. These aerodynamic accomplishments were previously not thought possible for birds because of the complex flight dynamics and sensory feedback that would be required to perform such a feat
So, it seems that you are confused, not I. "The basic interactions are encoded, not the global flocking pattern. The global pattern emerges from the simple rules." You are really trying to defend the undefendable. The "simple" rules you quoted are obviously aimed at achieving the flocking pattern. So, if they are encoded, their necessary outcome, the flocking pattern, is encoded too as an aimed result. Regarding how simple they seem to you (but obviously not to the authors of the Nature paper, and certainly not to me), just try the following: a) Take a couple dozen model airplanes b) Encode those three simple rules in some software in them, so that c) As soon as you start them flying, unguided, they can easily and effectively fly in a V formation equivalent to what we observe in birds. Then, and only then, we can measure how "simple" your rules are.gpuccio_{April 30, 2016
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Origenes: your idea seems to be that since we can explain a V formation bottom up from the level of individual birds, we can also explain embryo development bottom up from the level of individual molecules (and ultimately fermions and bosons). No. Our position is that an argument that bottom-up directional organization is inconceivable is fallacious. gpuccio: 1) What are those basic rules? The seminal experiment is Reynolds, Flocks, herds and schools: A distributed behavioral model, Computer Graphics 1987. Reynolds used three simple rules for his "boids": Separation - avoid crowding neighbors (short range repulsion) Alignment - steer towards average heading of neighbors Cohesion - steer towards average position of neighbors (long range attraction) This shows how global patterns in flocks emerge from simple interactions between the birds. These have been extended by direct observation of various species. For instance, see Young et al., Starling Flock Networks Manage Uncertainty in Consensus at Low Cost, PLOS Computational Biology 2013. gpuccio: 2) Why do you believe that they are “basic”? Individuals following these basic rules regarding their neighbors shows how the global pattern can emerge. They are basic because they can then be modified to suit a particular niche or environment, such as starlings above. gpuccio: 3) Why do individuals follow those rules? Where are they written? Because flocking has a number of advantages, both as predator and as prey, and because the rules are simple and directly related to other behaviors, there is a clear evolutionary pathway. gpuccio: 4) Is the transmission of those rules (that is, information) genetic/ epigenetic, or are those rules learned each time de novo by each individual, for some incredible luck and talent? As with most complex vertebrates, they inherit some instinctual behaviors, then refine them through learning. gpuccio: 5) ... Do you believe that “complex flight dynamics” and “complex sensory feedback” are the result of a few “basic rules”? You are confused. Flight precedes flocking. The global pattern of the flock is due to the interaction between the individuals. gpuccio: 6) Do you think that learning to walk is based on a few “basic rules”? No. But we're not discussing learning to walk or learning to fly, but how flying organisms organize into flocks. gpuccio: Obviously, there is not an external supervisor which tells each bird how to fly. Good. gpuccio: The difference is that in a2) and c2) the coordination is due to genetic/epigenetic factors, and the behaviour is therefore specific of a species. This is the key. The basic interactions are encoded, not the global flocking pattern. The global pattern emerges from the simple rules. gpuccio: In no such cases a bottom up explanation can be proposed, because bottom up systems, where individuals simply make adjustments to their local conditions, as you suggest, generate situations like those I have given in the first part of my post #87 We know that global patterns can emerge from simple interactions. We can show it in silico, and we can observe it in vivo.Zachriel_{April 30, 2016
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Zachriel: As I really believe that you are confused here, I will try to explain my point even more clearly. Let's take the three examples of "Coordinated distributed decisions" which I have given in my post #87: a2) Fishes swimming in formation b2) A coreography c2) Birds flying in formation Now, it should be rather clear that there is one difference between examples 1 and 3, and example 2. The difference is that in a2) and c2) the coordination is due to genetic/epigenetic factors, and the behaviour is therefore specific of a species. In example b2), instead, the coordination is explicitly external (the coreographer). Humans as a species have many coordinated behaviours which are based on genetic/epigentic coordination (for example, walking, as you have suggested yourself). But some specific coreography is not an endowment of the species: humans do not all repeat a same coreography at particualr times. In cases a2) and b2) (as in all cases of specific repeated bevaviours based on species specificity) the coordination is obviously in the genome(epigenome. In cases b2) as in all cases of specific coordinated human activities which are not "instinctive" to the species) an external coordination, or an internal coordination by a specific individual (for example, in the design of art) is necessary. But in all cases, a coordination is present, and is responsible of the complex functional achievement. In no such cases a bottom up explanation can be proposed, because bottom up systems, where individuals simply make adjustments to their local conditions, as you suggest, generate situations like those I have given in the first part of my post #87: a1) Fishes swimming in aquarium b1) Passersby in a street c1) Birds (flying randomly) where no specific functional coordination can be observed.gpuccio_{April 30, 2016
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Zachriel: "The proximate cause is that some birds individually follow basic rules based on their relationship to their neighbors." Well, a few simple questions on that: 1) What are those basic rules? 2) Why do you believe that they are "basic"? 3) Why do individuals follow those rules? Where are they written? 4) Is the transmission of those rules (that is, information) genetic/ epigenetic, or are those rules learned each time de novo by each individual, for some incredible luck and talent? 5) Regarding the paper in Nature: "These aerodynamic accomplishments were previously not thought possible for birds because of the complex flight dynamics and sensory feedback that would be required to perform such a feat" Do you believe that "complex flight dynamics" and "complex sensory feedback" are the result of a few "basic rules"? Do you believe that "complex flight dynamics" and "complex sensory feedback" are the result of individual bottom up learning, or do you think they are based on genetic/epigenetic information?? 6) Do you think that learning to walk is based on a few "basic rules"? Are you aware of the extremely complex biological information which is necessary at the level of the body, the nervous system, and so on, to achieve that task? Do you think that information is learned each time by each new human? Or is it based on genetic/epigenetic information? Why do we walk while horses don't? You grossly equivocate on the meaning of "supervisor". Obviously, there is not an external supervisor which tells each bird how to fly. But there is an internal supervisor, the genetic/epigenetic information in the specie Geronticus eremita, which tells each individual how to behave, and gevies each individuals the tools to behave that way, so that a V formation is achieved, according to very complex laws of aerodynamics that none of the birds understands, but which are the foundation of that specific and complex genetic/epigenetic information in the species Geronticus eremita. That genetic/epigenetic information works top down to achieve the V formation. How can you doubt that? The simple fact that only some species can do that should be enough to convince you. You are free to believe that the genetic/epigenetic information was achieved in the course of natural history by the bottom-up magical process of neo darwinism. That is your faith, and I am OK with others' freedom to choose their personal faiths. But to argue that the V formation is each time the result of bottom-up mechanisms, and not of the top-down results of genetic/epigenetic information in the species, is complete folly, and I am really amazed that you insist on such a wrong concept.gpuccio_{April 30, 2016
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Zachriel, your idea seems to be that since we can explain a V formation bottom up from the level of individual birds, we can also explain embryo development bottom up from the level of individual molecules (and ultimately fermions and bosons). I find it absurd that you choose to compare birds with molecules, but to make the point you can also offer ice crystal formation. Next follows a well-known discussion about the differences between order (V formation / crystals) and organization (embryo development). And of course you will argue that the differences are gradual and not in kind. - - -Origenes_{April 29, 2016
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gpuccio: Excuse me, why do you think that some birds fly in such a complex and efficient formation, while others don’t? The proximate cause is that some birds individually follow basic rules based on their relationship to their neighbors. The ultimate cause is that it can lead to reproductive success, depending on the bird's niche. gpuccio: Do you think that they know the laws of aerodynamics? No more than a human has to know the laws of gravity in order to walk. The bird learns to find the sweet spot, where the effort is least, and in time with its forward neighbor. Nor is that a "supervising control" of flock formation. It's an individual behavior that results in birds flying at an angle to the wake of the bird in front. There is no "supervisor" that tells each bird where to go. It's bottom-up organization. gpuccio: Why and how do bees build behives? Not through a "supervising controller", but the collective action of individual bees following basic rules of interaction. It's easier to model with ants, but the principle is the same. It's bottom-up organization. gpuccio: The only possible explanation is the the genome-epigenome of those species has the information about the flight, the formation, and the roles. The innate instinct of the bird is to follow certain basic rules of flight. It is the individual actions that make the pattern. Again, flock and swarm behavior is simple to simulate. It's bottom-up organization.Zachriel_{April 29, 2016
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Zachriel: Are you out of your mind? "individuals making adjustments to their local conditions"??? Excuse me, why do you think that some birds fly in such a complex and efficient formation, while others don't? How do you think that they have "awareness of the spatial wake structures of nearby flock-mates, and remarkable ability either to sense or predict it"? Do you think that they know the laws of aerodynamics? Why and how do bees build behives? Why and how do beavers build dams? The problem of apparently very intelligent instinctive behaviour in animals is certainly unsolved, but how can you deny that it must have its foundation in genomic and epigenomic configurations? Bees don't learn each time how to build a hive. It's not that their personal intelligence, or intuition solves the problems involved. They behave that way instinctively, and therefore it is obvious that the behaviour has its foundation in their genomic and epigenomic constitution (information). When birds fly in a V formation, solving complex problems of aerodynamics, it's not because of their genius as engineers: they are programmed to do that way, and the interactions between them are obviously programmed: they happen in the same way for the same species. It's not that ibis build each time a different configuration, solving problems each time in a different way. The functional solution is in their genome and epigenome, it is not a sum of individual decisions: it is rather a sum of individuals applications of the same program, which is complex enough to include separate roles for individuals during the development of the procedure. Exactly like it happens in cell differentiation. How can you believe that this is the result of unguided bottom-up organization? Your idea has no sense, it is really not even a credible hypothesis. "individuals making adjustments to their local conditions"? Excuse me, the individuals have in principle the same genome-epigenome, with all possible inter-individual variations which are certainly nor aimed to get a V formation. Local conditions are certainly random and variable. They have no information about how birds can fly in a V formation. The individuals do not learn individually how to fly in formation. Some species do it, others don't. The formation implies different roles. The only possible explanation is the the genome-epigenome of those species has the information about the flight, the formation, and the roles. I cannot even begin to understand how you think that the outcome could regularly come from unguided "individuals making adjustments to their local conditions". I think that here you are really confused.gpuccio_{April 29, 2016
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gpuccio: Well, I dont know “what is the supervising control for an avian flight formation”. Nothing in what you posted indicates any evidence of a "supervising control". Rather, everything points to individuals making adjustments to their local conditions resulting in a global pattern, that is, bottom-up organization. This doesn't "prove" that embryogenesis is bottom-up organization — that would require looking at the details — but it does show that the argument that bottom-up organization can't occur is false.Zachriel_{April 29, 2016
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Zachriel: From Wikipedia:
Coordinated formation flight A wide variety of birds fly together in a symmetric V-shaped or a J-shaped coordinated formation, also referred to as an "echelon", especially during long distance flight or migration. This pattern of formation flying is resorted to so as to save energy and improve the aerodynamic efficiency of birds.[8] The birds flying at the tips and at the front interchange positions in a timely cyclical fashion to spread flight fatigue equally among the flock members. The wingtips of the leading bird in an echelon create a pair of opposite rotating line vortices. The vortices trailing a bird create an underwash which creates an induced drag for the bird creating it; at the same time these vortices create an upwash which can aid the flight of any bird following.[9] In a 1970 study the authors claimed that each bird in a V formation of 25 members can achieve a reduction of induced drag and as a result increase their range by 71%.[10] Studies of waldrapp ibis show that birds spatially coordinate the phase of wing flapping and show wingtip path coherence when flying in V positions, thus enabling them to maximally utilise the available energy of upwash over the entire flap cycle. In contrast, birds flying in a stream immediately one behind another do not have wingtip coherence in their flight pattern and their flapping is out of phase, as compared to birds flying in V patterns, so as to avoid the detrimental effects of the downwash due to the leading bird's flight.[11]
From Nature:
Upwash exploitation and downwash avoidance by flap phasing in ibis formation flight Nature, 2014, doi:10.1038/nature12939 Abstract: Many species travel in highly organized groups1, 2, 3. The most quoted function of these configurations is to reduce energy expenditure and enhance locomotor performance of individuals in the assemblage4, 5, 6, 7, 8, 9, 10, 11. The distinctive V formation of bird flocks has long intrigued researchers and continues to attract both scientific and popular attention4, 7, 9, 10, 11, 12, 13, 14. The well-held belief is that such aggregations give an energetic benefit for those birds that are flying behind and to one side of another bird through using the regions of upwash generated by the wings of the preceding bird4, 7, 9, 10, 11, although a definitive account of the aerodynamic implications of these formations has remained elusive. Here we show that individuals of northern bald ibises (Geronticus eremita) flying in a V flock position themselves in aerodynamically optimum positions, in that they agree with theoretical aerodynamic predictions. Furthermore, we demonstrate that birds show wingtip path coherence when flying in V positions, flapping spatially in phase and thus enabling upwash capture to be maximized throughout the entire flap cycle. In contrast, when birds fly immediately behind another bird—in a streamwise position—there is no wingtip path coherence; the wing-beats are in spatial anti-phase. This could potentially reduce the adverse effects of downwash for the following bird. These aerodynamic accomplishments were previously not thought possible for birds because of the complex flight dynamics and sensory feedback that would be required to perform such a feat12, 14. We conclude that the intricate mechanisms involved in V formation flight indicate awareness of the spatial wake structures of nearby flock-mates, and remarkable ability either to sense or predict it. We suggest that birds in V formation have phasing strategies to cope with the dynamic wakes produced by flapping wings.
Emphasis added. Well, I dont know "what is the supervising control for an avian flight formation". Neither seem scientists to know. It seems, however, as you can see, that it is some very complex sum of functions, certainly rooted in deep and complex genetic and epigenetic information. Whatever the explanation may be, it does not seem to be a "simple case".gpuccio_{April 29, 2016
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Origenes: Don’t get your hopes up The argument was raised that bottom-up relationships can't result in global organization. If you don't understand simple cases, then it's unlikely you would recognize more complex examples.Zachriel_{April 29, 2016
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Zachriel: What is the supervising control for an avian flight formation?
Don't get your hopes up, Zachriel. Whatever it is, it does not produce something that is ...
... even vaguely comparable to the complexity and functional order in C. elegans’ first division: http://www.wormbook.org/chapters/www_asymcelldiv.2/asymcelldiv.2.html [Gpuccio]
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gpuccio: http://betterphotography.in/wp-content/uploads/2011/05/v-formation-rajesh.jpg I think the concept is clear. In all the examples in the second set, some supervising control, based on specific information, gives order and function to the outcome. What is the supervising control for an avian flight formation?Zachriel_{April 29, 2016
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Origenes @90 Interesting comments.Dionisio_{April 29, 2016
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// follow-up #86 // The problem that materialism has with "function", is that it is cannot be understood in isolation, but requires the context of a larger whole instead. Legs, arms, head, muscles, organs, and cells are all functional to the whole. IOWs it is in conjunction with a whole that the parts make (functional) sense and are unified. Yet IOWs when we speak of "function" we explain the parts from the level of the whole. And obviously this in direct contradiction to the ambition of materialism. — Why does a cat have eyes? So it can see. — Here are some of the questions wrt function that spook materialists: Why would the parts be in functional submission to a larger whole? What is the bottom-up explanation for this top-down hierarchical relationship between the whole and the parts? We see a reflection of the same hierarchical whole-part-relationship in written language. One cannot explain the context (the message) in these sentences bottom-up from the level of the characters. Obviously, the characters lack the tools and intelligence to produce it. Instead each character is in "functional submission" to the (larger) context. The characters derive there functionality (meaning) from a higher level. NB as with biology, we observe several levels of contexts/wholes: words, sentences, paragraphs, stories. IOWs it is the context that explains the parts and not the other way upwards :)Origenes_{April 29, 2016
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