Is “Directed Evolution” Darwinian? [with addendum]

Do you consider white fur on a fox to be a fitness variable? --michaels7 It depends upon the fox and its environment. a) is it fox in a snow-covered environment much of the time and b) is there in fact variation in the coloration of the fox's fur? c)does the color variation contribute to the probability of a successful hunt? If the coloration impacts its success at hunting, it almost certainly would be a fitness variable. There are also other things to consider, such as how mate choice may be influenced by color. My problem in “understanding” issues with NS is one of clarification between core and non-core variables for fitness. It's often not an easy thing to distinguish. Researchers try to gather as much information as possible about the system in question, but even then mistakes can be made and in many cases we still don't know. As Jerry indicated genetic drift plays a much larger role than people often assume. One thing which helps narrow the problem, though, is to consider relative fitness among organisms. This allows you to only focus on those traits that are, in fact, variable in the population under study. So while the length of the adult femur in a T-Rex likely contributed to its absolute fitness (whatever that is), it would be a non-factor in its relative fitness equation if all adults had the same length femur. (This was an admittedly contrived example, but hopefully illustrative of the point.) In other words, it's important to know what the variable traits are. One can only empirically test how a certain trait influences fitness of a species when there is *no* existing variation in that trait in question by introducing a new mutation for the trait and seeing how it fairs in the population. Hope that helps somewhat. great_ape

Atom, You said "Organisms X and Y are two different allele types (variations) of the same species." I have no idea what you are talking about so maybe some examples are in order. Consider the following. Organism X at time t1 (e.g. the year 1970) has a population frequency distribution d1 (e.g. 40%) of some allele (e.g. fur coloring). At time t2 (e.g. the year 2000) the frequency distribution for this allele is d2 (e.g. 50%) and it is considered substantially different from d1. What are the causes for the changes in this frequency distribution? Biologists and geneticists have hypothesized two main causes; the first is something they call natural selection based on environmental pressures and second is called genetic drift which is based on chance. There could be others such as a migration of species members but these are the two main ones. If you want to suggest other processes, then go ahead. If you want to eliminate one of the two main processes, then go ahead. But in either case you have to have evidence and reasoning to back up what you want to say. If you want to make the definition of natural selection more precise, then go ahead but I doubt anyone will believe that the process is non existent and does not act in the environment. jerry

Your examples of organisms x and y is inappropriate. Focus on variations of x alone.

Organisms X and Y are two different allele types (variations) of the same species. Better? Atom

natural selection or whatever you feel comfortable calling it is only applicable to a population. Your examples of organisms x and y is inappropriate. Focus on variations of x alone. You are literally comparing apples and oranges with a whole milieu of allele difference maybe as much as humans and bananas. So looking at one allele that may be common to both organisms may not be meaningless but most likely inappropriate. jerry

A short follow-up: Can fitness be defined apart from differential reproduction? (As a set of envrionmental constraints and phenotypic traits, for example) Imagine a desert environment shared by two organisms, X and Y. Both live in the same exact location and share the same constraints. X needs to drink 10% its body weight in water each day to survive; Y needs 50%. Organism X in this enviornment will reproduce and have 3 offspring each generation. Organism Y will have 100. Generation times are the same as are times of reproduction. Q1: Which organism is more fit, in this environment? (If you say X, then fitness has no bearing reproductive success.) Q2: If organism Y is more fit, then that means that those traits are more fit, by your definition. (When its traits "interact" with the environment it produces more offspring, meaning it has a greater survivalability.) So if this is the case, lower water consumption has a negative correlation with fitness. But for two other organisms, P and Q, also living in the exact location and environment, maybe the opposite is true. But in all cases, we can't define fitness in relation to an ideal set of traits, since a trait will give us different results in the same environment; we can't know beforehand what the outcome will be. So we then define fitness based not on possession of this or that trait, but on actual outcome success. This poses the problem of circularity. Either way we lose. I invite your discussion. I may be missing something. Atom

jerry, great_ape, I appreciate your interaction on the topic. jerry, I recognize that this isn't the biggest problem for Darwinism, but this is just a single thread discussion on one weblog. I have a suspicion that many people are interested in seeing these issues worked through, however. A couple quick items: great_ape, good analogy with F=ma. I wanted to think about this before I responded. You don't need to respond back, I won't press for answers. Let's take gravity again. You are correct that we can associate the label "force" simply with the outcome, ma, an accelerated mass. In the same way, we can associate the label "Natural Selection" with the outcome, differential reproduction. But then we'd need to ask "what causes the 'force'"? For gravity, I'd be foolish to reply "the accelrated mass (ma) is the cause of the force." Imagine a universe with a single object at constant velocity. It begins to accelerate. Was that accelration caused by "the mass accelerating (ma)"? If so, the acceleration was uncaused. So if we identify the force with the outcome (effect) we now need an explanation for the "force", since the outcome still needs an explanation. For gravity we have one: bent spacetime or graviton exchange. Notice, "acceleration" is not needed to explain the force. In the case of NS, yes we can also identify it with the outcome. But then we need to explain the cause of "NS", since we still need to explain the cause of the outcome. And invoking "differential reproduction" or even "differential fitness" (which is based on differential reproduction) is the same as saying "the differential reproduction caused the differential reproduction". In fairness, you brought up environment interaction which I'm guessing you will say "causes" the differential reproduction. How it does so apart from differential reproduction, I have yet to see explained. Atom

Apparently genetic drift explains more changes in population allele frequencies than natural selection. This is what the population geneticists say. To me this whole argument is over minutiae. If there is a change in the frequencies of alleles it could be due to environmental factors that led one set of alleles to increase in frequency and I would say that this is an example of natural selection or it could be due to statistical differences due to chance that end up favoring one set of alleles over another. Modern biologist and geneticists recognize there is a problem with the term "selection" in natural selection and sometimes use the terms "natural interaction" or "natural fit." In any given situation it may be impossible to figure which is happening or what combination is happening. If you have a frequency change, then it might be interesting to see which may be operating but it may not be answerable unless some experiment is possible. Throw out the term fitness if you want. Change the term selection to something else if you want. It doesn't add or subtract anything from the discussion. The underlying processes are still there and easy to understand. This all takes away from the central discussion. Whatever you want to call the processes involved in allele frequency changes, they are a minor, minor, minor processes in terms of the evolution debate. They can be very important for medical research but in terms of evolution they are at best a side show. That is the important point. Focus on this and we may get someplace, not whether the proper terminology is being used which current biologists already admit. jerry

Question, Great_Ape, Do you consider white fur on a fox to be a fitness variable? My problem in "understanding" issues with NS is one of clarification between core and non-core variables for fitness. I think there is confusion in these areas in relation to micro vs macro outcomes which no experiment has yet to overcome. and yes, the typing slows down. Michaels7

For the record, I also think the "outcome" explanation of fitness is inadequate for much the same reason Lewontin does. And I'm not sure it is fair to say modern evolutionary theorists think of fitness purely in terms of outcome. "Some theorists" does not imply a consensus. It is probably fair to say that in experiments, for the sake of quantitation, fitness is effectively treated that way. If you're working with flies, for example, you might measure fitness in terms of viable offspring. Now that I see your excerpts, I think that Lewontin's essay was one of our assigned readings way back when. great_ape

great_ape, thank you for your response. If you feel you have explained yourself as well as possible, feel free to let your responses remain, as I won't press past that point. In the essay Sal linked, Lewontin explains that the definition you and jerry are using was that used by Darwin, but is not that used in Modern Darwinian Theory. They use the definition I refer, that based on outcome, which I (and others) find problematic. But it seems that an outcome based definition is the only one that "works" for doing any kind of quantatative work. Two excerpts from the essay. Sal already posted portions of these two excerpts but they highlight the very problems I bring up:

The difficulties of the concept of fitness are, unfortunately, much deeper than the problem of frequency and density dependence. The problem is that it is not entirely clear what fitness is. Darwin took the metaphorical sense of fitness literally. The natural properties of different types resulted in their differential “fit” into the environment in which they lived. The better the fit to the environment the more likely they were to survive and the greater their rate of reproduction. This differential rate of reproduction would then result in a change of abundance of the different types. In modern evolutionary theory, however, “fitness” is no longer a characterization of the relation of the organism to the environment that leads to reproductive consequences, but is meant to be a quantitative expression of the differential reproductive schedules themselves. Darwin’s sense of fit has been completely bypassed. The natural properties of organisms lead to differential reproductive schedules and these must somehow be mappable onto a quantitative function, fitness that can enter into formal prediction structures.

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There is no obvious common feature that would have allowed us to predict these classes. How, then, are we to assign relative fitnesses of types based solely on their properties of reproduction? But if we cannot do that, what does it mean to say that a type with one set of natural properties is more reproductively fit than another? This problem has led some theorists to equate fitness with outcome. If a type increases in a population then it is, by definition, more fit. But this suffers from two difficulties. First, it does not distinguish random changes in frequencies in finite populations from changes that are a consequence of different biological properties. Finally, it destroys any use of differential fitness as an explanation of change. It simply affirms that types change in frequency. But we already knew that.

Atom

Atom, One last thing. I took a graduate seminar on the philosophy of biology several years back with one of the main players in the field. I remember from that course that issues such as yours have come up in the literature over the years, and I only wish my memory served me better so that I could reference relevant articles and arguments. I just wanted to point out that, while I do think you're wrong, I don't think the conceptual issues surrounding NS and evolution are as clear and obvious as some folks make them out to be, and I find it very understandable that disagreements can ensue as people try to get the bottom of just what these terms signify in reality. Ultimately, however, what matters to me is whether there are useful and meaningful distinctions to be made by invoking these terms in the manner they are invoked. And I think there are very few who would claim that there are no such meaningful distinctions to be made. great_ape

Atom, I don't think I can my position any more clearly than motthew has. Personally, I think you have lost yourself in linguistic analysis, as has been the case with many-a-problem in philosophy. I will, however, attempt to answer your questions, then I will likely bow out b/c the thread is becoming unwieldy. (Is it just me, or when we hit > 120 posts or so there is an annoying lag with typing, etc.?) 1) Is differential reproduction required (in the causal antecedent sense) as a prerequisite for NS to occur? (you used the word prerequisite earlier) Yes. If differential reproduction did not result from the environmental "forces" doing the filtering, then we would not refer to that combination of environmental factors as contributing to "natural selection." Again, "natural selection" was darwin's attempt to put a label on a certain phenomenon in nature consisting of the interaction between environment and traits and the differential reproduction that ensues. The whole system: environment + traits + ensuing differential reproduction is what we refer to as "natural selection." 2) Is differential reproduction the result of “natural selection”? Again, linguistic issues. You're banking on the common linguistic sentiment that something can't be both part of the definition of a something *and* the result of that something. Yet consider F=ma. Would you make the argument that the acceleration of a body can't be caused by a force, because acceleration is necessary to define force to begin with? 3) Does not the “selecting” occur as replicators reproduce against a backdrop of environmental factors and constraints (self-selecting as it were by their acts of reproduction)? If not, when exactly does the act of “selecting” take place? When the environment was first set up in the big bang? Every moment? Or only when things actually reproduce and survive? It occurs precisely when things reproduce and survive, differentially, based on environmental influences. That is, when a process meets the criteria outlined for "natural selection." Is this process different from other material/biological processes and worthy of its own title? You bet. And the fact that Darwin received such accolades for putting his finger on why it's different and noteworthy is a testament its being a well-applied label. Also, I should add, NS is a population-level phenomenon. It happens when a *population* of organisms begins to change as a result of the interaction of the environment and their respective heritable traits. Again, I think the term "force" is questionably relevant to this discussion and may add more confusion than its worth. I prefer "process". And clearly the process of natural selection is distinguishable from other processes, such as genetic drift, etc. The word "force" is often and understandably used because, again, it's a blanket label/metaphor for diverse environmental factors leading to differential reproduction. Feel free to not call NS a force, if it makes you feel better. But just be fair and treat artificial selection the same way. A quick analogy. "Fire" is what we call a certain chemical rxn between a range of substances and oxygen. Fire is a process. The transformation of a substance (e.g. wood to ash) is part of the definition of the process of fire. Yet according to your philosophical deconstruction of "natural selection," it would not be accurate to say that fire burns wood and produces ashes. Think about it. Because in a certain restricted semantic sense, you could be correct about some aspects of the usage of "NS" as a label. Yet have you thereby accomplished anything of any significance to the real world? Have you unveiled anything that wasn't already understood? 4) If differential reproduction is required to cause “Natural Selection”, then how can it also be the result of “Natural Selection”? (see #3) great_ape

MatthewTan, I believe that current mammals have over 200 or more different cell types, each working with one or more of the other cell types. Quite a complicated system to develop by design let alone by random events and still getting all the "bugs" worked out. Another good analogy. jerry

Re: Comment #123 by gpuccio Interesting and insightful “soliloquy”. I think gpuccio has a strong point. Increasing complexity not only does not really improve survival "fitness", but becomes a "burden" opening itself to multitude of potential "bugs" in the "operating system". MatthewTan

The combination of alleles and environment can lead to differential reproduction depending upon the particular combination.

The combination of alleles and environment may lead to the differential aspect of differential reproduction once the reproduction actually begins to take place. The reproduction and the "act" of selection are one in the same. If an organism has the right combination of alleles for an environment but withholds from reproducing, then the "selection" has changed even though environment and alleles have not. So it is the organism that selects itself, in a sense. Some are better at doing so than others. The environment just provides the arena, with hazards and constraints. Natural Selection, then, is not a force. It is merely a description we give to what happens when replicators out-replicate one another. In other words, it is a description of differential reproduction. As I said in my first post on this...

Natural “Selection” on the other hand is a-causal; it doesn’t cause differential reproduction, because it IS differential reproduction. What does differential reproduction cause? Differential allele frequencies…but then again, isn’t that what differential reproduction refers to anyway, since we talk about populations on the level of genes? So differential reproduction “causes” differential reproduction.

If Natural Selection is a force, what does it cause? What does it require? Does it require the phenomena it is supposed to cause? Atom

I am aware of ecothermic animals for which homeostasis is less important so my opening comment could be limited to most endothermic animals. jerry

Good work motthew. I don't see anything controversial with your mathematical abstraction. I'd like to focus in more on "who is doing what" (environment as backdrop of constraints vs. as "active" filter), but I like the way you're describing it. Since I have taken so much time in tearing down the popular (mis?)understanding of NS as "force" separate from the result of differential reproduction, in other words what it is NOT, I probably owe it to all the partcipants to explain what I think NS actually IS. I do think a phenomena exists and it is repeatable. I just differ on "who is doing what" and on whether or not we can define it in a non-circular way. Hopefully I can pull away from my lovely girlfriend long enough this weekend to write up a short summary of what I think NS is. Lets hope. Atom

Can we agree that homeostasis is good for the prolonging of life? I am sure it is not the only variable but it seems like a very healthy situation for living organisms. So that organisms with alleles that promote homeostasis are more likely to reproduce and have more offspring because they will probably live longer. Also organisms with alleles that disrupt homeostasis are more likely to die and not reproduce and thus have less offspring. Also the alleles that promote homeostasis in one environment may not promote it in another environment. And vice versa. The combination of alleles and environment can lead to differential reproduction depending upon the particular combination. How hard is to understand. It is not circular; it cause and effect. jerry

I wonder if some mathematical terminology might not help me get my point across (this is dangerous for me to do since I only minored in mathematics and have forgotten much of it). Please bear in mind that this discussion is probably worse than the proverbial elephant going down a slide. I'm not intending to deal with details, just provide a theoretical framework. Suppose we have a equation for fitness f(p,e) where p is a certain phenotype and e is an environment. The result of the function is a real number from 0 to 1, representing the scale from totally unfit to totally fit. The phenotype is, of course, evaluated in the context of the given environment, and phenotypes which produce higher values of f will be more reproductively successful than other phenotypes in the same environment. Now, it's true that specific traits in the phenotype cannot tell us its overall fitness for an environment, but that's why we have black box fitness function that gives us a phenotype's overall score. An individual of a given phenotype is of course going to have wildly different success in reproduction. We could possibly predict the pattern of individual's success by using a statistical bell curve centered at the individual's phenotype's f(p,e) score. A certain subset of phenotypes for a given environment will, of course, score closer to 1 than the rest will. That means this subset (however wildly different their traits may be) of phenotypes will dominate reproductively, and thus the environment acts a preset filter and unintelligently directs the phenotypes in it toward certain outcomes. While my theoretical fitness function is designed to be a universal, unchanging function, the trouble is that both phenotype and environment are in a constant state of flux. How strong is this flux? Sometimes it can be extremely chaotic and other times only be wiggling around a little bit. This messes with the directional aspect that exists when using constant values for f(p,e). In actuality p and e would have to be some sort of differential equations. For breeding programs, however, the environment variable would have to be substituted for a goal (g). So we have a new but similar function f(p,g). In this function, however, constant variable are used. So we can accurately predict the overall outcome. I'll stop there and wait for input. motthew

Yes, differential reproduction is *required* for natural selection in the sense that it is necessary to *fulfill* the full criteria for “natural selection.” *BUT JUST AS IMPORTANT* for meeting the criteria for natural selection is the *action* of various aspects of the environment towards *generating* that differential reproduction. It is this latter component of the criteria that I think Atom is neglecting in his argument.

great_ape, I will ask you to be straight-forward. (No "metaphorical" terms are needed to precicely and quantifiably describe the FORCE of gravity, mind you.) 1) Is differential reproduction required (in the causal antecedent sense) as a prerequisite for NS to occur? (you used the word prerequisite earlier) 2) Is differential reproduction the result of "natural selection"? 3) Does not the "selecting" occur as replicators reproduce against a backdrop of environmental factors and constraints (self-selecting as it were by their acts of reproduction)? If not, when exactly does the act of "selecting" take place? When the environment was first set up in the big bang? Every moment? Or only when things actually reproduce and survive? 4) If differential reproduction is required to cause "Natural Selection", then how can it also be the result of "Natural Selection"? Here is that same double-talk applied to gravity: For the falling of a body to occur we need: 1) the falling of a body, 2) *disparate* environmental factors which interact with the falling body, helping it along its way down (density factors, air particle collisions, solar photons, etc) and 3) any other prerequisties or disparate causes you want to throw in there. If you have all those factors (don't ignore any of them Atom!) then you will get the result of the falling of a body. You see, once you include the result as an explanation for how the result was caused you have lost your way. It doesn't matter what else you throw into the equation at that point. Atom

DanaMagee, One problem with birds is that they have an oxygen delivery system that is different from any other class of animals on the planet. It is uniquely suited to flight and without it birds would not be able to fly. It seems so unlkiely the might TRex which is similar to reptiles would have the same unique oxygen delivery system. Even if they did, where and why did it develop. It is not just small difference but a major reconstruction. jerry

gpuccio, Wonderful soliloquy! This philosophcal analysis you did, along with all the unliklihoods that must be assumed to support the opposite Darwinist viewpoint is very convincing. The problem is that the current holders of the keys to the world won't let this discussion get out. Even many who are supposed to be God's disciples on earth will not even let the discussion proceed. We have to keep on fighting. jerry

[...] Is directed evolution Darwinian? [...] Questions on natural selection « Omnipotent Grace

Wow, this thread has grown so quickly that I scarcely had the time to read it. That's the proof of one thing I have always thought, that NS is anything but simple. Only a very tricky concept could have generated so much discussion in such a short time! I'll try some more elaboration, just to add to the pool. The environment. Is it random or not? That's important because, as I have already written, there is little doubt that NS, however tricky and elusive the definition may be, is related to the "interaction" between the environment and the organism. So, if the environment is random, the only non random component of NS remains the organism, that is the already existing information plus the variation induced by mutation, which is by definition random. In that sense, NS could be considered random in regard to the creation of new information, as the only non random component is the already existing information. But is the environment random? And if yes, in what sense? I don't know if the environment is random in absolute. That depends if you consider the existence of a planet like ours only the random product of random forces in one of many random universes, or if you entertain any less drastical and more teleological view of reality. But that's not the point. The point is if the environment is random in regard to life, and in particular in regard to the new information necessary for important transformations in life. Let's make an example. At a certain time in the past, if we have a stable environment and stable organisms, what is the role of environment in NS? Has it only a "censorhip" role, in the sense of eliminating random errors in organisms? Or has it a "permissive" role, intended as boundary, for new organisms with new information? Probably both. There is no doubt that the environment, even if stable, is a constraint. Life as we know it would not be possible on Saturn. But the environment can also change. If it changes, life that was possible could become impossible, and vice versa. So we can say that the environment is certainly significant for the existence of life, but if we believe that its being what it is was not designed, then its relationship with the appearance of life is random, and if we believe that its fluctuations are not designed for life, then its relationship with further modifications of life is random. In other words, unless we believe that environmental characteristics and fluctuations are intended to help or modify life in a certain direction, their influence on life can be considered random. In that scenario (non designed environment) environmental conditions would act as a background randomly favouring or hampering life, because the laws which govern its temporal development have no pre-connection with life. In that case, it is life and only life which acts non randomly, adapting to the fluctuations of environment, or changing to interact differently with a stable environment. In both cases, the mechanism of that adaptation or transformation remains a mystery, it is certainly connected to the nature of life itself, and it is best explained by the concept of design. But the problem is that I do believe (while darwinists certainly don't) that the environment and its fluctuations may have been designed, at various levels, to help life. After all, I believe in a designer. But even in that case, even if the designer has in some way planned the environment for life, I still think that the role of environment is only passive, "permissive". It's a brilliant passivity, if you want, as is suitable to the designer, but always a passivity. Indeed, in all discussions about NS, a point is always underestimated: the characteristics of life itself. I see it this way. Too much fuss has been made of concepts like surviving fitness, reproductive advantage, and environmental landscapes and niches, and the result is that our reasoning has become biased, and we can't any more see what has always been under our eyes. And what is under our eyes is life itself, its obvious characteristics and properties, its apparent purposes. Surviving is not all. In any landscape, what are the entities which survive better? I would say, certainly, inorganic entities. Stones are very difficult to destroy, some of them have existed for aeons. Molecules, atoms, barions, are very long lasting, sometimes almost immortal. Life, on the other hand, is extremely frail, in all its manifestations. The reason for that is very obvious. Love is not realized because of the basic laws of nature, as darwinists still think. Life is realized "in spite" of all laws of nature, perhaps not violating them, but certainly manipulating them against all odds. That's why abiogenesis is still such a complete mystery for everyone. Because life cannot come out of inorganic matter, unless some really hard and fundamental event (we could say "miracle") takes place. Life is the only way the second law of thermodinamics can be ridiculized, without violating it. Living beings are so improbable that they can survive only through an incredibly complex inventory of continuous magics, and still only for a short span of time. Life is so improbable and frail, that the only way it has to survive is by cloning itself before dying, so that the unlikely miracle may be perpetuated in spite of all contrasting realities. But that's not all. Not only I really don't understand how one can think that life arises as a necessity from inert matter, but I don't understand either how one can suggest that the increasing complexity of life in progressively higher organisms may have as its own purpose "a better reproductive fitness". Are we kidding? I know no living being reproducing itself better than bacteria, the simplest living organisms. Bacteria are perfect: they live, they reproduce in an extremely efficient way, they exploit the environment certainly better than we do. They are beautiful, they are clever and cooperative (see the Shapiro paper), and, above all, they are many. Think about it. The simplest living species, the first one to appear on this planet 4 billion years ago, is still the prevailing living thing here. Why add complexity to that, to attain more reproductive fitness? Is the environment non randomly preferring elephants to bacteria? Why? Are humans better than arthropods, in regard to survival? Are they better than rats, in regard to reproduction? Why the added complexity? Was it the environment? The fact is, the increasing complexity in progressively higher beings is not really necessary for higher fitness: it is necessary for higher functions. Life "evolves" not because it has not already found efficient ways to reproduce or to survive. Life evolves to do "new things", things which were impossible in the simpler forms. And, although some (but, absolutely, not all) of this new things can be usefully recuited to help survival, survival in itself is not their motivation. Because, in reality, complexity provides new functions, but in itself it undermines survival. Life is extremely unlikely in a bacterium, but it becomes ever more unlikely and frail in a fish, in a bird, in man. Complexity is frail, as every PC programmer (or even simple user) well knows. That reminds me of operative systems. Who remembers the wonderful simplicity and stability of 16 bit Windows? (I am old enough to remember) So, why has Microsoft devised increasingly complex OSs, and still does, requiring higher and higher resources, higher and higher error managing (not always successful, I'm afraid), and higher and higher competence (and patience!) in the user? The answer is simple: because these new OSs, however complicate, however frail, "do more" than their ancestors. They are more powerful, and so they can manage more complex information, manage video and 3D rendering, true multitasking, and so on. So, I really think that function, and not mere survival, is the real motivation of increasing complexity in living things. And function is related to the inherent mechanisms of life itself, and of its main expression, that is consciousness. So, movement evolves so that living beings can move, and is then exploited to help survival, and compensate for the lower fitness intrinsecally related to higher complexity. The eye, in its various implementations, is necessary to see, to perceive the world in a new dimension of representation, and not only to survive. But it can help survival. The purpose of life is to express itself, to express qualities and experiences which are inherent to life and consciousness. They are expressed as higher functions, to know the environment and interact with it, and not only to survive without any goal. The higher organisms must pay a very heavy cost to be able to express these new functions: their bodies must become bigger and more complex, intelligently manage an incredible number of cells, highly intricate immune systems must be designed to defend them from insults, billions of billions of neurons must control what takes place in the inner world of the body, and interpret and organize myriads of information from the outside, and correctly respond to them. The chance to survive, even for short periods, is brought beyond any reasonable limit of likelihood. But, luckily, the designer is up to the challenge: he knows his task. So, excuse me for this long soliloquy, but sometimes, when I hear and read about randomness and the environment as "shaping" a whole living universe, an universe before which we should just feel inclined to bow in reverence, I lose my (scarce) self-control. gpuccio

http://www.cnn.com/2007/TECH/s.....index.html Now if Behe has no trouble with Common Descent then I assume he should have no trouble with a Bird-Dino link. Having "no trouble" with a bird-dino link (being able to accept the possibility) is not the relevant issue. The relevant thing is being able to be skeptical of it -- namely not accepting the certainty based on a CNN report. Frankly, I'm more fascinated at the unquestioned acceptance that protein can survive 68 million years. tribune7

If you accept Common Descent then you should have no problem believing in a Dinosaur - Bird connection right? For Old Earth Creationists this shouldn't be much of a problem either. For instance "there could potentially be NUMEROUS ancestors (perhaps each with a unique body plan?) and that evolution produced various versions of organisms from those established themes". Who knows. Scordova is right though we shouldn't reject scientific findings from the secular world just because of our bias against them. DanaMcgee

What are Dr. Dembski's views on the Bird-Dinosaur link? Take a look at this: http://www.cnn.com/2007/TECH/science/04/12/dinosaur.reut/index.html Now if Behe has no trouble with Common Descent then I assume he should have no trouble with a Bird-Dino link. DanaMcgee

Great_Ape, "Yes, differential reproduction is *required* for natural selection in the sense that it is necessary to *fulfill* the full criteria for “natural selection.” *BUT JUST AS IMPORTANT* for meeting the criteria for natural selection is the *action* of various aspects of the environment towards *generating* that differential reproduction. It is this latter component of the criteria that I think Atom is neglecting in his argument. Hmmm, not speaking for Atom, but I think he is being a good reductionist, yes? He's picked up on a valid point I think. Intelligent agency at the very least speeds up what the environment does, but does not stop there. It leaps over environmental considerations for "survival" with the unique creation of curious minds utilizing breeding techniques creating species based upon specialized and directed mutations for artificial consumption of the mind. What would normally only appear as short lived errors in any environmental surroundings and blip out as bad mutations - are kept alive by artificial means for whimsical curiosities in some cases. Still, I do not see how selection, plus random mutation, and environment converge to new life forms - without a centralized, animated code programmed to conserve information, but allow varience on the edge. This is what we observe today. Enjoyed this discussion everyone. Ps. Lucy is in trouble btw.... http://creationsafaris.com/crev200704.htm#20070410a Michaels7

Motthew? or Matthew? "There are important qualitative differences. Importantly, in breeding, those with the best selected-for traits are only allowed to mate with others with the best selected-for traits; in the wild organisms are allowed to mix freely, which is a serious hindrance." This is a good point. But not just a hindrance. In the wild, some artificially selected "best" traits could be a killer. In my above example the hairless cat survives due to the benevolent curiosity of individual breeders. http://en.wikipedia.org/wiki/Sphynx_(cat) "Wild organisms" living in the wild would not survive for long with such best selection procedures by us curious business minded and playful humans. Natural Selection is not a force. It is the end result of the environmental surroundings and available gene pool. Michaels7

#49, Atom, Very good. I almost posted the same subject matter last night, but my comments grew to long. Will try again, especially after Great_Ape, Salvador responded with good follow thrus. Environment is random. No animal would survive on Saturn. Lets truly step back. We have one "safe habitat" for life in our solar system(please, lets not argue ove Mars or moons). In our "safe habitat" we have more environmental influences within safe parameters. Sure, some are extreme to us - artic pole - produces polar bears. But allow that polar bear to migrate south, interact, you have part of the normal environmental influences wher most life flourishes at greater rates. Extreme environments cannot suffice to replace artificial selection, only point to selective qualities that are pre-determined within the gene pool influenced by environment or artificial choices. Dave's dog breeding example shows different boundary or limits. Or better, take the hairless cat(please). Bred uniquely for people with odd taste, would not survive in normal environmental surroundings. Artificial selection pushes the extreme mutations past even extreme environments. While mutations survive, switched off in normal environments. The breeder captures the mutated offspring and reproduces beyond population normals. Artificial selection creates artificial normality of mutational traits that would otherwise a)die off, b) limit numbers, low percentage. So we have... 1) "Normal boundary" genetic conditions within certain environmental thresholds. All genomes drift back to this boundary in normal environments. Call it a "Blemished gene pool" 2) "Extreme boundary" genes in exteme environments, randomly directed by environmental surroundings of hot, cold, moist, dry. "Exteme edge boundary gene pool" 3) "Artificial broken boundary" genes which would not go past certain population contraints in "normal or extreme boundary" conditions - like the hairless cat, just like a hairless polar bear would not survive. There are no beneficial traits - except - in the eye of an intelligent beholder. What I cannot agree to is these minima/maxima conditions lead to any novel type cell forms or macro structures. I think we mistake migration paths across great environmental boundaries with the equivalence of creating new species. While original migration may take time for specialization of traits - hair color, webbed feet, it only takes a generation or two for those specialized features to be absorbed back into the great "Blemished gene pool" Michaels7

Atom wrote: But this doesn’t have much to do with either: A) defining NS as a force and answering what exactly it “causes” (other than differential reproduction, which is necessary for natural selection to occur in the first place) or B) showing how we can define fitness without ultimately having that definition reside in greater differential reproduction, even if removed by one or two steps. But I’d like to hear more of your thoughts on the topic. You can help me sharpen my own thoughts.

Lewontin essentially pointed out that NS is a force when it's a force, and it's not when it's not. Thus, NS entirely superflous and can't be invoked as a general principle. Check out this devastating crtique of fitness by Lewontin in 2003 Santa Fe 2003 Stanley Salthe considered it a nail in NS's coffin, so I credit Salthe with pointing me to the article:

In modern evolutionary theory, however, “fitness” is no longer a characterization of the relation of the organism to the environment that leads to reproductive consequences, but is meant to be a quantitative expression of the differential reproductive schedules themselves. Darwin’s sense of fit has been completely bypassed. .... How, then, are we to assign relative fitnesses of types based solely on their properties of reproduction? But if we cannot do that, what does it mean to say that a type with one set of natural properties is more reproductively fit than another? This problem has led some theorists to equate fitness with outcome. If a type increases in a population then it is, by definition, more fit. But this suffers from two difficulties. First, it does not distinguish random changes in frequencies in finite populations from changes that are a consequence of different biological properties. Finally, it destroys any use of differential fitness as an explanation of change. It simply affirms that types change in frequency. But we already knew that.

Those were the highlights, but the rest of the article is worth reading. The only time fitness is meaningful is in the repeatability of results, i.e. we can predict how a bacterial population will evolve inside a persons body in response to an antibiotic. But this isn't much of an insight in that we expect similar outcomes for similar situations!!!! The interesting question is whether selective forces exist to create large-scale biological innovation, not just change. The notion of similar outcomes for similar situations gives no insight into the forcefulness of NS as a means of creating large scale innovations. Wind and rain can change the shape of mountain. Mount rushmore is a mountain with a changed shape. Does that mean wind and rain shaped mount rushmore since wind and rain can shape mountains? Absolutely not. There is an analogous difficulty in asserting NS can effect the kind of biological change that can create large scale biological novelty. scordova

Atom wrote: But this doesn’t have much to do with either: A) defining NS as a force and answering what exactly it “causes” (other than differential reproduction, which is necessary for natural selection to occur in the first place) or B) showing how we can define fitness without ultimately having that definition reside in greater differential reproduction, even if removed by one or two steps. But I’d like to hear more of your thoughts on the topic. You can help me sharpen my own thoughts. Lewontin essentially pointed out

scordova

I can't believe I'm still watching this thread so closely, but...

“non-random” ... seems designed to conflate natural selection with intentional selection, by using a fuzzy definition of “non-random” to make it sound like both are directed. Natural selection is not random with respect to the environment. However, the environment itself is random, by which I mean, it doesn’t act with any intentions or goals in mind.

Since I'm the one who used the term non-random, let me defend my use of it. I in no way meant to imply that an environment acts with intentionality. Non-randomness is not synonymous with intentionality. Lots of things are non-random without being intelligent. Objects unhindered by air resistance will fall at 9.8 m/s/s on earth. Acceleration due to gravity is non-random. That doesn't mean gravity has any goals. I say natural selection in a given environment is non-random, although it does fluctuate. Breeding programs are also non-random. That does not mean, however, that natural selection is exactly the same thing as a breeding program. There are important qualitative differences. Importantly, in breeding, those with the best selected-for traits are only allowed to mate with others with the best selected-for traits; in the wild organisms are allowed to mix freely, which is a serious hindrance. motthew

Calling directed searches "Darwinian" is tantamount to defining Darwinism away. It is to conflate natural selection with selection simpliciter, which renders the "natural" part meaningless. If we use that definition, then anytime anyone selects anything, we can call it "natural selection", in which case, what good is the concept? It is precisely the point of natural selection that it is undirected, ie, there are no intentions or goals involved. Darwin specifically contrasted this with animal breeding, which, like evolutionary algorithms, is directed selection, in which goals are involved. If you ignore or equivocate on this crucial distinction, you render the concept of natural selection vacuous. And as Bill says, it's an abuse of the language to boot. If you can't speak clearly and consistently, you aren't thinking clearly and consistently. Btw, the claim that natural selection is "non-random" is true in one limited sense, but also misleading almost to the point of culpability. That commonly uttered statement seems designed to conflate natural selection with intentional selection, by using a fuzzy definition of "non-random" to make it sound like both are directed. Natural selection is not random with respect to the environment. However, the environment itself is random, by which I mean, it doesn't act with any intentions or goals in mind. It just happens to be the way it is at any given point in time (unless the environment itself is being controlled to achieve someone's intentions, in which case we're back to intentional selection). Deuce

"A) defining NS as a force and answering what exactly it “causes” (other than differential reproduction, which is necessary for natural selection to occur in the first place)" --Atom This thread has jumped forward quite a bit since last I was here. Several of you have made some excellent points. One more attempt to convince Atom... As Darwin himself noted in the quote J provided, "natural selection" is essentially a metaphorical term, a linguistic term that blanketly refers to all the disparate *environmental causes* that, when interacting with particular organismal traits, yield differential reproduction among organisms. In the case of artificial selection, you don't need such a blanket term; you can simply envision a breeder. Yet Atom, you are willing to say that the breeder is a causal force but not the disparate environmental mechanisms involved with natural selection. I do not understand the disconnect. (I rather dislike talking of forces and causality because of metaphysical connotations, but I simply assert here that natural selection is *no less* a force than is artificial selection despite the presence of intelligence in the latter). Yes, differential reproduction is *required* for natural selection in the sense that it is necessary to *fulfill* the full criteria for "natural selection." *BUT JUST AS IMPORTANT* for meeting the criteria for natural selection is the *action* of various aspects of the environment towards *generating* that differential reproduction. It is this latter component of the criteria that I think Atom is neglecting in his argument. As for defining fitness without circularity, it all rests in the specific details of individual biological instances. What relative fitness means for bird beaks in the context of Darwin's finches, for example, resides in just *how* the beak physically/materially *contributes* to differential reproduction among finches. Not simply the differential reproduction itself. The informative content rests in the details. Differential reproduction, without any associated fitness, is simply genetic drift. If anything, contemplating the notion of genetic drift should illuminate things a bit. Genetic drift, by definition, entails differential reproduction, but genetic drift is decidely NOT natural selection. So what distinguishes genetic drift from natural selection? What constitutes that difference is the crux of this whole discussion. It is the selective "pressure," and it comes from diverse environmental sources. great_ape

I'm not arguing arguing for the predictability of natural selection. I'm not arguing for evolutionary storytelling of natural selection. I'm not arguing for natural selection as evidence for evolution. I'm not even arguing for the usefulness of natural selection. What I am arguing for is that natural selection is is not a meaningless concept, it is quite real, and is the non-random component of differential success in reproduction. Any acknowledgment that different ecologies have different types of organisms living in them, is, in my mind, a recognition of what I've just said. motthew

Can an unconscious director write a script?

You haven't seen many movies lately, have you? DonaldM

I just love the PT gang. They can always be counted on to trip over their own tongues! DonaldM

:) @ j. Sal, welcome into the discussion. You bring up the point of similar organisms needing to fulfill similar constraints, which makes sense due to their sharing the same "pieces of machinery" for their replication. Thus one change in machinery that leads to better differential reproduction should cause a similar response in similar machinery elsewhere. If they're gonna survive, they need the same mods, the ones that cause greater differential survival. But this doesn't have much to do with either: A) defining NS as a force and answering what exactly it "causes" (other than differential reproduction, which is necessary for natural selection to occur in the first place) or B) showing how we can define fitness without ultimately having that definition reside in greater differential reproduction, even if removed by one or two steps. But I'd like to hear more of your thoughts on the topic. You can help me sharpen my own thoughts. Atom

Atom (60, 78):

I honestly want to understand what is at the root of NS and if the concept can be framed in a non-circular, or even causal way. ... I’m pressing only because I want straight, simple, answers.

How about this: Charles Darwin, OOS:

Several writers have misapprehended or objected to the term Natural Selection... [Natural selection] implies only the preservation of such variations as arise and are beneficial to the being under its conditions of life... It has been said that I speak of natural selection as an active power or Deity; but who objects to an author speaking of the attraction of gravity as ruling the movements of the planets? Every one knows what is meant and is implied by such metaphorical expressions; and they are almost necessary for brevity. So again it is difficult to avoid personifying the word Nature; but I mean by nature, only the aggregate action and product of many natural laws, and by laws the sequence of events as ascertained by us.

Hence, natural selection is simply determination by "the sequence of events as ascertained by us." Helpful? j

The situations where survival of the fittest is an appropriate and somewhat useful metapor is when there are reproducible situations that get identical oucomes. For example, two petri dishes with the same kind of bacteria and identically treated with the same antibiotic will get the same results. Survival of the fittest in one context accurately predicts the survival of the fittest in the next, and this will help us predict what the surviving organism will look like if they survive at all. I can, for example by applying pesticide to an insect population have an idea of how another insect population will evolve if were dealing with similar populations of the same species as in my control group. This is helpful to drug development. I point out this is Blythian evolution, not Darwinian evolution. Where survival of the fittest is a worthless and useless metaphor is in the are of a population surviving out of pure luck. Technically, they had the trait of being lucky and thus were the most fit. Totally useless.... And even though the metaphor is useful for predicting evolution in the present day, it doesn't bode well for Darwinian evolution. In almost every case we have preservation of species, not origin of new ones!!!!!! Salvador scordova

Ok they're showing up immediately now...Thanks Dave! Apollos

DaveScot said:

Are most or all of your comments showing up right away?

They were being posted immediately until I added that pseudo code sample in this thread yesterday, then I think I got flagged as spam from there on out. Supposedly Akismet will correct it eventually if they're marked as "not spam" (Their web site says it can take a day or two). Apollos

To put it another way: When assesing fitness, we only consider traits that help or hinder net reproduction. (A true statement.) Those organisms with these traits (the beneficial ones) will have higher differential reproduction than those without them. (Another true statement.) Therefore, the traits which cause differential reproduction will cause differential reproduction, which then explains why when we see differential reproduction these traits were the cause. (A true statement due to its logical form. So a tautology.) "Traits which cause x will cause x, which then explains that why when we see x these traits were the cause." Convoluted, but logically true and the essence of what you're saying. Atom

...but then I go on to find specific reasons that they aren’t fit instead of stopping there.

But motthew, your "reasons" are only reasons because they lead to or take away from survivalibity in the end. Why not say that they aren't fit because they're not "red" enough? Because "redness" doesn't help nor hinder survivability/reproduction. Thus, it doesn't affect their "fitness." You are simply removing the problem by one step then pretending it goes away. "Frogs are fit because of x. X is defined as fit because of y. Y is defined as fit because it leads to greater survivability. Therefore, frogs are more fit due to x isn't circular reasoning..." - see the problem? Atom

Atom: It still sounds to me as if you are in fact using it in the rhetorical sense. You're claiming that in the phrase, "the fit survive," "survive" and "fit" are semantically equivalent, because we define what is fit by what survives. If fitness is defined by survivability, then you're quite right. But I disagree that this is how fitness is being defined. Frogs aren't fit for the desert (in part) because they need lots of water for their reproduction. This is one instance of defining fitness. I use the fact that frogs don't survive well in the desert as an indicator of their lack of fitness for the desert, but then I go on to find specific reasons that they aren't fit instead of stopping there. See the difference? motthew

The first definition from your link: "Tautology (logic), a statement of propositional logic which can be inferred from any proposition whatsoever " This is what I mean when I use the term. A statement that is always true can be inferred from any proposition whatsoever, even from none. I am not using it in the rhetorical sense. Atom

motthew, a tautology is a statement that is always true due to its logical form. An argument of the form "if x then x" is always true, regardless of what we plug in for x. Even "if x and y and z and q and p and l...then x" is still always true. It doesn't matter if we "add" more information (y,z,q,p, etc) or not. Atom

"I was questioned by great_ape for saying that NS is not a force, in the sense that what is causes is the same as the cause itself, or in other words, it “causes” nothing.)" NS, ie, the environment, does seems to be a cause. It is a non-random cause of death. NS can only subtract, it can never add. The novel information must come ultimately from a source. Darwinistas lean on random mutation ultimately without bothering to probe the implications of any particular view of the source of such randomness. "Random" ultimately is no different than simply saying "unknown" or "unpredictable." It is a negative term conveying ignorance only. So what is RS+NS really? It is the non-random environment acting upon molecular effects (via death to some) from some unknown or unpredictable source. That's it. No more no less. (All of the anti-ID nonsense is simply the (generally unstated) philosophical premises of the claimant that having nothing whatsoever to do with RM+NS.) mike1962

I hope someone got something out of that rather lengthy exchange. Haha. I know I did. motthew

So, to collapse the chain of how we defined a given trait as beneficial, we can say that long fur is ultimately beneficial in the cold because it helps an organism reproduce.

A tautology is not a circular argument, a tautology is a restatement of something so that no extra information is given. Are you saying that you said nothing of any information value in the following statement?

Let us stick with the example of long fur for now. We say it is beneficial because (special definition) it helps retain heat. Retaining heat is beneficial because it helps an organism survive, which helps it to reproduce.

Of course you've added information! You told us that fur retains heat, and heat helps organisms survive (ignoring any one of a thousand factors). Again, I say, survival of the fittest tells us that we can discern reasons for why some organisms thrive, and that in turn shows us that natural selection has endpoints though they are without willful intent and ever fluctuating. Maybe it is useless as a statement in and of itself, but when you apply it to a certain situation, it's quite clearly useful. motthew

Is it fair to say that you’re essentially saying something like this: Survival of the fittest gets us nowhere, because whereas we can theoretically understand the reasons why some organisms will reproduce more successfully than others, the fitness landscape is so comlicated in such a constant state of fluctuation that a clear trend toward organisms with certain features can never be properly established?

In a word, no. I am not saying that. I am taking it a step further: for any special definition of fitness you come up with ("long fur is more fit in a cold environment") it can always be shown that it is a circular definition, even if a couple steps removed. (My original point, however, was not the logical circularity of NS, which I already felt was established. I was questioned by great_ape for saying that NS is not a force, in the sense that what is causes is the same as the cause itself, or in other words, it "causes" nothing.) Let us stick with the example of long fur for now. We say it is beneficial because (special definition) it helps retain heat. Retaining heat is beneficial because it helps an organism survive, which helps it to reproduce. (If survival didn't ultimately aid in reproduction, it would become irrelevant to our abstract view of Natural Selection: we are only concerned with replicators out-replicating against a constraint space). So, to collapse the chain of how we defined a given trait as beneficial, we can say that long fur is ultimately beneficial in the cold because it helps an organism reproduce. Fit because it helps reproduction. Better reproduction because it is fit. The circle. Atom

Oh, I contradicted myself. I should have said "Natural selection alone isn't meant to explain much," instead of saying that it's not meant to have any explanatory power. (Extracting foot from mouth) motthew

Atom: Okay. Is it fair to say that you're essentially saying something like this: Survival of the fittest gets us nowhere, because whereas we can theoretically understand the reasons why some organisms will reproduce more successfully than others, the fitness landscape is so comlicated in such a constant state of fluctuation that a clear trend toward organisms with certain features can never be properly established? If so, I partially agree. There is no single end goal of natural selection. That which is labeled "fittest" is extremely elusive and always changing. But there are some factors in classifying the fitness that are clearly dominant and not so unstable: desert vs. tundra vs. rainforest, etc being one of the biggest. And thus we can say with some degree of confidence that certain factors brought about the dominance of certain types of organisms. If it still bothers you that this is a tautology then I'm not sure what else to say about it. Natural selection alone isn't meant to have explanatory power. Supposedly coupling it with the development of novel traits is. And thus my main point is, just because there is no teleological intent behind something, does not mean that there is no directional force in it. motthew

Mistake! What I meant was: A: That which is fittest survives. B: X is fittest. Therefore: X survive. (A good example of begging the question, as well.) motthew

Thank you for the answer motthew.

Phrase 2, on the other hand, is what I think “survival of the fittest” is really getting at. It’s a recognition that when we look at a given environment, we can find reasons that certain types of organisms can thrive in it.

True and agreed. But it doesn't solve our problem or escape the circle. "we can find reasons that certain types of organisms can thrive in it." - true: it is because they have traits which allow them to survive. Which traits are these? It depends on the envirionment. It may be low water consumption for desert, or long fur for the cold. But how do we define low water consumption or long fur as a "trait which allows it to survive"? By the net results of what happens when you put those traits in those environments. Those traits that survive are the survivors, thus are the beneficial/fit traits. You're saying, one step removed, "The reason some organisms suvive in environment A is because they have trait X. Trait X helps it survive/reproduce, so is thus fitter. We know this because it survives better with trait X than without it. Therefore, organisms with trait X will survive/reproduce better than those without it." A tautology still. Atom

I'm actually arguing with a friend in a chat about this right now, and he's helped me to once again refine my thinking. Logically: A: That which is fittest survives. B: X survives Therefore: X is fittest. In this formal sense "survival of the fittest" is circular reasoning, a tautology. But ignore that specific phrase for a moment and think about these phrases instead: 1) "Some things survive", 2) "There are reasons some things survive." Phrase 1 gets us nowhere. It's an entirely true statement but we can't do anything with it. Phrase 2, on the other hand, is what I think "survival of the fittest" is really getting at. It's a recognition that when we look at a given environment, we can find reasons that certain types of organisms can thrive in it. Granted, there are a thousand factors in an environment, so it's often difficult to really understand why certain organisms survive and others don't. But there are some factors that are so obvious they develop a clear an understandable relationship. Take again for example the desert. It's obvious why frogs don't dominate in the desert. They have to have water for their reproductive cycle. My friend pointed out that fish actually do live in the desert, and he's right! But it's telling that we're amazed that fish live in the desert. It shows that we are able to predict statistically, though not particularly, what kinds of organisms will thrive in certain kinds of environments. So while "survival of the fittest" is a poor way of expressing it, what it's really getting at is that we can take what we know about what organisms live where, and discern some of the major factors for why they're there. I'm arguing for the self-evidence of what has unfortunately been labeled "survival of the fittest" and "natural selection." What use it is to evolutionary theory is another matter. motthew

"survival of the fittest"? Darwinism is a religion of death. DanaMcgee

motthew, please explain what "survival of the fittest" is, if not "survival of the survivors". If you have reached a clear, non-circular definition of Natural Selection as a force, then please explain it. Then we can move past this "quibble" (to use jerry's assesment.) We can explain gravity as a force in two or three sentences. Please do the same for NS as a force and clear up any misunderstandings I may have. Atom

Okay, I'll go back on my word (oops!) and respond again:

Actually, we label the FORCE which CAUSES the falling of the bullet “gravity”, not the falling itself. Or else we’d have a useless tautology: “the falling of the bullet causes the falling of the bullet.”

No, we say “the bending of spacetime/graviton exchange(different and separate from the falling of the bullet) causes the falling of the bullet.” We have a cause logically separate from the effect in the case of real forces.

Well, you caught me oversimplifying and conflating scientific ideas. I didn't want to complicate the matter. But I can counter by simply taking it down to the fundamental levels that you want to take it down to. Gravity is, according to General Relativity, a manifestation of the shape of spacetime. But what is the explanation for the shape of spacetime, not as a description of the interaction of the parts of the spacetime system, but rather the underlying causes for the spacetime's existence in the first place? Eventually we always get to a point in science where, at least for a time, we can describe what we observe or logically derive from observations, but are clueless as to the underlying causes of it. It's no use to pick on "survival of the fittest" because it's a self-evident phenomenon that we don't have an underlying explanation for. It does not make it a valueless proposition. I might note that thanks to this discussion, today is the first day that I've clearly understood that "survival of the fittest" is actually quite different from "survival of the surviving." The first is not a tautology, the second is. Which is really what I've been trying to work out in this conversation all along. motthew

By the way, as a filter or even 'force' isn't a better name for Natural Selection simply 'death'? This use would get Dawkins out of his circularity when he says that Natural Selection (allelic frequency in surviving populations) is guided by Natural Selection (removal of alleles from reproducing population). It can't be both the cause and the effect, so it should be limited to one or the other. Charlie

Ken Miller is a weisel haha DanaMcgee

DaveScot,

Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.

Thanks. It was exactly the Weisel 38 I had in mind when I said 'random' was a metaphysical concept to Darwinian defenders. Oh, and pre-Dover Ken Miller biology textbooks. Charlie

"In most of these situation you can analyze what it is about the allele that lets the organism fit better into the niche such as longer fur. Some differences may not be obvious and actually be due to drift. ” Why did you leave that out? It answers the question you asked.

I am sorry for leaving that out. I left it out because it is also circularly defined, as I thought I made clear. What about longer fur defines it as beneficial? It allows an organism to retain heat, which allows it to survive better. Suvival is included in "reproduction" as a necessary step in it. Increased survival is unimportant if it simultaneously causes sterility, for example. What matters is the net effect. So increased survival, in as far as it matters to NS, is only important in what results it has for net reproduction. So the definition of a "beneficial trait" still boils down to "that which in the end allows an organism to out-reproduce". Atom

motthew, thank you, I am redefining and sharpening my ideas on NS in the process as well. I like your bullet analogy. It has a "tendency" to fall, which we label "gravity". Actually, we label the FORCE which CAUSES the falling of the bullet "gravity", not the falling itself. Or else we'd have a useless tautology: "the falling of the bullet causes the falling of the bullet." No, we say "the bending of spacetime/graviton exchange(different and separate from the falling of the bullet) causes the falling of the bullet." We have a cause logically separate from the effect in the case of real forces. In the case of NS, we say the "tendency" causes the "tendency." Differential reproduction of differentially fit traits, which are defined as the differentially successful alleles, leads to differential reproduction of differential alleles. This differential reproduction "leads" to a differential population of alleles. But "a differential population of alleles" is what differential reproduction is/describes. Atom

Atom, Please! Here is what you said "In a cold environment, organisms with alleles better suited to the cold will end up reproducing more." This is an excerpt from my comment that you used and then you said: "What makes you say that their alleles “better suited” to cold? Is it not because they survive/reproduce better than those without those alleles? (Is there any other way to assess fitness, other than by net results?)" You left out "In most of these situation you can analyze what it is about the allele that lets the organism fit better into the niche such as longer fur. Some differences may not be obvious and actually be due to drift. " Why did you leave that out? It answers the question you asked. jerry

I'm not trying to attribute purposeful action to the environment. I'm trying to point out that something can bring about a specific result simply because it is what it is. Let me use an analogy. If you fire a gun, no matter which direction, according to physics, the tendency of the bullet is to hit the ground (it won't necessarily hit the ground, but it is the tendency, which we label "gravity"). Likewise, in a desert, no matter what kind of organisms live there, the tendency of the population is to be dominated by those that require the least water. So in both artificial and natural selection scenarios, there is a tendency toward a certain result (or a certain subset of results). That is not to say the scenarios are more similar than dissimilar, though. This is a fascinating thread. I think I've refined my thoughts on natural selection more in one afternoon than I have in years. I'm not sure I'm helping the conversation progress, though, so I'll hold off commenting any more until some inspiration hits. Thanks for the great conversation, Atom and others! motthew

Matthey Tan, I do not know what Dembski is exactly. He is not a YEC and he supports an old earth. That does not mean he isn't friendly with the YEC's or doesn't think they have been very helpful to ID. What does it mean to be a creationist? People have different definitions of the term. I found reading the Dover documents helpful because in it he deals with invalid criticism of his beliefs in science. I doubt that no one would have asked a YEC to testify at Dover. That would have been insane. They were trying to distance themselves from YEC. He didn't testify for reasons having nothing to do with religious beliefs. jerry

jerry, please don't get frustrated with me. I'm pressing only because I want straight, simple, answers.

In a cold environment, organisms with alleles better suited to the cold will end up reproducing more.

What makes you say that their alleles "better suited" to cold? Is it not because they survive/reproduce better than those without those alleles? (Is there any other way to assess fitness, other than by net results?) There is not some "platonic ideal" that we compare organisms against and say "this one is fitter"; no, fitness is determined soley by results, which leads to all the problems discussed thus far. Atom

Charlie https://uncommondesc.wpengine.com/education/can-38-nobel-laureates-be-wrong/

Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection.

This excerpt from a letter to the Kansas school board by the Wiesel 38, a group of 38 Nobel prize winners, echoes the position of NAS and AAAS on evolution. Natural selection isn't really a guide. It's a filter that works really well at conserving the essential aspects of species by killing anything that wanders too far from the norm. Geneticist Guiseppe Sermonti, in his book "Why is a Fly not a Horse" points out that NS, based on actual observation of what it does instead of what the chance worshippers wished it did, is a conservative mechanism that operates to conserve the essential characters that define a species. One needs to keep in mind that as far as can be determined from the fossil record approximately 999 out of every 1000 species that ever lived became extinct without splitting off any new species (an evolutionary dead end) after an average span of 10 million years. They appear suddenly, remain essentially unchanged for millions of years, then die off suddenly. RM+NS handily accounts for the unchanging period and sudden extinction. Extinction occurs as recessive deleterious mutations accumulate in any species with obligatory sexual reproduction until there are so many of them the genome is no longer robust. This can be seen in most purebred dogs where natural selection has been thwarted and artifical selection allows deleterious mutations to rapidly accrue. Purebred dogs are prone to a litany of genetic disorders that would quickly make the breeds become extinct in the wild. The sudden appearance is what begs for a credible explanation. This is summed up in the commonly heard phrase "The question isn't about survival of the fittest but arrival of the fittest." DaveScot

"And y is not a real cause in that case." - meaning, if we invoke y to explain y, we haven't really added anything to our dicussion. It is like saying "blindness causes blindness". Would we call blindness a "causal force" in that case? I think that is analagous to the situation we have been outlining. Differential reproduction against a bacdrop does the "selecting" which has a result of "selected organisms", which really means differential reproduction. Atom

Atom, I give up. Natural Selection is such an obvious process. It is neither circular nor tautological. It is not completely analogous to artificial selection but so what. In a cold environment, organisms with alleles better suited to the cold will end up reproducing more. Substitute warm, wet, dry, mountainous, etc and you will get examples of natural selection. In most of these situation you can analyze what it is about the allele that lets the organism fit better into the niche such as longer fur. Some differences may not be obvious and actually be due to drift. NS is not circular or tautological. It is common sense. Now maybe some people use it in circular fashion but I do not think population geneticists do. There are obviously zillions of more factors than I have named including other species that will affect what alleles get passed on because some of the population possess them. It is a simple process and there is nothing mysterious about it. In such things as malaria the array of alleles may be complicated and hard to tease out but the basic process is in evidence. jerry

Ok, let's see if we can't analyze any differences we may have.

So you’re saying that the environment sets a tendency for which organisms will be successful in it.

The environment is the backdrop of constraints, but it does NOT set any tendency; the "tendency" is the result of the differential reproduction against this backdrop. (Both taken together). And once we include differential reproduction in the "cause", we defeat ourselves, since we also say that it is the effect. So we say that y + z causes y, which is a tautology, but useless. And y is not a real cause in that case. Atom

Again I ask my original question, what does Natural Selection cause? More specificially, what does it "cause" that isn't a part of the process itself or a simple translational restatement of the initial definitions (ie "It causes organisms that survive/reproduce better to survive/reproduce better")? Atom

Atom: Forgive me, I'm confused as to where we disagree, now that I think about it. You're saying that "natural selection" can be defined as:

Those organisms with traits that allow them to effectively reproduce better will reproduce better.

I agree with this. As for the ramifications of it, I think we might have some differences. But you agreed with my statement:

The environment plays a factor in which ones die.

So you're saying that the environment sets a tendency for which organisms will be successful in it. And I say that this is somewhat (though far from entirely) analogous to dog breeder providing a tendency for which organisms will be successful in his breeding program. Where do we differ? motthew

Thank you motthew. Let me attempt to analyze your ideas.

The tautology argument hinges on the idea that there’s no reasons for which organisms dominate in reproduction.

I agree, there is a reason that some organisms dominate in reproduction. It is because they have those traits which allow them to dominate in reproduction. You gave the example of needing less water in the desert as such a trait. What about needing less water is advantageous? It allows an organism to survive better. What about surviving better is advantageous? It allows an organism to dominate in reproduction. In other words, traits are only advantageous ("fit") in as far as they help an organism dominate in reproduction. Which is the same as saying the following: Those organisms with traits that allow them to effectively reproduce better will reproduce better. The "reproducing better" is the differential reproduction I've been discussing, and it is where all the "action" takes place.

The environment plays a factor in which ones die.

Yes, as the backdrop of constraints. The organisms self-select against this backdrop by differential reproduction (which includes survival, of course). See my comments above. Atom

Dana, I know. Banter doesn't always blog well, I guess. Honestly, living in the land of medicare I have some left-leaning tendencies myself. Charlie

"How much evidence is there really against Intelligent Design? I’m asking this in complete and utter seriousness. And don’t give me that bad design equals no design bit." What elese do they got Dana? How about "ID = religion/theocracy/the end of western civilization"? ;) Atom

The ultimate question here, as I see it, is this: Can the environment act as a predetermined "goal" in natural selection, and so be analogous to an intelligent agent working toward an intended goal?

NS is a description of differential reproduction which only “leads” to itself, differential reproduction. And because of differential reproduction, we have the very real fact that more organisms with “fit” traits will exist than those without them. But that is a tautology.

The tautology argument hinges on the idea that there's no reasons for which organisms dominate in reproduction. If organisms that die before reproduction die on a completely random basis, then the tautology argument would be valid. But they don't. The environment plays a factor in which ones die. For example, organisms that need very little water are going to thrive in a desert whereas organisms that need a lot of water won't. So, the environment is not an intelligent goal per se, but there is a tendency toward an end result. But it is a clumsy tendency, and one I don't have faith in the way many evolutionists do. motthew

I'm only kidding. DanaMcgee

Hi Dana, I'm not even a socialist. Charlie

How much evidence is there really against Intelligent Design? I'm asking this in complete and utter seriousness. And don't give me that bad design equals no design bit. DanaMcgee

Charlie are you some kind of Darwinist or something? DanaMcgee

Apollos I just happened to see a couple of your comments in the Akismet spam bin. I'm not sure why Akismet is flagging them as spam. I approved them right away. You're not being moderated so if a comment of yours doesn't show up right away that's what happpened. Most days lately there's way too much spam (1000 or more) to sort through it looking for mistakes so some could get lost. Are most or all of your comments showing up right away? DaveScot

You all have an excellent discussion going here. I almost hate to gum up the works, but here is a quote on natural selection from the expert. I like to see it repeated as often as possible just for fun.

Natural selection is anything but random. Natural selection is a guided process, guided not by any higher power, but simply by which genes survive and which genes don't survive. That's a non-random process.

Richard Dawkins. http://www.beliefnet.com/story/178/story_17889_1.html Natural selection is guided after all - by natural selection. As for 'random', I have a simple vision of how the word is used. Darwinist's mean unguided, undirected, atelic, unintelligent, unplanned, dependent upon chance, etc. when they say "random". That is, until somebody calculates the improbabilities of such processes resulting in given features or increasing information. At which time "random" becomes "unpredictable given what we know now". But they don't tell the public this (and they don't mean this) when they are using the word to /describe/support the theory. They don't offer it as an admission of ignorance but as a claim to metaphysical knowledge. My two cents. Charlie

Jerry: Is Dembski a creationist? Re: 42 and 43 Thanks for the link given. But they are so many articles. So, I chose the more obvious one talking about Henry Morris. This is from the concluding para: Dembski: "Toward the end of my visit, John noted that ID fell short of a full CREATION MODEL, but then commended ID for conclusively showing the bankruptcy of Darwinism. HE WAS RIGHT. As a limited tool for dislodging materialism, developing the concept of design, and applying it to biological systems, ID is the best thing going. I would therefore like to encourage Henry Morris and all young-earth creationists to view intelligent design as a FRIEND in the destruction of Darwinian materialism and in developing the scientific understanding of design in nature." From these words, Dembski appears to be a creationist, though not in the sense of "biblical" creationist. By "creationist", I mean not believing in evolution. Am I right? I am aware the Michael Denton, Michael Behe, and Mike Gene are (non-Darwinian) evolutionists. So, I still have not got the answer to the question: have Dembski ever proclaimed that he "would remain committed to creationism regardless of what the evidence showed." MatthewTan

BTW, I hope you guys don't think I'm trying to be difficult or play naive. I honestly want to understand what is at the root of NS and if the concept can be framed in a non-circular, or even causal way. If so, great, we all gain in understanding. But until then, I am convinced that the current framing is unimpressive, non-causal and even highly circular. That is why I mention that when people start saying "But NS can do this and that..." I step back and say "Really? Can NS do anything?" I hope we can come to an agreement on whether or not it can. Atom

Jerry, I agree, it may seem like a quibble, but I don't think it is. I'm sorry if it comes across that way. But I think people ascribe to NS what it is incapable of, because they envision it as an agent, when it is not. You wrote...

But in natural selection, conditions in the environment act to affect the passing on of certain alleles

So, environmental constraints exist. Organisms either fulfill them (which means they reproduce in greater numbers, since that is the only net effect we care about) or they do not (under-reproduce). Those that do fulfill them reproduce more, which is another way of saying they pass on more of their alleles. But what is the defnition of those that fulfill them? Those that reproduce more. Differential reproduction in full circularity. Now, you can focus in on the "fulfillment" aspect of the constraints (which I believe you equate with "selection"). How does this fulfillment occur? By differential reproduction. Those organisms that fulfill those constraints are by defition those out-reproduce their competitors. What else would it mean to fulfill constraints? How would that be measured, except by effective output? This is the circularity inherent in thinking of NS as a force. NS is a description of differential reproduction which only "leads" to itself, differential reproduction. And because of differential reproduction, we have the very real fact that more organisms with "fit" traits will exist than those without them. But that is a tautology. True, of course. But useless. And definitely not causal. Atom

motthew, Thank you for your critique of my post. I will try to explain better. You wrote:

Thus, nature prevents those with “undesirable” traits from reproducing, just as a human prevents dogs with undesirable traits from reproducing in a breeding program

Preventing some from reproducing and allowing others to reproduce more are two sides of the same coin, or rather, of the same equation. We are talking about a "difference" between two quantities; I can create the difference by either giving more to one side or by taking some away from the other side. It is the same thing. So again, we have a process of differential reproduction, where some organisms are prevented from reproducing due to accidents or whatever. The environment is the backdrop: some organisms thrive (out-reproduce) and some don't (under-reproduce). The environment doesn't do the selecting, the differential reproduction does the selecting, or rather, it is the selecting. If the environment stays the same and the organisms either produce more or produce less from personal choice, the "selection" has changed yet the backdrop has not. Thus it wasn't the environment that did the "selecting", it was the act of differential reproduction itself. As things out-reproduce they are "selected", remember that. Their differential reproduction is their selection. Atom

gpuccio, I assume that in the case of the finches and moths there was no mutations at all but just a change in frequency of existing alleles due to some environmental change and over time the environment will change the frequency back again or alter it differently. Technically this is natural selection and evolution but it is trivial. It is interesting that this is all they have. jerry

Someone mentioned in a earlier comment that whereas WEASEL totally misses the point of RM+NS (I quite agree, you've all done quite enough to demolish it), a program that took an already meaningful phrase and had it mutate and select for new, different but meaningful phrases could be interesting. Such a program require not only that mutated letters would produce not only real words, but words that go together syntactically and semantically. And without any specific end target. Has anyone ever worked on a program that does this? It would be very interesting. motthew

I think this all serves to highlight something I've long considered: Agent causation behind the universe or broad natural forces is difficult to prove, due to the scope of those forces and the problem of discerning intention. On the other hand, random/purposeless activity is just as hard (or perhaps, even harder - we know for certain that agent causation exists on some levels) to prove, largely for the same reason: If you're not certain what would have been intended to begin with, how can you assert an action is unintentional? It all comes down to philosophy in the end. But here's the problem from this ID-sympathetic person's perspective: 1) Both of these views clearly fall more into the realm of philosophy. Darwinists insist one view is scientific and essentially fact, and the other is not. 2) A person can "do good science" while holding either one of these views, because understanding mechanism can be done apart from discerning intention and ultimate causation. Darwinists insist that even entertaining the thought of intelligent order will result in bad or even no science. I think it's clear that Darwinists are wrong on both 1 and 2, and the debate has never really been about 'protecting science', but protecting a worldview that requires an exclusive claim to science for morale reasons. nullasalus

Atom, Regarding comment #46: The distinction your making between natural and artificial selection is interesting, but lacking. Let me make sure I understand you correctly: You're saying that in the artificial scenario, selection is a separate and earlier action to differential reproduction. Whereas, in the natural scenario, selection and differential reproduction are one and the same. This idea makes sense if we're only considering the production of a single generation. But consider it as an iterative process. Once the offspring are born, a subset of them will die before they reproduce themselves. Thus, nature prevents those with "undesirable" traits from reproducing, just as a human prevents dogs with undesirable traits from reproducing in a breeding program. But that doesn't make artificial and natural selection the same thing. The force of artificial selection is much stronger: a person takes one male and one female that are most likely to give the desired result. Natural selection allows all the population to freely mix, severely diluting the most desirable traits. At the very least, this means that natural selection is a very slow and inefficient process, and possibly so inefficient that is not able to do much beyond certain limits. How to discover those limits, well.. we've been debating that for almost two hundred years. motthew

Atom, If you want to argue that in artificial selection the use of the word selection is more appropriate that is fine. But in natural selection, conditions in the environment act to affect the passing on of certain alleles so Darwin used the term selection to contrast this process with the obvious one everyone understood which was artificial selection. If you do not think that Darwin's use of the term "selection" is appropriate then it is your prerogative to do so. Darwin was rhetorcist supreme and his choice of words had their desired effect. The process happens and you can call it what you wish but everyone knows the term, natural selection. Since the process is real and obvious, your objection is coming off more as a quibble than one of substance. I personally don't care what the name is and if it is an inappropriate use of the term "selection." What ever you want to call it, the process has trivial effects and that is what should be hammered. Quibbling with the actual meaning of the term "selection" itself based on its dictionary denotation distracts from the main issue and I am not sure what it gets anyone. jerry

"But to be fair, we must remember that differential reproduction depends on the “interaction” between the organism and the environment, so the environment has some role in the equation, although passive."

I agree. It does play a role which is passive; it is the backdrop. The "interaction" is what takes place as the replicators out-replicate each other, the environmental constriants providing the backdrop. The end result is the same as the process: differential reproduction. Therefore, I still hold that NS is not causal. Atom

Atom: "It is backwards: differential reproduction is the “cause” of what we label selection, which is just describing the end result of the process, which is differential reproduction. Again, differential reproduction is the “cause” of differential reproduction." I think you are correct in you statements. That's what NS is. But to be fair, we must remember that differential reproduction depends on the "interaction" between the organism and the environment, so the environment has some role in the equation, although passive. gpuccio

jerry, your post is a very clear and balanced evaluation of the problem. I have just one comment: we have two kinds of alleged examples of NS, and they are very different in their meaning. In the first kind, we know the specific mutation we are talking about, like in the much discussed scenarios of sickle cell disease, antibiotic resistance, OP resistance in mosquitos. All the cases in this group seem to share three constant characteristics: a) The mutation is a single, simple mutation, ususally a single bp variation. We are therefore in the legitimate field os spontaneous random mutations, occurring with reasonable frequency. b) The mutation involves, invariably, some loss of information in the protein which has mutated, more or less serious. c) The mutation may involve some indirect advantage in specific environmental situations, ususally related to the modification-damage of the interested protein (never to the appearance of a new function), and so it can be "selected" in that context with the mechanisms you described: in the end, the prevalence of the mutated allele may be higher than expected. In the second kind of examples that you cite, instead, (finches, moth, bears, etc.) we know nothing (at least, to my understanding) of the molecular basis of the supposed mutation. That's a very important difference, in my opinion, because we can have no idea of what is really happening, or of the mechanisms involved. All of these examples seem to reflect some simple, positive adaptation to the environment, and so they could be considered a little bit "higher" than the examples in the first group, which don't even deserve the name of "adaptations". But my problem is: if we don't know the molecular mechanism, how can we be sure that it is RM + NS? As we are no more in the naif times of Darwin, I think that we can define something a "mutation" only if we are aware of the specific underlying genomic variation: otherwise, how can we know that it is not a true "adaptation" (in a Lamarckian sense), and not a darwinian phenomenon? We have seen a great revival of Lamarckian concepts in a new form in the last few years, including all we know (and especially all we still don't know) about epigenetic inheritance. So, to sum up, you are perfectly right: the few well known examples of RM + NS are at best responsible of trivial variation inside the species. But still, there is a difference between those examples in which the molecular basis is known, and our inferences are more detailed and justified (and yet, even in these cases, not all is necessarily as it is supposed to be, as we have discussed elsewhere), and those other examples where everything is highly hypothetical (finches, etc), and whose fortune in the darwinian community seems to be more a sentimental and cultural question (which I can understand: depriving a darwinist of his finches would certainly be pure cruelty!) than a scientific one. And, finally, a note about genetic drift: why is everybody in the darwinian community so excited about that? It seems obvious that it is a purely random phenomenon. Either it happens or not, either it is relevant or not, it is totally irrelevant to the problem of information buildins: at best, it is a random variation of random variation, adding nothing to the power of RM. In other words, we know existing information can vary in a certain number of random ways: be it single nucleotide substitution, single nucleotide deletion or addition, microdeletion, macrodeletion, chromosomal alterations, gene duplication, genetic drift or whatever else, who cares? What is the difference? gpuccio

For the sake of everyone (including myself) let's take a step back and again contrast Artificial and Natural Selection. In Artificial Selection you have a group of organisms and an agent. Before any reproduction occurs, the agent will select which organisms will be allowed to reproduce. (Like a dog breeder does.) This is a definite action. Thus, the selection takes place prior to any reproduction occuring. After the selection takes place, the selected organisms are allowed to reproduce, which is the differential reproduction. It is clear that the artificial selection is an actual cause that exists prior to differential reproduction occuring and causes the differential reproduction. Now let us replace the agent with nature. Take a group of organisms that have not reproduced yet. Nature has a set of constraints that exist there as a back-drop. Nature has done no selection yet, since no reproduction has yet occurred. Now the organisms are allowed to reproduce, some producing more than others. This is the differential reproduction (or differential allele passing), which is described as the result of some organisms reproducing more than others. Those organisms that reproduced more are the ones that are "selected." When and how did the "selection" take place in this second scenario? The act of reproducing more IS the act of selecting. Contrast this to the first scenario, where the act of selection is separate from and temporally prior to the act of differential reproduction. Organisms are "selected" as they out-reproduce their neighbors; in other words, the organisms "select" themselves. But if this act of differential reproduction is where the selection occurs, how can selection be said to be the cause of differential reproduction? It is backwards: differential reproduction is the "cause" of what we label selection, which is just describing the end result of the process, which is differential reproduction. Again, differential reproduction is the "cause" of differential reproduction. Atom

Hey Jerry, Thank you for your time as well and the discussion. Now, I know that differential reproduction takes place; I never denied this. I also know that those organisms that have traits which allow them to reproduce more (differential reproduction) will be the ones that produce more (tautology, since we identify and assess the fitness of those traits by actual reproductive success), and therefore over time there will be more of those types of organisms around (another obvious statement, since the survivors survive). You wrote:

Natural selection is a process that produces differential offspring of certain alleles.

Are you saying that Natural Selection "causes" differential allele frequencies? If so, how is that any different than the process itself, which is just the description of organisms mutating and trying out their different configurations agianst a fitness backdrop of constraints by out-reproducing each other? NS is or at very least includes differential reproduction (differential allele passing) as a prerequisite for the process to occur. How can you then say this differential reproduction is an "effect" of NS? Atom

Atom, Natural selection is a process that produces differential offspring of certain alleles. Why? Sometimes it is not obvious but sometimes it is. When an allele or combination of them make the organism more likely to survive to reproduce then the term survival of the fittest applies. Genetic drift is the major cause for allele frequency changes in the population so this is not natural selection. But there are cases where some allele combinations lead to differential reproduction because it leads to success for the organism. It is not circular because it tries to identify the relevancy of an allele or combination of them for survival and reproduction variations. Whether this happens much is another story. We have had these discussions here recently, namely, the sickle cell debate and it seems there are not too many obvious documented cases. Darwin's finches and the peppered moth (if it happened) are trivial cases of NS which probably did not involve any new allele creation. Polar bears and grizzly bears can mate but white fur is probably a better survival allele on the polar ices and a brown color better for forrest areas. Again a simple example. Given that NS can happen, the real story is not that it can happen but that it is really a trivial process and yet the Darwinists must have it as their magic process. It is the non random part of their theory but as I said before it is "ho-hum." It is embarrassing that they embrace it so fervently. jerry

Matthew Tan, Why don't you read what Dembski actually says. He has several things on his other site. http://www.designinference.com/ Read Dembski's two very content full essays he wrote for the Dover Trial. Nearly everything written about ID and Dembski, Behe etc is false or distortions of their positions. Read what Dembski and Behe say and then what Darwinists write about them. I have never seen an honest Darwinist. According to a Darwinist if you believe in God and believe he had something to do with the world, you are a creationist. jerry

Did Dr. William Dembski say this? This is from a Amazon.com's book reviewer: http://www.amazon.com/gp/product/0393050904/103-9385963-4546267?ie=UTF8&tag=origiresou-20&linkCode=xm2&camp=1789&creativeASIN=0393050904 "The creationist community, on the other hand, is both narrow and narrow-minded. Many of its most prominent advocates, for example, including William Dembski, have publicly proclaimed that they would remain committed to creationism regardless of what the evidence showed." MatthewTan

DaveScot said:

I usually just grab the system timer count in microseconds and use one or more of least significant digits as my random number.

I imagine this would work just fine, as long you weren't grabbing successive numbers in a loop, where I would worry that the timing interval between iterations might stabilize. I haven't tested it in this fashion, I've usually just relied on system provided random number functions. (For integer random numbers, call FRand() and multiply by the desired random number sample: FRand() * 100 for a 1 to 100 or 0 to 99 result) Apollos

Of course agency can affect natural processes so here we have a force outside of normal natural processes that can affect outcomes. If we assume the agency has free will, that is it is not determined, then we can say we have two forces not the three we usually postulate. Namely, law and agency. But if there is no free will, then there may be only law.

Thanks for this, Jerry. It seems reasonable to me that free will is indeed a factor, after all I'm the one writing this now, not purposeless forces. I guess my initial thought wasn't too far off the mark if I'm right about free will: randomness may be an artifact of perceptual limitations, an "optical illusion" of sorts. Predictability may not always be within our ability to reason, but it may not ever be unreasonable. Apollos

As for fitness landscapes, I understand the concept. They are contraints that replicators must fulfill to reproduce more or less offspring, depending on how well they fulfill these constraints. (Assuming no "noise" from chance events.) But notice, it is the organism itself which either exploits these constraints or does not; nature does nothing but is merely the back-drop for these exploits. And of course, by exploiting the constraints, I mean out-reproducing the other replicators. Yet again we return full circle to differential reproduction... Atom

gpuccio, pleased to meet you as well. I agree, NS does describe "something", there is something going on. And I also agree it is not a "force" as some overly enthusiastic supporters claim. great_ape, thank you for taking your time to dissect my ideas. I appreciate your courteous interaction on the topic. I hope not to bore you or waste your time.

Natural selection includes the entire *process* that yields differential reproduction, not just differential reproduction itself. The prerequisites for the algorithm of natural selection are usually something like as follows: a) excess offspring b)the presence of heritable variation c) differential fitness / reproductive success based on that heritable variation.

Your answer is telling. You said that one prerequisite for Natural Selection was "c) differential fitness / reproductive success based on that heritable variation" also known as differential reproduction. (How else can "fitness" be measured? An organism is only as "fit" as the extra fraction of offspring it produces.) But you also said that the end result is differential reproduction: "...the entire *process* that yields differential reproduction" So, if I understand you and Darwinists correctly: Natural Selection is a process that requires differential reproduction as a prerequisite to yield differential reproduction. You see my problem with that? To me it is like saying that the loss of hearing causes deafness. You conflate cause with effect, and show that Natural Selection has no causal power. Maybe you can be clearer, what does Natural Selection cause? Atom

Dave, thanks for the response.

No one knows if there is such a thing as truly random. The answer to that would spell the difference between a deterministic and non-deterministic universe.

This cuts right to the heart of my inquiry. I'll check out the Scripps research link as well. Apollos

Apollos, The concept is indeed of importance and fits this topic as much as a discussion of natural selection does. In another recent post, gpuccio, discusses how what may appear random is the result of a multitude of forces. Since we are unable to understand how they interact the distribution of results are impossible to predict and are best described by a probability distribution. But each result is determined and could be predicted if we only understood all the forces involved. Now I do not understand quantum mechanics but it is based on random processes and for most of his life or even till he died, Einstein really believed that they were not random but determined and that we just did not understand what caused the randomness. Some have said that they really are random and if you could rewind the clock you would get a different answer which would not be true under a determined universe. So if there is really no randomness but just a lack of knowledge on how an individual result came about, then the entire natural world is determined. Under this scenario, life if it came about by natural causes would be the result of law and not chance. So if someone set up the initial conditions and life appeared it was a result of the initial conditions and the laws of the universe. Of course agency can affect natural processes so here we have a force outside of normal natural processes that can affect outcomes. If we assume the agency has free will, that is it is not determined, then we can say we have two forces not the three we usually postulate. Namely, law and agency. But if there is no free will, then there may be only law. I am rambling on but I think this is an essential question that we throw around without really thinking about it very much. Others may want to comment on the idea that randomness is really not random. jerry

Appolos Random loosely means unpredictable. To be more precise truly random means there is not and never will be a means of prediction. No one knows if there is such a thing as truly random. The answer to that would spell the difference between a deterministic and non-deterministic universe. Pseudo-random is often used in computer science to describe algorithmic methods of producing random numbers where predictability exists only if you know or can deduce the algorithm. Evolution pundits tend to abuse the term by implying that random mutation is truly random (with respect to whether or not any given mutation is advantageous) - a totally blind process. This is not proven but rather taken as a matter of faith in The Church of Saint Charles Darwin. It may very well not be blind at all and lots of recent research indicates it isn't. The case we usually note here is the Scripps research which found that bacteria control the rate of mutation and step on the gas pedal when there are toxins in the environment. Here's an analogous situation. An accomplished dart player doesn't always hit the bullseye but few people would characterize his attempts as random or blind. More and more what was thought to be blind chance is not at all blind but merely imperfect as the dart player is imperfect but not blind. The bacterial mechanism reported by Scripps is not blind. It knows there's a target and when there's a reason to hit it. It just doesn't know exactly where the bullseye is located. Designers call what the bacteria is doing the "shotgun" method. A shotgun blast contains many projectiles that cover a wide area compared to a rifle shot. It's less efficient but your aim doesn't have to be as good. By the way, in generating random numbers in personal computer applications where reproducibility isnt' a requirement and consecutive samples are separated by many milliseconds or more I usually just grab the system timer count in microseconds and use one or more of least significant digits as my random number. There are a lot of asynchronous events of varying duration happening in a typical PC so the precise number of elapsed microseconds from one sample to the next is sufficiently unpredictable. If I need a lot of samples quickly I'll usually grab the timer count and use that as the seed for an algorithmic pseudo-random number generator. That's more or less de rigueur in game programming. For higher quality random numbers, again where reproducibility isn't a requirement, a convenient source is a sound card. Crank up the amplification on an open MIC input and use one or more of the least significant digits from consecutive samples of the A/D convertor. In that situation you're reading semiconductor noise in the amplifier. DaveScot

Dana, Atom: perhaps I would not describe myself as "a socialist of sorts", but I am certainly not right-wing. And I definitely am an ID advocate. So, good to meet ya both. gpuccio

great_ape: if your discussion is strictly about the "causal" word, I think we can find a compromise specifying better the terminology. I think what Atom means (and in a sense it is a good point) is that it is wrong to conceive NS as an actin (and theresore "causal") force. On that I agree. NS is not a force, in any sense that a force is defined in natural sciences. But you are right that, is something called NS happens, it must have a cause. Assuming for an instant that NS happens according to darwinian paradigm, then the "cause" of what Atom correctly calls "the result" can be best described as an interaction between the reproductive ability of the organism (depending on the total biological information it owns) and the resources available in the environment (and obviously the obstacles and limitations inherent in the same environment). So, the environment (call it nature, landscape, or any other name) is only part of the equation. The other part is the active biological information in the organism. And there is no force in action, only a process which can, but not easily or simply, be described as the result of complex necessity laws shaping an interaction. But the real proble, beyond the "causality" problem, is that of information. Excuse me if I am repetitive, but that's the real question. You say: "By drawing a very straightforward analogy, humans play the same role in artificial selection that the environment plays in natural selection." Well, let's analyze better the differences. It is not only a problem of different agents (landscape against intelligent agent). We can view it as a problem of information. By definition, the "landscape" has no specific information neither about the organism's already existing information nor about the new information necessary to have a "new" organism (in other words, the necessary variation to express a new function. The only role of "landscape" is a blind one: allowing or denying resources of which it knows nothing, creating or subtracting obstacles of which it knows nothing. In that sense, the landscape is a totally random factor. It certainly obeys the laws of physics and necessity, but there is no explicit link between those laws and the organism. The landscape is, after all, a "blind watchmaker", even for Dawkins. For me, it is blind, period. The real "teleological" element, the only non random element in the NS equation, is not in the environment, but in the organism: the organism is certainly not random, and the information it already owns is its non random heritage. In the case of intelligent causality, instead, the scenario is completely different. The material cause of the variation can or not be the same (random variation, see the weasel example and my previous post about antibody maturation). But intelligent agents can use, and indeed use, other "causes" of variation: a programmer does not write his code through random variation of the letters and selection of the right ones (although he could). A programmer usually directly "types" the correct letters. And even if the intelligent agent decides to use random variation as the means of modification, he will always have to exercise intelligent causation, through any available method, to select the result. Because, you see, that's the only way that he can impart the new information he already knows to the existing pattern. Tha fact is, darwinian model cannot do that. In darwinian model you have three components: RM, landscape, and existin organism. Of these, two are completely random, in respect to the "new" complex, functional information which should emerge. They are RM and landscape. Please note that landscape is certainly random in respect to the new information because it has no knowledge of what that new information must be, even if it can be a limiting or enhancing factor in the interaction with the "new" organism which will have the "new" information" (with its inherent function). Let's pretend, to be clear, that the new information is an oredring algorythm. Let's pretend that the landscape can, in an interaction with an organism, positively enhance the new ordering function. Still, the landscape is blind, so it has no idea of how an ordering algorythm should be written to get that function. In other words, it has no information about the information which has to be created, even if it can have a role in the interaction once the new information is created. So, we have random mutation, random environment. But yes, we have a non random factor: it is the information alredy existing organism. But, that's exactly the information we want to "increse". In our example. the existing organism does not include on oredering algorythm. That's exactly what it should acquire, to become a new organism. And, making exception for small variations, usually not functional, or only indirectly functional, like those examples we have often discussed, and in absence of any functional coninuity of ordering algorythms (and, believe me, of any more than basic function in the world), there is only one way the old organism can "learn" the new algorythm, be it an ordering algorythm or a new enzyme, or anything else: it has to come from outside. The point is, it is not necessary that an intelligent agent be the direct cause of that information imparting. He can also be the indirect cause, in the sense that the information can be written somnewhere (always by an intelligent agent) and, at some point in time, transferred to the organism. But the point is, there is no way in the world of having CSI unless an intelligent agent has created it. So, you see, we can call a selection "intelligent selection" if the information (in the sense of CSI, that is prespecified, or compressible, or functional information, that is a rare, very rare island in the ocean of possibilities) is already known to the system and can therefore be "cloned" on a new "hardware". That's the only true "selection" I know. The agent, or the information he has already created, "selects" something which is already known, already available. So, in that context, the only real cause of the new information is the existing information, although many intermediate causes of different nature (random, not random) can be used. We are, perfectly, in the "weasel" paradigm (thank you, Dawkins). We are in the paradigm of ID. gpuccio

Would anyone care to comment on the concept of randomness? It comes up often (over 20 uses in this thread), and I sometimes get tripped up by whether the concept is concretely real, or a useful perceptual limitation. For instance, if I take a digital stopwatch that displays thousandths of a second -- each time I push "stop" I'll get an apparently random number at the third decimal place. This might prove useful, but isn't truly random, as the reading is determined by exactly when I press the stop button. Using random numbers in a computer program is as easy as asking for one; but building a random number generator (a Pseudo Random Number Generator) requires pre-established lists of "random" numbers, such as from decimal places in Pi. These might be indexed based on the sum of the last three decimal places from a high-resolution timer (similar to the stopwatch method above). It is illusory randomness, and can have the benefit of being predictably repeatable. Testing "background" noise is another method, but randomness would seem to be illusory there as well. Although not necessarily predictable in any meaningful sense, urban noise for instance, would be determined by cars, voices, fans, doors opening and closing, airplanes, etc, each the product of some sort of deliberate action. A coin flip is apparently random, but if it lands in the hand at least, is determined by the force applied to spin it, the distance it travels, etc. I guess I'm wondering about the philosophy of the nature of randomness, whether it objectively exists. The concept is useful in a variety of applications, but is there room to interpret it as a convenience of perceptual shortcomings? If this is too off-topic, please disregard. Apollos

I've never seen the "weasel" program run, but I think I understand what it attempts to show. If I'm correct, it demonstrates exactly the opposite of what it claims, making it a perfect example of framing and no more valuable to knowledge of the subject than the video demonstrating evolution (and may instead subtract from the sum total of human knowledge, ironically paralleling that RM does little more than damage existing information). My understanding of the "weasel" program: A string of apparently random characters magically transforms into a recognizable, ordered statement. I'll use my own text for the example. A string: "uwocaeqnrbw pkmvxz" ...steadily becomes... "intelligent design" ...apparently by random selection. The fact is, that the target pattern must already exist in the code of the program (or some other data source) exactly as it needs to appear, letter for letter. A pseudo code example might look like this: templateStr[] = "Intelligent Design"; randomStr[] = "uwocaeqnrbw pkmvxz"; foreach( character chr ) in randomStr[] {   while( randomStr[chr] <> templateStr[chr] )   {     randomStr[chr] = GenerateRandChar(a...z);     display( randomStr[] );   } } For each index in the random string, a random character is generated until it matches the corresponding character in the template string. Each time a random character is generated, the random string is displayed, completing the illusion of random activity "generating" specified information. It is misdirection, prevarication. The program takes a deliberate path around the truth. Where it could simply { display( templateStr[] ); }, it instead jumps through hoops to "simulate" a blind search for a meaningful pattern. Perhaps there is more going on in the weasel program, but it most likely amounts to the same. The target pattern must be a template, and every successive "generation" would have to compare itself against that template. If a program could change a meaningfu statement one letter at a time -- with each generation conveying specific meaning -- and transform it into a new statement with different but equally specific meaning, I wuld be more impressed, but that would not skirt the design issue. Apollos

"Artificial selection is teleological and intelligent directed. So they are very different." --jerry I'm not claiming they are the same; I agree that the presence/absence of intelligence is a crucial distinction. However, here I am simply claiming that the two manners of selection are not different in the sense that one is causal an the other is not causal. Atom, I think the weak point of your argument is illuminated by the quote from Darwin you have provided. To put it in your terminology, nature/environment (including other organisms) are acting as "force A". There is a reason that Darwin describes it in the fashion that he does; there is a sort of agency at work in his opinion; it's just not an intelligent one. Natural selection includes the entire *process* that yields differential reproduction, not just differential reproduction itself. The prerequisites for the algorithm of natural selection are usually something like as follows: a) excess offspring b)the presence of heritable variation c) differential fitness / reproductive success based on that heritable variation. Included in the notion of "differential fitness" and, similarly, "differential reproduction" is the concept of a fitness landscape. It's a sort of equation, with various parameters, that determines how successful a given individual will be based on its genotype/phenotype. My main point here is that this fitness equation is *determined* by the environment of the organism in very much the same way as a human, during artificial selection, determines the "fitness" of individual traits by deciding which animals to breed. It's strange that you're willing to extend "artificial selection" beyond the confines of the results to see the "force" at work, but you are unwilling to consider natural selection beyond the "result" of differential reproduction. Now, I agree with Jerry, that there is a large difference between intelligence being involved and nonintelligent processes, but I don't think this has anything to do with "causality" as such. Perhaps you are instead getting at the fact that one scenario has "intelligent agency" and the other does not? I think the fact that you naturally envision nature as an agent of action is why you're unwilling to assign nature/environment the very same role. great_ape

When dealing with the writings of such complex people, it is often times difficult to sum up what the heck they are actually talking about. The good thing about Tom Wright is that he tends to be a straight shooter. DanaMcgee

Hey Atom, good to meet ya. Yeah it's not as big a contradiction as it first seems. I know Bishop Tom Wright (Anglican) is orthodox theologically and is a social conservative. Yet he is on the Left (although he claims "never to have been a party man") politically. I think from what I can muster from his writings that he advocates some kind of decentralized distributivism ala G.K. Chesterton. DanaMcgee

"I am an ID advocate and a socialist of sorts."

Hey Dana, me too. :) Atom

By the way, what I meant by Communism was the Marxian brand. I am an ID advocate and a socialist of sorts. DanaMcgee

I guess an even easier way to cut to what I am getting at is by asking the question: If Natural Selection refers simply to Differential Reproduction, what is Differential Reproduction the cause of? Be careful how you answer. If you say "greater complexity", that can be shown false; some replicators replicate more in a simplifed state. If you say "Differential Allele Frequencies" then that is just another phrase for "Differential Reproduction", on the level of genes. If you say "Greater Fitness", what is the general definition of "Fitness"? Atom

"two" not "to" Also, if you say the variations themselves are what cause the effect in scenario B, then the causal aspect of NS refers to these variations (mutations) as the force. Since variation is random in Darwinism, then NS is a random cause. This is the point I am making. We also see that NS is no magic wand; organisms must do all the hard work themselves. Atom

Great Ape, Let me try to elaborate a bit. Natural Selection is another name for Differential Reproduction. Some organisms have a higher net reproduction turnout than others; thus, these are said to be "selected" by "nature". What we really mean, when we examine it, is that some replicators replicate more than others and the offspring of these will exist in greater numbers. (A tautology.) Now, this point has been brought up by others, but that is not the force of what I am trying to say. Let's say we have to "forces": force A and force B. Force A examines all organisms, decides that those with a certain trait should be the ones who reproduce, then allow those to reproduce in greater numbers. The result is differential reproduction and the cause is Force A: Force A causes differential reproduction. Then we have force B. Let's say in the absence of force A, all organisms reproduce at whatever rate they choose, with all the uncertainty of reproduction. Some of these are stronger, or faster, or usually just luckier, so they reproduce more than others. The net effect is the same, and we label the EFFECT Force B. Notice, Force B describes the end result, differential reproduction, not the cause of that result. That is the thrust of what I am saying. People tend to see NS as a "force" capable of doing something further, when no, it is a description of the end result. Sompare this to the words of Darwin (notice how he makes NS an almost intelligence like force):

"It may be said that natural selection is daily and hourly scrutinising throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life."

I am not aware of anyone else making that precise point. So any folly inherent in my argument is strictly my own I guess. :) Atom

The source of most of the world's evil is not religion, like the organized atheists decry. Rather, it is Darwinism, an acid which destroys all goodness, beauty and meaning it touches. I think in Fred Hoyle's book the Intelligent Universe, Hoyle predicted that if the paradigm of thought didn't change from nihilistic Darwinism to something along the lines of Intelligent Design then society and the human race were destined for destruction. How can you can you convince true blue atheists/naturalists that they may in fact be mistaken? After all isn't Darwinism, like Communism simply a substitute religion? DanaMcgee

great_ape, As you said the other day about natural selection, the environment including other organisms shape reproductive success and they are non- teleological forces. Artificial selection is teleological and intelligent directed. So they are very different. Yes in some ways they are the same but in essence very different. Interesting thing is that NS affects humans in a lot of ways but human reproduction is still mostly unaffected by NS. jerry

DaveScot, wonderful post! I think you have very well defined the possible range of what is usually called "microevolution": creating variation which is, in essence, random and unrelated to complex function. That's reasonable, and observable. Instead, the mere idea that the repeated sum of a great number of this kind of variations can generate complex new information and function is simply ridiculous. GilDodgen, regarding the Weasel program, I perfectly agree with you that it is a wonderful example of how a random search can generate CSI if you already have the specified information you are trying to generate. The secret of that program is that the program already knows the final information, and so it can use a random search which "builds", step by step, the final result, by comparing each random bit obtained with the right sequence, and fixing it. That's easy, although it still requires some search, due to the random method of inducing variation. It's what we can call: "design through random variation and intelligent selection according to a specific plan". I really can't understand how any sentient being can use that example to promote the concept of darwinian evolution! In darwinian evolution, by definition the final information to be obtained is not known to the system, neither as a whole nor in any of its parts, and the supposed "fixing" has to happen according to function, not to recognition of information. That simply cannot happen, for two important reasons, each of which would be enough to rule out the theory from the realm of reasonable thinking: a) The space of functions is not continuos. You cannot pass from one function to another, different one, through a continuous number of modified functions, even if that continuity is reduced to single bit variations. After all, functions are not real numbers, not even natural numbers. A function is usually separated from another one by an ocean of non functional combinations. Functions are islands in the sea of possibilities. That's, in my opinion, a simple way of understanding Dembski's ideas about specification, and why CSI, and especially functionally specified complex information, can never arise from the noise of random variation. b) Many of the functions we observe in living beings are IC. Behe has shown that very simply, many years ago, and nobody has been able to answer that. All the attempts to show a reasonable way to IC biological machines has been, at best, pitiful. IC is a milestone in the ID thought, and that concept alone should be enough for anybody to reject darwinism. But the weasel program shows us very well how everything changes if we alredy know the information we want to implement. In other words, if we have a design to guide us. Then, random variation becomes a powerful tool to induce new configurations which define progressively narrower search spaces, fixing the bits already obtained, until the search space becomes narrow enough to allow the final result. I think we have a very good example of a "weasel" mechanism in the process of antibody maturation. The development of the immune system, both T and B, is really a marvel from the point of view of design. Here, speaking for simplicity only of the B part (antibody response), the B precusror undergoes somatic DNA mutations (random?), whose final result is to create a repertoire of receptors (membrane immunoglobulins in virgin B cells), which we can imagine as a well distantiated number of different antibody configurations, something like a great number of small islands in the sea of possible configurations, so that most "epitopes" occuring in nature (that is, the reacting sites of antigens) can be in some way recognized. This process of controlled mutation to attain a diversified, punctuated repertoire of combinations covering the search space of epitopes (a large, but not extremely large search space, given that an epitope is usually 3-20 aminoacids)is in itself really astounding, but not so astounding as what happens after. First of all, the repertoire must be intelligently "depleted" of all self-antigens, but we'll not enter into details of that. But, when an epitope of a foreign antigen is recognized (through a very complex and controlled procedure, involving the processing of the antigen by very intelligent antigen presenting cells, and then the stimulation and regulation by a T helper lymphocyte), the specific B lymphocyte begins to proliferate, giving birth to a clone of effector cells (plasma cells, secreting antibodies) and memory cells. But here comes the really amazing part. The initial antibodies are usually weak, their specificity for the antigen is only approximate. And then, a process of "maturation" starts. Well, this process, for what we know of it (which is not much), is very similar to the weasel program. A very intensive process of hypermutation starts, but it implies only the small segment of DNA which codes for the antibody receptor site, or the very near regions of DNA. Out of many mutant cells, only those with higher specificity for the original antigen are selected. Well, that's the interesting part: the results of a random (but very, very focused) hypermutation, whose mechanisms still defy us, are selected by matching them with a pre-existing information: the original antigenic epitope. And, even if the details of how that happens are not known, you can bet that it will certainly be a very intelligent and controlled procedure, involving the antigen presenting cell and various regulatory T cells, not to speak of lots of specific cytokines and other factors. In other words, the organism prepares itself by building a very intelligent random repertoire for all necessities, then recognizes and processes and stores a specific information from the environment (the antigen), then reacts to it with the means available in the repertoire (immature antibodies), and finally refines its response through a very controlled process of random (but not "natural") hypermutation followed by very intelligent selection, utilizing the original information (the antigen) to select the maximum function. This final process is very similar to the weasel program. It demonstrates how a very intelligent, designed process, utilizing a preformed information, can implement it in a new clone (the only difference is that, in the case of antibody maturation, the information contained in the antigen, in other words its form and chemical properties, is duplicated in a mirrored form, as an antibody, like in building a keyhole on a key). And, obviously, exactly like the weasel example, antibody maturation has immediately been presented as a proof of darwinian evolution... Well, Shakespeare's works will never be cloned by typing monkeys, that's for sure, but his beautiful words in Hamlet's monologue or in the even more beautiful Sonnet LXVI, about the subversion of values in human experience, about beholding "right perfection wrongfully disgrac'd" and "simple truth miscall'd simplicity", will always comfort and reassure us in this jungle of meaninglessness. gpuccio

DaveScot, wonderful post! I think you have very well defined the possible range of what is usually called "microevolution": creating variation which is, in essence, random and unrelated to complex function. That's reasonable, and observable. Instead, the mere idea that the repeated sum of a great number of this kind of variations can generate complex new information and function is simply ridiculous. GilDodgen, regarding the Weasel program, I perfectly agree with you that it is a wonderful example of how a random search can generate CSI if you already have the specified information you are trying to generate. The secret of that program is that the program already knows the final information, and so it can use a random search which "builds", step by step, the final result, by comparing each random bit obtained with the right sequence, and fixing it. That's easy, although it still requires some search, due to the random method of inducing variation. It's what we can call: "design through random variation and intelligent selection according to a specific plan". I really can't understand how any sentient being can use that example to promote the concept of darwinian evolution! In darwinian evolution, by definition the final information to be obtained is not known to the system, neither as a whole nor in any of its parts, and the supposed "fixing" has to happen according to function, not to recognition of information. That simply cannot happen, for two important reasons, each of which would be enough to rule out the theory from the realm of reasonable thinking: a) The space of functions is not continuos. You cannot pass from one function to another, different one, through a continuous number of modified functions, even if that continuity is reduced to single bit variations. After all, functions are not real numbers, not even natural numbers. A function is usually separated from another one by an ocean of non functional combinations. Functions are islands in the sea of possibilities. That's, in my opinion, a simple way of understanding Dembski's ideas about specification, and why CSI, and especially functionally specified complex information, can never arise from the noise of random variation. b) Many of the functions we observe in living beings are IC. Behe has shown that very simply, many years ago, and nobody has been able to answer that. All the attempts to show a reasonable way to IC biological machines has been, at best, pitiful. IC is a milestone in the ID thought, and that concept alone should be enough for anybody to reject darwinism. But the weasel program shows us very well how everything changes if we alredy know the information we want to implement. In other words, if we have a design to guide us. Then, random variation becomes a powerful tool to induce new configurations which define progressively narrower search spaces, fixing the bits already obtained, until the search space becomes narrow enough to allow the final result. I think we have a very good example of a "weasel" mechanism in the process of antibody maturation. The development of the immune system, both T and B, is really a marvel from the point of view of design. Here, speaking for simplicity only of the B part (antibody response), the B precusror undergoes somatic DNA mutations (random?), whose final result is to create a repertoire of receptors (membrane immunoglobulins in virgin B cells), which we can imagine as a well distantiated number of different antibody configurations, something like a great number of small islands in the sea of possible configurations, so that most "epitopes" occuring in nature (that is, the reacting sites of antigens) can be in some way recognized. This process of controlled mutation to attain a diversified, punctuated repertoire of combinations covering the search space of epitopes (a large, but not extremely large search space, given that an epitope is usually 3-20 aminoacids)is in itself really astounding, but not so astounding as what happens after. First of all, the repertoire must be intelligently "depleted" of all self-antigens, but we'll not enter into details of that. But, when an epitope of a foreign antigen is recognized (through a very complex and controlled procedure, involving the processing of the antigen by very intelligent antigen presenting cells, and then the stimulation and regulation by a T helper lymphocyte), the specific B lymphocyte begins to proliferate, giving birth to a clone of effector cells (plasma cells, secreting antibodies) and memory cells. But here comes the really amazing part. The initial antibodies are usually weak, their specificity for the antigen is only approximate. And then, a process of "maturation" starts. Well, this process, for what we know of it (which is not much), is very similar to the weasel program. A very intensive process of hypermutation starts, but it implies only the small segment of DNA which codes for the antibody receptor site, or the very near regions of DNA. Out of many mutant cells, only those with higher specificity for the original antigen are selected. Well, that's the interesting part: the results of a random (but very, very focused) hypermutation, whose mechanisms still defy us, are selected by matching them with a pre-existing information: the original antigenic epitope. And, even if the details of how that happens are not known, you can bet that it will certainly be a very intelligent and controlled procedure, involving the antigen presenting cell and various regulatory T cells, not to speak of lots of specific cytokines and other factors. In other words, the organism prepares itself by building a very intelligent random repertoire for all necessities, then recognizes and processes and stores a specific information from the environment (the antigen), then reacts to it with the means available in the repertoire (immature antibodies), and finally refines its response through a very controlled process of random (but not "natural") hypermutation followed by very intelligent selection, utilizing the original information (the antigen) to select the maximum function. This final process is very similar to the weasel program. It demonstrates how a very intelligent, designed process, utilizing a preformed information, can implement it in a new clone (the only difference is that, in the case of antibody maturation, the information contained in the antigen, in other words its form and chemical properties, is duplicated in a mirrored form, as an antibody, like in building a keyhole on a key). And, obviously, exactly like the weasel example, antibody maturation has immediately been presented as a proof of darwinian evolution... Well, Shakespeare's works will never be cloned by typing monkeys, that's for sure, but his immortal words in Hamlet's monologue or in the even more beautiful Sonnet LXVI, about the subversion of values in human experience, about beholding "right perfection wrongfully disgrac'd" and "simple truth miscall'd simplicity", will always comfort and reassure us in this jungle of meaninglessness. gpuccio

"Natural “Selection” on the other hand is a-causal; it doesn’t cause differential reproduction, because it IS differential reproduction." --Atom I have to say again that this line of reasoning is highly suspect. By drawing a very straightforward analogy, humans play the same role in artificial selection that the environment plays in natural selection. The only sense that artificial selection is different consists in the entity or entities that are doing the filtering (i.e. that are defining which individuals differentially reproduce.) Yet how it is, under any common understanding of causality, you find artificial selection to be *more* causal than natural selection completely escapes me. Is this an argument you developed yourself or did you read it somewhere? If so, I'd like to find out what the original source is. great_ape

"Dave, This is such a good essay (#16), why don’t you repost it as a new topic so it won’t be lost in the comments here?" Please do, DaveScot. I've copied it and saved it to a word doc.... but it would be cool if you'd post it as its own topic - easier retrieval. Tedsenough

Dave, This is such a good essay (#16), why don’t you repost it as a new topic so it won’t be lost in the comments here? On the WEASEL program: A main point to note is that a letter is preserved in a given position even though it still produces complete gibberish, because it is known in advance that this letter will need to be in this position in the future to reach the goal. (For example HREJDF would be replaced with HREJDL because the L is in the right place to produce WEASEL later on, even though both strings are complete gibberish.) This is precisely NOT what Darwinian evolution is all about. How Carl Sagan could not have noted this is completely beyond me. GilDodgen

DaveScot writes: "The question then becomes one of how many such agencies exist in the universe, what forms they can take, did any of those possible forms predate humanity, and did they have the physical means, motive, and opportunity to accomplish the things we see here without violation of any known laws of physics." This seems to be a crucial question, so I just wonder, is there any other research directed at this other than the SETI project? Dizzy

I understand that the ID position is that the protein itself had to have been designed, not the variations that can occur through mutation. Proteins don't automatically warrant a design inference. It depends on the function of the protein and interdependencies on other proteins. A signalling protein could easily get a random mutation that slightly modifies a biologically active site making it more or less able to bind with a target and that can change a whole downstream cascade of events with large scale ramifications. I think I read recently that such a site has been implicated in whether a dog turns out to be a large or small breed, for example, as the cascade result is how much growth hormone is produced. It's not the sole determinant though as you can cross a large breed sire with a small breed bitch and the puppies never turn out so large the mother can't bear them. On the other hand some proteins that are components in intricate molecular machines and because their shape must critically match the shapes of other components for the machine to function variations that change the shape would cause the machine to not work without simultaneous variations that change the shape in other proteins. These simultaneous changes seem to go far beyond any reasonable odds of happening together. Click on the "Categories" sidebar Molecular Animations to see some examples of this type of molecular machinery. People have found this one particularly compelling for its simplicity, ease of understanding, and difficulty in imagining how it could have evolved ex nihilo. The problem it solves is DNA supercoiling which must have been a problem from the very first DNA molecule, all forms of life have one or both these machines in them, so it presents a classic chicken/egg problem with only one protein involved. What came first, the DNA molecule that has to have a topoisomerase family enzyme in order to be unwound for replication and reading or the DNA molecule that carries the information required to construct a topoisomerase enzyme? And this is a very very simple machine made of a single protein unlike many others you'll see in that animation series in which the machines are formed of multiple proteins. A ribosome in particular is composed of many different proteins and ribonucleic acids working together. The whole machine must be assembled and working in order produce the parts that make the up machine that makes the parts! This particular machine is also present in every form of life and is so basic (it's the machine that reads the coded information in a gene and builds a protein according to the coded assembly sequence) no life as we know it is possible at all without it. How'd that happen without a designer envisioning the entire machine in abstract then building all the hundreds of interlocking pieces that make it up simultaneously? It's like proposing that you can build an automobile by starting off with randomly shaped chunks of metal and just randomly changing the shapes until they all fit together into a working automobile. To compound the problem you need a fully working automobile to gather the parts together to make an automobile. This is the story the chance & necessity pundits ask you to accept and take as a matter of materialistic faith that, impossible as it sounds, eventually science will reveal how it was done without intelligent agency. And speaking of dogs, that brings up what appear to be fundamental limits on variation that mutation and selection can produce. Dogs are possibly the most widely varying species on the planet while still remaining a single species. In 20,000 years of artificial selection and preservation of variants that never would have survived in the wild there hasn't been a single variant with an anatomical feature not characteristic of canines nor has a new species of dog emerged. Not even something as simple as a retractable claw. The variations are entirely limited to the deleterious (dogs are predisposed to a large litany of genetic disorders) and the cosmetic. You can get big dogs and small dogs (change in scale) you can get wide variation in ratio of body part size (change in aspect), you can get broadly different coloration, patterning, coat length and thickness, and that's about it. What artificial selection and preservation can't accomplish seems to be even farther beyond the scope of natural selection and preservation which is restricted in that any variation must be either nearly neutral or decidedly beneficial in order to have the selection value required to fix the variation within the population. Island species are another good example of these limits. Isolation on an island for millions of years and the quite different environmental pressures (or lack thereof) drives selection at an accelerated rate for island species. The result is often dwarfism or gigantism but never any variation on the level required for evolution writ large like the appearance of a novel cell type, tissue type, organ, or body plan. In short, the observed limits of highly accelerated natural selection over millions of years are same kind of limits in variation you see in dogs through thousands of years of artificial selection but nothing beyond that. It appears there is something other than random mutation and natural selection that produces the fundamental differences between the higher taxonomic categories. Intelligent agency solves all these problems. We already know for a fact that intelligent agency with the capability or near capability of building or modifying complex organic machines in defiance of impossible odds of random assembly is extant in the present universe. That agency is us. The question then becomes one of how many such agencies exist in the universe, what forms they can take, did any of those possible forms predate humanity, and did they have the physical means, motive, and opportunity to accomplish the things we see here without violation of any known laws of physics. For example any agency in a remote galaxy would be prohibited from influencing anything in this galaxy because of the limitation imposed by the speed of light barrier. Given that normal matter and energy compose only a small fraction (5%) of what makes up the universe it seems premature to rule out exotic forms of intelligent agency that could very well be composed of non-baryonic matter that we only suspect exists through indirect observation of its gravitational effects on normal matter. In fact what we consider normal matter and energy may be the minority component and thus really an atypical form in the big picture - the froth on the top of an unplumbed ocean. Hubris is rampant in the halls of science today. Of course that's nothing new. The history of science is littered with disgarded theories that were once thought to be writ in granite. Thinking we have a fundamental understanding of nature where that understanding is lacking only in the fine details is something that has plagued inquiry since the getgo. DaveScot

Fross asked about our canine friends: Good question: Certainly this is directed, and thus we get the small ones who can fit in holes like Dachsunds to chase small animals, the very obedient working dogs, fight with each other for sport, and those who just sit around the house gaining weight. Some would argue we've done a great disservice. There is genetic damage evident, as in hip displaysia in German Shepards and just the general dumbness of some breeds compared to the wolf. Interestingly, they can all interbreed. Discover Magazine featured an article on Man's Best pal a few years ago portraying them as "they've been evolving for 12,000 years--so what's up with man's best friend." Sorry--"they" have not been "evolving" so much as being bred for whatever purposes we thought for them. Be that bad or good. But sorry again, IMHO Pandas Thumb does not get the brownie point on directed evolution any more than cute articles in Discover. As to Dawkins mechanism for weeding out superfluous letters, he is a weasel if he thinks this has not been answered in so many places before. And it has. His lock and gear mechanism analogy can be used to argue anything. You have but to know the code. Both Canines and Gears require Design parameters to make them bark or say what we want. Wakefield Tolbert

I read the PT response a day or two ago, and just couldn't see why Dembski was wrong. I try to be objective, but the Darwinists have become increasingly dishonest in their representations of Darwinian processes. I say dishonest because I think it's intentional. Also, if I see another Darwinist write that "so and so" doesn't "understand" evolution I'm going to scream. RM+NS = everything - yeah that's a tough one. After I figure out the math behind general relativity I'll try to tackle the intricacies of Darwin's super-theory, which supposedly is too complex to be grasped by physicists, doctors, mathematicians, engineers, and even some biologists. But the guys at PT can spell it all out for us. shaner74

Fross, Artificial Selection is definitely not Darwinian. It is causal; it actually causes something, namely differential reproduction. Breeders see the variation they like or the ones that are "on the road towards" what they want and cause those to reproduce more. Natural "Selection" on the other hand is a-causal; it doesn't cause differential reproduction, because it IS differential reproduction. What does differential reproduction cause? Differential allele frequencies...but then again, isn't that what differential reproduction refers to anyway, since we talk about populations on the level of genes? So differential reproduction "causes" differential reproduction. What Truth and insight. Anyway, Artificial Selection is VERY ID, since it is: a) causal and b) has as its cause intelligence. I don't see how it can not be considered ID. Atom

Check out this design inference (implicit): http://www.enterprisemission.com//NukingJupiter.html jaredl

What Fross is talking about seems to be what Dr. Yoshikawa (a theist) is talking about. DanaMcgee

It is interesting that in the book Cosmos, Bios, Theos. The book is a collection of interviews with famous scientists about their views on the origin of the universe, life, Homo sapiens and their view on God. If they have one Professor Shoichi Yoshikawa a Senior Research Scientist and Professor, Department of Astrophysical Sciences, Princeton University puts forth a similar view. He writes. What is your view of the origin of life? I understand Darwinian Theory, and I believe the theory explains some of the cases of evolution where the external conditions remain static. For example, the development of organisms on an isolated island can be understood within the framework of the theory of evolution. However, it is very difficult for me to believe that all the evolution or, more precisely, the existence of all the varieties of DNA chains and egg cells can be accounted for by the mechanical processes only. What is your view on the origin of Homo sapiens? In particular, the origin of Homo sapiens may not be understood completely. The seemingly random events of nature, such as glacier periods, the apparent size of the moon versus the sun, volcanic eruptions, the existence of microorganisms (viruses, bacteria, and so forth) have influenced the development of the human beings. Were they just coincidences? Also the concept of beauty (music, poetry, paintings and so on) appears to be shared by many. The mechanical explanations could be advanced but... How should science approach these questions? Specifically the origin of the universe and the origin of life? The origin of the universe can be understood on a scientific level. It does not conflict with religion. The origin of life could be explained by the theory of evolution. However, it is equally possible that, during the birth of a new organism, the selection of a new set of genes is somehow influenced by a metaphysical force. I think God created the universe and life. Homo sapiens was created by God using the process that does not violate the physical laws of the universe significantly or none at all. I believe that the hidden variables of Quantum Mechanics are under God's control. I am a fan of Roy Abraham Varghese. Here are two of his most famous books. http://www.amazon.com/Cosmos-Bios-Theos-Scientists-Universe/dp/0812691865 http://www.thewonderoftheworld.com/Sections1-article9-page1.html DanaMcgee

I realize that natural selection can only work on what's extant. In the paper cited above, mutations caused protein variation, at which some were selected for their properties by people. This happens in nature too via natural selection, no? I understand that the ID position is that the protein itself had to have been designed, not the variations that can occur through mutation. What I didn't realize was that the ID position also considers breeding programs, eugenics, (possibly sexual selection) etc or anything else that uses conscious selection to fall under the ID banner. I think this is one of those rare things that both sides agree on, (mutations can cause variations that can be selected for) and I don't think that it's correct to say that it falls soley under Intelligent Design. Intelligent selection maybe. :) Fross

Carl Sagan and Ann Druyan said,

"it comes down to the SAME THING.[emp mine.] Dawkins’s arbitrarily chosen twenty-eight letter sequence, toward which his selection was aiming, was METHINKS IT IS LIKE A WEASEL…by forty-one generations, we’re there."

I'm amazed when I read some person or other who says they were influenced by Carl Sagan's alleged brilliance. And yet he is impressed by Dawkins's WEASEL program. Even my 14 year old son picked up on the lunacy of the WEASEL program as being any kind of help to the blindwatchmaker idealogues. And Sagan couldn't see it? Maybe he didn't want to. Who knows. At any rate, yes, the weasel program shows how accumlated small changes compared against a preset [read: intelligently designed] goal can lead toward that goal. Wow, that's earth shattering. As if dog breeders and pidgeon breeders didn't know that already. But how is this like blindwatchmaker evolution? Does Dawkin's little program demonstrate the alledged power of RM+NS in building up CSI without an intelligently designed preset goal? If not, what's the point of WEASEL? Oh, right, to show us how how accumlated small changes compared against a preset [read: intelligently designed] goal can lead toward that goal. OK, then. Thanks Richard for demonstrating something obvious, that has no bearing on blindwatchmaker production of CSI. mike1962

OT: good memory there's this great little jazz bar in Helsinki. Freezin cold winter drive from St. Petersburg and we find this little oasis of Americana jazz, playin old tunes, Sunny Side of the Street, classics from Sachmo and some big band tunes. Words & Music by Dorothy Fields & Jimmy McHugh, 1929 Recorded by Jo Stafford, 1945 (#17)

G7 C C/B Bm7-5 E7 Grab your coat and get your hat, F Bm7-5 Bb9 Leave your worries on the door - step; Am Am+7 D9 D7 Just direct your feet F G7 C To the sunny side of the street. G7 C C/B Bm7-5 E7 Can't you hear the pitter-pat? F Bm7-5 Bb9 And that happy tune is your step! Am Am+7 D9 D7 Life can be complete Dm7 G7 C On the sunny side of the street. Bridge: CM7 C7 Gm7 C7 Gm7 F I used to walk in the shade with those blues on parade; D9 Am7 D7 G7 G9 But I'm not afraid -- this rover crossed over! G7 C C/B Bm7-5 E7 If I never had a cent, F Bm7-5 Bb9 I'd be rich as Rock - e - fel - ler, Am Am+7 D9 D7 Gold dust at my feet Dm7 G7 C On the sunny side of the street.

Michaels7

This unjustified conflation is made again and again by Darwinists (as you know). Carl Sagan and Ann Druyan, Shadows of Forgotten Ancestors, p. 127:

An illuminating computer experiment analogous to the evolution of a short DNA sequence was performed by biologist Richard Dwakins. He starts with a random sequence of twenty-eight English-language letters (spaces are counted as letters): WDLTMNLT DTJBKWIRZREZLMQCO P. His computer then repeatedly copies this wholly nonsensical message. However, at each iteration there is a certain probability of mutation, of a random change in one of the letters. Selection is also simulated, because the computer is programmed to retain any mutations that move the sequence of letters even slightly toward a pre-selected goal, a particular, quite different sequence of twenty-eight letters. (Of course natural selection does not have some final ACGT [DNA base] sequence in mind, but -- in preferentially replicating sequences that improve, even by a little, the fitness of the organism -- it comes down to the same thing.) Dawkins's arbitrarily chosen twenty-eight letter sequence, toward which his selection was aiming, was METHINKS IT IS LIKE A WEASEL. ...by forty-one generations, we're there.

(Boldface added.) And in nature, those with "improved fitness" are better able to survive, and those who survive are more fit. Get it? ;-) __________ Fross: "Would something like dog breeding be considered ID? (and therefore something like eugenics?)" Millenia of dog-breeding somehow didn't cause people to institutionalize the application of the same principles to humans. This all changed very soon after Darwin claimed that man was an animal with no inherent, fundamental differences from other animals. j

"Can natural selection not be seen as a director? I realize it’s not conscious, but it is a mechanism that directs." It appears NS can "direct" accumulative deleterious mutations "over time" for extinction... "Mutation Rate Catastrophy" http://creationsafaris.com/crev200704.htm#20070409a hattip: creationsafaris.com A nice summary review from CS:

"Think of it: neo-Darwinists have pinned their hopes on the rare, mythical “beneficial mutations” to generate novelty, and for natural selection to save every blessed tidbit in its sieve, leading to the wondrous variety of adapted life (wave the magic wand of millions of years here). But now, their own mechanisms have turned on them. Beneficial mutations (if there are such things) actually trigger a mutational arms race. This subverts natural selection, begins a mutational meltdown, and sends the population off the cliff to extinction."

Original paper: Complete genetic linkage can subvert natural selection http://www.pnas.org/cgi/content/abstract/0607280104v1 This is getting hilarious. This is in direct opposition to conservation of genes across hundreds of millions of years. I've never seen a more hodge-podged goooop of guessing games and contradictions in my life in one field of study. Maybe I'm naive, but only in politics can one waggle so much tongue in different directions and get away with it. Materialist evolution is in deep trouble. Michaels7

fross Can natural selection not be seen as a director? I realize it’s not conscious, but it is a mechanism that directs. Can an unconscious director write a script? The problem is that natural selection works with what is already extant. The question is whether NS is capable of abstraction. How does it work to create the abstract genetic code - a code which requires the products of code translation to replicate the code itself? The ability to work with abstraction is a hallmark of intelligence. Where there's a code there's a coder. Natural selection is no coder. It might modify existing codes within the confines of no abstraction with random change as the only input of variation but how does it create the code in the first place? DaveScot

It is frustrating isn't it. They really need to adopt the term a-telic evolution, although I guess that would give the game away wouldn't it. I guess nobody really expects honesty from many in the darwinist camp at this point. Jason Rennie

Would something like dog breeding be considered ID? (and therefore something like eugenics?) Can natural selection not be seen as a director? I realize it's not conscious, but it is a mechanism that directs. The above study seems to indicate (I put the lay in lay person) that they're causing these proteins to mutate and then they're selecting the ones with the properties they set out to get. So the design isn't going into the pre-selection materials, but design is being applied in the selection event. I thought ID had problems with the random aspect of the pre-selection materials mutating to something with useful properties that could be selected. (either by people or natural selection) Fross

Directed evolution requires a director. Any director that I can envision uses intelligence in the process of directing. Directed evolution is unquestionably an ID position. bFast

...pro-ID scientists...

Had you not mentioned it, I would have missed the fact Matti Leisola is listed in www.dissentfromdarwin.org I then looked at Steve Reuland's response and realized on top of Leisola being listed in dissentfromdarwin, Leisola participated in a creationist conference. The fact Leisola succeeded in this endeavor is news in itself. Matti Leisola is a Professor at Laboratory of Bioprocess Engineering Helsinki University of Technology. Congratulations on another pro-ID paper passing peer review!!!! scordova