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Metaphors, Design Recognition, and the Design Matrix

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Here are excerpts from The Design Matrix by Mike Gene:

Metaphors such as “fear”, “cost”, “abhor” and “angry”, commonly share the projection of consciousness onto the world. Metaphors such as these represent the human tendency to view the world through anthropomorphic glasses. However, the metaphors employed by molecular biologists are not of this type.
….
Metaphors typically break down when we begin to take them literally.

[but] The design terminology that is used in the language of molecular biology does not break down when interpreted literally
….

there is a basic and literal truth to the use of design terminology in molecular biology–these technological concepts are just too useful. Metaphors are certainly useful when explaining concepts to other human beings, yet the design terminology often goes beyond pedagogy–it provides true insight into the molecular and cellular processes. An understanding of our own designed artifacts, along with the principles required to make them, can guide the practice of molecular biology.

Why is it that some metaphors are no where near as effective for describing biology as well other metaphors, especially design metaphors?

Mike Gene recognizes qualitatively the enigma that others recognize quantitatively. There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems. Recognition of these coincidences is the recognition of specified complexity, and recognition of specified complexity is the recognition of design. Outside of biotic reality, there are no other assemblages of matter in the universe which fit design metaphors more exactly than those found in biology.

I liked Mike’s book, but I especially liked Chapter 3. Chapter 3 suggests the fact that biology is well described by design metaphors is a clue that biological systems (like birds, plants, and bunnies) are intelligently designed. UD readers are invited to read about the other clues which Mike outlines in his book, and the consilience of these clues constitutes The Design Matrix.

Notes:

From wiki:

Metaphor (from the from Latin metaphora; see the Greek origin below) is language that directly compares seemingly unrelated subjects. It is a figure of speech that compares two or more things without using the words “like” or “as.” More generally, a metaphor describes a first subject as being or equal to a second object in some way. This device is known for usage in literature, especially in poetry, where with few words, emotions and associations from one context are associated with objects and entities in a different context. A simpler definition is the comparison of two unrelated things without using the words “like” or “as”, the use of these words would create a simile. For example,she is a button.(as cute as a button)

Comments
Here is a direct quote from post #60 at Uncommon Descent: (https://uncommondescent.com/intelligent-design/metaphors-design-recognition-and-the-design-matrix/#comments):
"I came here to Uncommon Descent specifically to offer an antidote to the atheist inspired Darwinian mysticism being presented by Allen MacNeill. So what does MacNeill do? He promptly disappears. I will let others interpret his departure as they choose. I ssy he didn’t have the stomach for a confrontation. I will continue my pursuit of Allen MacNeill at his weblog - “The Evolution List” as I recently linked."
This is such a gross mis-characterization of what happened at UD that I can only assume that you are either demented or just plain despicable. I have at all times treated you with the utmost in courtesy, and this is how you respond. You are hereby banned from THE EVOLUTION LIST permanently, and all of your comments there have been removed.Allen_MacNeill
March 25, 2009
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Thank you jerry but I do not "debate." I confront and expose.JohnADavison
March 25, 2009
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Scordova Thanks for the plug of my 2005 paper - "A Prescribed Evolutionary Hypothesis" It is unfortunate that you did not include Schindewolf's text commenting on the similarities shared by the placental and marsupial Saber toothed cats. That commentary ends as follows - "The similarities of form are present in such details as the structure of the large flange on the lower jaw, DESIGNED TO GUIDE AND PROTECT THE UPPER CANINES." (Caps in italics in the original). I mention this to remind IDists that Schindewolf wrote those words in 1950 when many of you were not yet born. I was a mere 22 myself! Let's give credit to those who were the original IDists, Otto Schindewolf, Robert Broom, Leo Berg, Reginald C. Punnett and William Bateson. "There is nothing new under the sun."JohnADavison
March 25, 2009
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"It doesn’t get any better than this." Yes, it would if you were able to debate Dawkins or Myers.jerry
March 25, 2009
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I came here to Uncommon Descent specifically to offer an antidote to the atheist inspired Darwinian mysticism being presented by Allen MacNeill. So what does MacNeill do? He promptly disappears. I will let others interpret his departure as they choose. I ssy he didn't have the stomach for a confrontation. I will continue my pursuit of Allen MacNeill at his weblog - "The Evolution List" as I recently linked. I thank Uncommon Descent for giving me the opportunity to evoke this expected reaction. Why don't you now invite P.Z. Myers or Richard Dawkins to present their versions of the great mystery of phylogeny? I am itching to take them on as well. Only by inviting them can you have the pleasure of seeing them decline. It doesn't get any better than this.JohnADavison
March 25, 2009
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Can you elaborate on Darwin’s notion of ‘good’? I thought one of the points of his book is that fitness is defined by the evolutionary niche the creature finds itself in hence ‘good’ or ‘bad’ depends on the environment.
Darwin's notion of fit is more in line with the notion of inherent good (somewhat independent of context). Darwin regarded "Good" in the sense of what a designer would consider "good". He seemed to suggest nature would somehow nurture the exploration of "good" patterns. The modern notion of "fit" is nebulous and situationally defined, contrary to Darwin's notion. "Fit" is also poorly defined. See Lewontin in the Santa Fe Bulletin Winter 2003
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.
So the popular notion of what is fit (Darwin's notion) is not consistent with the notion of "fit" as defined by modern theory. In modern theory, when selection acts to destroy vision (such as blind cave fish), then that is in contrast to Darwin's notion that nature somehow nurtures into existence, and therefore would tend to preserve rather than destroy an eye. Darwin's metaphorical notions were literally wrong according to modern evolutionary theory. Lewontin notes it is hard to reconcile Darwin's notion of "fit" (inherently good characteristics) with the notion of "fit" in practice:
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.
Andreas Wagner notes that fitness is illegitimate in charcaterizing biological function. Wagner unwtingly supports Behe:
However, fitness is hard to define rigorously and even more difficult to measure....An examination of fitness and its robustness alone would thus not yield much insight into the opening questions. Instead, it is necessary to analyze, on all levels of organization, the systems that constitute an organism, and that sustain its life. I define such systems loosely as assemblies of parts that carry out well-defined biological functions.
"assemblies of parts that carry out well-defined functions"? As in Irreducible complexity. :-) Function, rather than fitness, is a better characterization of biology. But "function" is a design metphor. I pointed out in the link that some functional systems elude any measures of fitness since they are not visible to selection: Airplane magnetos, contingency designs.scordova
March 25, 2009
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I hope Allen's comments get posted immediately. I personally have learned a lot from Allen in the last couple years through what he has said and what he has recommended.jerry
March 25, 2009
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scordova @56
I am delighted you are here, but since I am a guest at UD, I must defer to those kind enough to grant me the privilege of being an author here.
Alternatively, you could interact with Allen in a forum where neither of you are subject to "moderation" by third parties. I, for one, would like to follow your discussion. Is there an open venue agreeable to both of you? JayMJayM
March 25, 2009
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Allen, UD is not my weblog, I am a guest here, I am under obligation to be supportive of those who have been kind enough to host my offerings. I am delighted you are here, but since I am a guest at UD, I must defer to those kind enough to grant me the privilege of being an author here. I'm appreciative of your comments. I hope you will not interpret the events of today as any sort of systematic attempt to suppress your valuable input to a dicsussion I started. Salscordova
March 25, 2009
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How sad; I would have thought that becoming a graduate student in a legitimate science might have given Sal a somewhat different perspective on the value of differing viewpoints in the advancement of science. Clearly, that is not the case.
Dear Allen, I have no jurisdiciton over who gets moderated into a "pending approval" queue. This queue is operated via computer, and I cannot add or remove the names that get automatically put in that queue. However, once you are in the queue, and you are commenting on a thread I author, I can release your comment from the queue. It was my fault for not seeing your comments in the "pending approval" queue earlier (I do not check it every hour). I check the queue only when I remember to. Sorry for the delay. Some of my comments on another thread are still not released, so I have to endure this as much as you. I have nothing against you, and I hope our history of interaction will assure you that I personally have no intent to suppress what you have to say. I'm sorry for the misunderstanding and I hope you can extend a little forebearance. regards, Salscordova
March 25, 2009
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iconofid, There’s no “improbable coincidence” at all. Both human designs and biological systems must function in the same environment, with the same physical restraints, and often solve the same or similar problems. We see similarities for the same reason that we see convergent evolution.
Thank you for your comment. Needing a solution to a problem is different from finding a solution to a problem. The need of a solution is no guarantee a solution will be found. The presumption in your argument is that if a creature needs to solve a problem, somehow it will (without any inelligent guidance) through mechanisms of selection. We know experimentally and observationally and theoretically this is not true. I have provided links that explain some of the reasons why above. "Natural Selection" exists, but it works more along the lines of Blyth's conception (preservation of species) versus Darwin's conception (origin of species).
We see similarities for the same reason that we see convergent evolution.
Convergent architectures make just as much sense under a design paradigm as they do under a mindeless paradigm. Convergent evolution cannot be used as an argument against intelligent design. For mindless processes to create convergence, one would have to show mutation and/or selection can converge on the same complex solutions. We know experimentally this is unlikely. We knockout enough genes in an organism, and the organism seems unable to coverge back on the solution that once made the organism functional. Thus converegent evolution via mindless mechanisms is still highly improbable. Convergent evolution via intelligent design is possible, imho. Long-time professor of biology, John A. Davison, used convergence arguments in his peer-reviewed paper to argue that convergence is an evidence of Intelligent Design: Prescribed Evolutionary Hypothesis
The so-called phenomenon of convergent evolution may not be that at all, but simply the expression of the same preformed “blueprints” by unrelated organisms. Example include marsupial “moles”, “wolves”, “anteaters”, “rabbits” (bandicoots), “squirrels”, including flying forms (phalangers), “woodchucks” (wombat), ”bears”, (koala), “mice” (Coenolestes) and most remarkable of all, saber-toothed cats. In Figure 1 Schindewolf presented pictures of the skulls of the marsupial Thylacosmilus atrox ( left) opposite that of the placental Eusmilus sicarius (right), the former from the Pleistocene of Patagonia, the latter from the Oligocene of South Dakota. The two forms are separated by thousands of miles spatially and millions of years temporally. Schindewolf’s legend beneath the figure is of special significance as it bears, not only on the questions raised here, but also, on the whole issue of Intelligent Design with which those questions are clearly related.
scordova
March 25, 2009
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Having now appealed to Sal Cordova's sense of fair play several times at Uncommon Descent and despite this having my comments deleted without explanation on multiple occasions, I must conclude that either Sal is being over-ruled by his UD overlords or he agrees with them that reasoned argument is not the point and that unanimity of propaganda is. How sad; I would have thought that becoming a graduate student in a legitimate science might have given Sal a somewhat different perspective on the value of differing viewpoints in the advancement of science. Clearly, that is not the case. Given that I have only limited time to prepare and research the posts and comments I make online, I will no longer be posting comments at Uncommon Descent.Allen_MacNeill
March 25, 2009
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scordova says: "There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems." There's no "improbable coincidence" at all. Both human designs and biological systems must function in the same environment, with the same physical restraints, and often solve the same or similar problems. We see similarities for the same reason that we see convergent evolution. Indeed, there are examples of convergence in the evolution of human technology, when the same or similar solutions are invented separately (bows and arrows, the automobile). We can even see it in the "designs" of very different species. Termites do complex buildings, air conditioning and agriculture.iconofid
March 25, 2009
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Joseph, I think in the short term there are random events that may determine who survives or not but in the long term, animals and plants seem to be adapted to their environment. You see different animals and plants at the equator then you do in the mountains or on the plains or at the poles. This wasn't random.jerry
March 25, 2009
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Can someone let me know why all my comments are being moderated? Have I broken a rule?GSV
March 25, 2009
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scordova “Natural Selection” can select defective organism over healthy ones (such as blind cave fish, wingless beetles, etc. etc.). This is not consitent with Darwin’s notion of “good”. In fact, “good” and “bad” are deeply metaphorical. Can you elaborate on Darwin's notion of 'good'? I thought one of the points of his book is that fitness is defined by the evolutionary niche the creature finds itself in hence 'good' or 'bad' depends on the environment.GSV
March 25, 2009
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https://www.blogger.com/comment.g?blogID=22102663&postID=8651024580496088104&page=1 I offer the above sequence from Allen MacNeill's "The Evolution List" as an answer to some of the questions that have been posed here.JohnADavison
March 25, 2009
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Dr. Kellogg wrote: My point is this: that a metaphor is tempting is a reason to avoid embracing it scientifically. It’s a reason to be suspicious.
But then on those grounds, one might then argue that the metaphor "natural selection" should be exorcised from science. "Natural Selection" as Darwin conceived of it is not what really happens in nature.
Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good. C.DARWIN sixth edition Origin of Species — Ch#4 Natural Selection
This doesn't happen in nature, in fact Darwin refuted this claim even in the subsequent pages of Origins when he effectively pointed out the success of random selection over natural selection. Natural selection has been unwittingly refuted by some of it's proponents such as Fisher and Haldane. The notion of "Haldane's Dilemma" has been used by ID proponents and neutral evolutionists to great effect. "Natural Selection" can select defective organism over healthy ones (such as blind cave fish, wingless beetles, etc. etc.). This is not consitent with Darwin's notion of "good". In fact, "good" and "bad" are deeply metaphorical.scordova
March 25, 2009
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Some organisms die and some live. Sometimes they die just because they were in the wrong place at the worng time. Sometimes they live not because they have better genes but that have better behavioral patterns. IOW acquired traits can and do outweigh genetically inherited traits. There is no way to predict what will be selected for at any point in time. So when people say "natural selection has been observed" all they really mean is we have seen some die and some live and we "think" we know why.Joseph
March 25, 2009
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Greetings, Sal: Once again it is extremely demoralizing to put time and energy into formulating reasoned responses to other peoples comments, only to find that one's own responses have vanished into "moderation limbo". Until yesterday I could at least see the comments I had attempted to post, headed by the phrase "Your comment is awaiting moderation". That at least allowed me to copy and paste them someplace else, so that my work would not be entirely wasted. Now, even that is no longer happening. My comments simply vanish as soon as I click on "Submit Comment", with no explanation as to why. Sal, I have always treated you as a colleague and a gentleman. At the very least, please explain what it was about my comments that caused them to be removed, so that I can avoid making such mistakes in the future. That's only fair, IMHO.Allen_MacNeill
March 25, 2009
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John, "Natural selection is anti-evolutionary and always was. It has always been a losing battle ending in extinction." I agree generally, but yet we have, you name it, several million species, mostly bugs etc. Where did all the variation come from for these guys? You say the first bird came out of a reptile egg but where did his cousins come from and where did the variation to fuel all the aves species come from? I find it hard to fathom that all of a sudden that reptiles are giving birth to birds or that a small colony of primitive birds generated the variation for all the bird species. Allen would say the variation came from his engines of variation but somehow I doubt all of it came that way because it seems the trend is to less variation within species over time, not more because of natural selection.jerry
March 25, 2009
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Natural selection is anti-evolutionary and always was. It has always been a losing battle ending in extinction. "Here I stand. I can do no otherwise." Martin LutherJohnADavison
March 25, 2009
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Salvador, I think the mistake that you and Mike are making is to conflate design terminology and metaphors with functional terminology and metaphors. To see this, look at this passage from chapter 3 of Mike's book:
Your body maintains an average internal temperature of 98.6 degrees Fahrenheit. When you are in a cold environment, without layers of clothing, your body quickly begins to lose heat and your core body temperature begins to decrease. Thermal sensors are activated to signal your brain that your body temperature is decreasing. In response, your brain attempts to compensate by signalling your muscles to begin short bursts of contractions which cause you to shiver. As you shiver, the muscle contractions work to generate heat, which in turn warms the blood that travels through them, increasing the body's core temperature. In essence, it's as if your body is activating a program to solve a problem posed by the environment... Biologists do not teach homeostasis to students by drawing from the fundamentals of chemistry and physics. Instead biology textbooks often introduce the concept of homeostasis by using a furnace and thermostat as an analogy for how such constant internal states can be maintained.
Mike would presumably agree with the standard ID argument that the complexity alone of the homeostatic system implies design, but here he is arguing for something more: that each system -- the biological system and its artificial counterpart -- contains a thermal sensor and a controllable heat source, and that the fact that the biological system can be so readily described in these "design terms", in Mike's view, should heighten our suspicion that it is, in fact, designed. In reality, though, these terms are not design terms -- they are functional terms. By this I mean that any system that performs the function in question -- maintaining a constant warm temperature in a variably cold environment, despite a lack of insulation -- must contain a part that plays the role of a temperature sensor and another part that plays the role of a controllable heat source. This is true whether the system is designed or not. You simply cannot have thermal homeostasis under these conditions without components that play these roles. If any successful system of thermal homeostasis must contain such components, then the fact that it can be described in terms of such components is inevitable. It therefore loses any significance, and you are left falling back on the standard ID argument: the system is complicated, so it must be designed.skeech
March 25, 2009
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I wasn't clear in my last comment. You said:
There is an improbable coincidence between the architecture of human-made systems and the architecture of biological systems.
The statement didn't make sense to me, because neither IDists nor evolutionists think that this is an improbable coincidence. (My comment about selection was not limited to natural selection. IDists, too, say that biological architectures were selected -- by a designer.) However, your subsequent comments indicate that what you meant was that you see an improbable coincidence absent a designer. Evolutionists, of course, don't see this as improbable; human designers select efficient structures and processes, and so does natural selection. One would therefore expect to see similar structures and processes between the two domains.Freelurker
March 24, 2009
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As for the problems involved with delayed appearance of comments due to long moderation queues, it's a little like corresponding via pen & paper mail. You just write what you want to write, not attempting to keep up with the flow or fit into the sequence, and trust your correspondence to figure out where your comment goes. I've been doing that with my friend and colleague, Hannah Maxson, for almost three years, and the time lag in our letters to each other runs about three weeks to a month and a half.Allen_MacNeill
March 24, 2009
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Greetings, Jon: Good to see you here. Sorry about the misunderstanding about my abilities to post comments here. My comments are apparently always held in moderation for periods lasting from an hour to more than a day, and so I assumed that they would never appear (indeed, some of them did disappear while awaiting moderation, only to reappear later). So, can we agree that natural selection is not a creative force in evolution? I think we can, and having gotten over that particular speed bump, can we go on to discuss the mechanisms by which you think phenotypic variation is generated, and why you think such mechanisms are no longer operative? I'm particularly interested in your semi-meiotic hypothesis for the origin of species; how exactly does it work? Yes, I've read your papers, but I'm not a cell biologist. Could you explain it in such a way that a reasonably well-educated undergraduate might understand it? I'd appreciate it, and think it might lead to some interesting discussions. BTW, I expect you are aware that, rather than completely rejecting Goldschmidt, Shindewolf, and the other macromutationists, Stephen Jay Gould believed that they were on the right track, so much so that his version of the theory of punctuated equilibrium depended on arguments that were quite similar to theirs. Indeed, he caught a lot of flack from the "modern synthesis" crowd for doing so, but time has vindicated some of his views, and may vindicate others as well.Allen_MacNeill
March 24, 2009
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Allen suggested: To kick off this discussion, let me pose a question: since the “engines of variation” are what produce new, and therefore presumably adaptive phenotypic variations, it seems reasonable to expect that, if there is anything to ID, one should be able to show empirically that the appearance of new variations is not random.
I think the way that a variation is suggested to not be of random origins is when it conforms to design metaphors, and does so in a way that defies probability. In fact this idea is consistent with the idea of specified complexity. We can't project very specific design metaphors (like decoder, computer, sensor) to rocks, rivers or any other kind of natural phenomenon, except biological organisms. When matter starts to conform to recognizable patterns associated with human design, it begins to suggests the variation had premeditation. Variation in and of itself cannot be what prods objects to look exquisitely designed. Neither do I think the sieve of "natural selection" will help the process along. A rock dropping on a car will cause variation in the car, but these aren't the sort of variations (accidents) that we would consider as the source of the car's designs. As far as I can tell, the sort of mutational change that we have direct knowledge of has very limited ability to create certain levels of designs. There is no question variation and mutation are engines of change, but it is the kinds of changes that are important. Improbable conformance to a design metaphor seems like a good standard for deciding if the source of variation is random (in the sense of mindless origins). As an example, protein interactions can be analogous to the lock-and-key or login-password metaphor. The strength of the metaphor is the strength of the improbability of the interaction. I thought that the exploration of binding site evolution could be a fruitful area of research. I was pleased that Durrett and Schmidt (very fine scientists at Allen's school) explored the issue Behe raised up regarding proteins. I felt their critique was one of the most well-reasoned, although I don't count Behe's hypothesis out. The numbers Durret and Schmidt came up with still appear pretty daunting for mindless origins of design. Finally, I don't insist that the conformance of biology to design metaphors constitutes an absolute proof of intelligent origins, but I would argue it makes the case compelling. If the designs in biology were not so compelling, if they were as common place as the air we breathe, we probably wouldn't be debating the topic.scordova
March 24, 2009
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The previous should say "Other variations of that gene are now gone." which has a completely different meaning.jerry
March 24, 2009
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"If it isn’t a mechanism- and I agree that it isn’t- how can it remove anything?" Two things. I think it is a process. Allen called it the summation of about 3 processes some time ago so I think it is a process but arguing over that is pointless. It happens. It removes variation because the processes favor some elements of the gene pool over others. And these processes will send some of the genetic elements into fixation. If an allele becomes fixed then variation has been removed from the gene pool. Other variations of that gene are not gone. Genetic drift also removes variation. A new environment will probably reduce variation as certain alleles will not be appropriate for it. Allen can probably say it better.jerry
March 24, 2009
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In #34 joseph asked:
"If [natural selection] isn’t a mechanism- and I agree that it isn’t- how can it remove anything?"
Natural selection can't "remove" anything, because natural selection doesn't "do" anything. As I pointed out above, it's an outcome, not a mechanism. The "engines of variation" are what "do" things in evolution, and it is those mechanisms (see the list here: http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html ) that produce the new variations that drive the changes we see in the fossil record, the genomic record, and the world around us. We are only just beginning to appreciate how extensive and how powerful these sources of phenotypic variation are, and how they work. I fully expect that, as we learn more about them, we will change our models of how evolution happens. That's where all the open questions in evolutionary biology are, and what makes it such a fascinating discipline to me.Allen_MacNeill
March 24, 2009
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