I object to evolution being made synonymous with natural selection. NS is an automatic process which not even ID-ers would regard as needing guidance. The ID argument is based on the complexity of the mechanisms that have given rise to life, adaptation and innovation, without which evolution cannot take place. 
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> dhw: That is why the attempt to synonymize evolution and natural selection ... i.e. to exclude the huge questions raised by these mechanisms ... is not acceptable to anyone who takes evolution and the design issue seriously.
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> MATT: Dawkins doesn't take it seriously? No, again the real issue is normative epistemology. You disagree to what valid evidence is. That's it in a nutshell. Science is not about finding 'truth' it is about models that work ... and however incomplete it may be, name an explanation that works better? There's none on the table...
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> Not for the first time you have quoted me, and then ignored what I've said. I stated that my reason for this whole discussion "is the issue of chance v. design". Nowhere have I questioned the model, and nowhere have I suggested there is a better explanation. I believe that evolution (micro and - still unexplained - macro) happened, I believe the theory of common ancestry, I do not question that natural selection happens, and I do not question the existence of the mechanisms for life, replication, adaptation and innovation. The sole issue here is whether the mechanisms could or could not have assembled themselves by chance. The design argument is that the greater the complexity, the greater the degree of improbability that chance could do it. "That's it in a nutshell." You may disagree with that argument, you may feel that since we can't know the answers, it's not worth asking the questions, but that is no reason for defining evolution in a manner that deliberately excludes the questions.-dhw,-I will point out that this discussion has been about Dawkins saying that the whole of life is explained by natural selection, which you take issue with. My job here has been to "be" Dawkins. -The mechanisms which brought about life are also responsible for how life changes. This is a separate discussion. Dawkin's statement is to look at what we've observed. The reason for what we see now is because of millions of years of selection at work. -Thus, the "whole of life."-Maybe I need more context for his claim, but I don't see anything wrong with it.

I object to evolution being made synonymous with natural selection. NS is an automatic process which not even ID-ers would regard as needing guidance. -> I stated that my reason for this whole discussion "is the issue of chance v. design". Nowhere have I questioned the model, and nowhere have I suggested there is a better explanation. I believe that evolution (micro and - still unexplained - macro) happened, I believe the theory of common ancestry, I do not question that natural selection happens.-Here is a form of natural selection which is an extreme natural challenge and causes the third largest extinction 450 million years ago. Hot to cold to hot again: -http://news.sciencemag.org/sciencenow/2011/01/how-to-read-a-prehistoric-thermo.html?ref=hp

MATT: It's in the language of biologists; an event that begins the process is called "selective pressure." While the organism is under pressure, it must find a way to adapt, behaviourally or molecularly. -'Selective pressure' is just another way of saying 'natural selection'. As we now know environmental or other pressures cause epigenetic modifications which become inherited.
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> At core, is selective pressure. I understand evolution to be destructive as well as constructive; selective pressure is the cause that moves an organism to continue to survive or become extinct.- Just another way of saying natural selection.
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> We need to consider what Dawkins is saying here. For natural selection to explain the "whole of life," we need to define what it is that it is selecting for. Ultimately we know that it is genes that are being selected for. I will have to dig up the name of the experiment done in the 1980's, but the experimenters deliberately knocked out a bacteria's natural ability to digest lactose. They then cultured these bacteria and reintroduced them into a lactose-rich media. What ended up happening was that the bacteria appropriated machinery that performed some other function, and used that (inefficiently) to again be able to ingest lactose. In this case the selective pressure was lactose, and the selection was for the new gene. -A very well-know study, new genetics, same species. Microevolultion, and it doesn't prove macroevolution. 
 
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> Modifying "what are we selecting for" the answer becomes clear: Selective pressure operates against only the genetic material that came before that date. The mechanism for change relies solely upon the collective history of the organism. Natural Selection explains both why organisms live and die out, and why we have the diversity we have today. Natural Selection works against existing genes to accomplish all of this. -Or works for the gene structure.- > So I think your #2 above is answered as it can be. In the Dawkins view, your question gets pushed all the way back to abiogenesis, because life is defined as a recursive function that consistently relies upon its prior states. Explanations such as the exact mechanisms that created eyes or sex are seen as only filling in the details of what is explained by what I discussed above. -Agreed

MATT: I am in agreement that natural selection is generally a passive process. However I think we both might be arguing over semantics. If we agree that natural selection is the filter--then we really only care about what the output of the filter is.
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> This is a new dimension to our discussions: who says the output is the only thing we really care about? You have missed the point of both the theist and the atheist agendas! So let me spell it out for you. The dispute is over whether the complexities of life's physical mechanisms are too great to have arisen by chance. Natural selection is irrelevant to the design argument ... it's a perfectly logical process whereby what survives is that which is most suited to survival (hence your 14 stages of horse). It would be unreasonable to deny this. By making out that evolution and NS are synonymous, the atheist can therefore argue that any questioning of evolution is unreasonable. What Dawkins calls "organized complexity" is not created by NS, but by mechanisms for replication, adaptation and innovation, without which evolution could not take place and Nature would have no variations to select from. These mechanisms have so far proved to be too complex for us to understand, let alone reproduce, and so theists claim that they have been designed. If you reject the possibility of design, you have no choice but to put your faith in the ability of chance to create the mechanisms ... but the idea of "faith in chance" is anathema to your atheist: hence the strategy of trying to make NS (which has no bearing on the design argument) synonymous with evolution. Ah Matt, what happened to my fellow sceptic's scepticism?-lol... I always think "scepter" when I see the British spelling "sceptic."-Remember; I'm trying to offer arguments I remember coupled with what we're reasoning about Dawkins' views--which again--I haven't read. -I don't see this is rewording evolution; natural selection is the process that culls organisms that were unable to respond to some change. -"Natural selection is the process by which traits become more or less common in a population due to consistent effects upon the survival or reproduction of their bearers." (Wikipedia)-Traits becoming more or less common. In other words, evolution is natural selection. Without natural selection, we have no theory of evolution.-It's in the language of biologists; an event that begins the process is called "selective pressure." While the organism is under pressure, it must find a way to adapt, behaviourally or molecularly. From beginning to end, "Natural Selection" is the process by which the organism moves from its original state to some state in the future. Rereading some sections of some of my books, I'm less inclined now to agree that natural selection is passive. -You are arguing I think, that the actual changes that an organism undergoes is a separate issue from that of natural selection, however, an organism must be under pressure of selection before it can perform the process of changing. -Therefore, since no change happens without selective pressure, natural selection explains the whole of why organisms change. -My attachment here is: Only at a very high and unrefined level. We're still not at the stage of knowledge yet.

MATT: I am in agreement that natural selection is generally a passive process. However I think we both might be arguing over semantics. If we agree that natural selection is the filter--then we really only care about what the output of the filter is.
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> This is a new dimension to our discussions: who says the output is the only thing we really care about? You have missed the point of both the theist and the atheist agendas! So let me spell it out for you. The dispute is over whether the complexities of life's physical mechanisms are too great to have arisen by chance. Natural selection is irrelevant to the design argument ... it's a perfectly logical process whereby what survives is that which is most suited to survival (hence your 14 stages of horse). It would be unreasonable to deny this. By making out that evolution and NS are synonymous, the atheist can therefore argue that any questioning of evolution is unreasonable. What Dawkins calls "organized complexity" is not created by NS, but by mechanisms for replication, adaptation and innovation, without which evolution could not take place and Nature would have no variations to select from. These mechanisms have so far proved to be too complex for us to understand, let alone reproduce, and so theists claim that they have been designed. If you reject the possibility of design, you have no choice but to put your faith in the ability of chance to create the mechanisms ... but the idea of "faith in chance" is anathema to your atheist: hence the strategy of trying to make NS (which has no bearing on the design argument) synonymous with evolution. Ah Matt, what happened to my fellow sceptic's scepticism?-The commentary above needs to be repeated over and over. It is the very clearest summary I've seen of the debating points between design and atheism.-That said, the use of the horse example is of especial interest: note that the horse has been bred back down to original size. This means the coding for advancing evolution is present in the final form of an organism, and can be reversed by selective breeding back to the beginning. This suggests to me that an argument can be made that the code for advancing evolution is present from the beginning of evolution, since the morphogenic pattern controls in the genome are fully maintained going forward or backwards.

MATT: Evolution is this case (Dawkins) is inference based on evidence. You tripped into my "inference is not knowledge" dogma once again...(Just trying to point out instances where your thinking parallels my own skepticism...I still don't think we're that different...)
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> Evolution and NS are not synonymous (see below), and I think you're being kind to Dawkins, who says that NS "explains the whole of life", which to my mind is not even an inference, let alone based on evidence. But I agree that inference is not knowledge, I do share your scepticism (even if I insist on spelling it the English way!), and we're not that different. On the epistemological thread, I'm confident we shall eventually come to an understanding, but the difference between us is that I tend to think more concretely than you do. On this thread, relating to evolution, both of us "accept" the basic theory, but there is one major difference between us, which is your focus on NS at the expense of adaptation and innovation. As far as the consciousness thread is concerned, I'm far more open to speculation than you are, but the reasons for that may perhaps come out later in our epistemological discussion.-Again, not having read any Dawkins--but having been a full-blown atheist previously--I assume that he for example, looks at the evidence of horse evolution, cut across about 14 skeletons at the Smithsonian, and concludes that there was a progression from horse 1 to horse 14; and that the explanation for each specimen was that it was under pressure of natural selection to reach the form it took. -When you look at palentological evidence at large, a similar story is told for many creatures. When you look at bacterial resistance, this is evidence on a micro scale for macro change. -I gloss over some details, but this is a fair representation of what I identify forms the whole of atheist ideology concerning evolution. -When you compare this explanation versus any others concerning how life has taken the form it does today--I find it a pretty convincing argument. So at this point generalizing to all of life is a natural next step. (Epistemology aside.) -Evolution and natural selection are seen as synonymous, but to writers (such as Massimo Pigliucci) he makes a distinction between what evolution was to Darwin compared to what evolution is to Evolutionary biologists today. Natural selection still plays a firm role. I don't have the time to read his book again, but the book "Denying Evolution" covers a great many of the objections you raise here, and at least offers a modern view on the current state of evolutionary biology. He does cover Gould, but in his view Gould still doesn't displace Natural Selection, only modifies it. He does tackle things such as the eye. It's just been about 6 years since I've read it and I do not recall his arguments around that.-If you're interested I suppose I could go dig up the relevant material and post it.


> In your book do you clearly delineate between Gould and Darwin? Because though I ran the simulation program myself, it was textbook stuff for me in undergrad. When I hear someone attacking "darwinism" (even though I know you don't mean it this way) to me it always means evolution writ large; I never went beyond the chemical levels, but it seems to me that Gould just filled in some gaps but admitted he didn't have any evidence...-I clearly described Gould and Eldridge's idea of punctuated equilibrium as some thing quite different.


> > David seems to see epigenetics as the answer ... certainly a more satisfactory solution than chance mutations ... but is there any evidence that epigenetic changes (a) produce new organs, (b) produce new species, and (c) are anything but short-term? (This is a genuine question, not a criticism.)
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> The best example I've seen is Reznick's study of guppies. Small guppies changed their size when presented to danger in a two year period, rapid by any theory. Large guppies did the same. Small to large, large to small. Same species but an 'immediate' adaptation. Does a series of 'dangers' or challenges finally cause the epigenetic 'rapid response team' genetics to drive the species to a new species? That is the 64 dollar question. Current research is looking at methods of rapid change, methylation, recombination,etc., not requiring mutation. These seem to cause only small adaptations, not a jump in species type. I'm not aware of other Reznick-like studies.
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> Of greater importance is that the genomic researchers have no idea why one series of amino acids is functional and when altered is not. It appears that most mutations lab-created are deleterious. Lab research trying to mimic evolution doesn't work. With 20 amino acids that are essential, available,and all used in various sequences, and with functional segments using 100 amino acids or more, the odds (according to one reviewer) are 10^170 against finding a new functional segment de novo.-Like I said... if we're going to crack this nut we really need to take an approach that doesn't try to mimic life's conditions until we know that we can create it in a test tube with ANY material, reagent, etc...