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UD Commenters Win One for the Gipper

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Below the fold I have reproduced an interesting comment thread in which ribczynski attacks ID proponents’ criticisms of macroevolution through NDE, and two ID proponents convincingly refute the Darwinist line.

 

DARWINIST’S ATTACK

 

ribczynski writes:

 

The following comments and questions are for those of you who acknowledge that natural selection and common descent are real (with the usual caveats about horizontal gene transfer), but believe that natural selection does not and cannot explain large-scale evolutionary changes (i.e. “macroevolution”).

 

[Note: In this discussion I will be using “natural selection” to encompass both heritable variation and selection, as is commonly done.]

 

1. When ID supporters ask for evidence of macroevolution, biologists point to the fossil record, molecular biology and comparative anatomy to make their case.  The more enlightened IDers accept these as evidence of evolution, but question whether such evolution can be explained as the result of unguided natural selection.  They ask for evidence that unguided macroevolution has been directly observed.

 

The problem is that macroevolution doesn’t happen on a short human timescale. Why demand a demonstration of rapid macroevolution when evolutionary biologists don’t even believe that it occurs? It doesn’t make sense.

 

Some, like jerry, will argue that Darwinians are just using time as an excuse:

 

Since there are no examples of macro evolution happening, Darwinists resort to all sorts of crutches, the most important of which is deep time.  They will say that don’t you see what can happen over millions of years and that is where they stop.

 

The question for jerry is this:  Is he prepared to provide a real-time demonstration of guided macroevolution? If not, why the double standard?

 

2. If a direct demonstration of macroevolution is not possible, then what about the indirect evidence of the fossil record, comparative anatomy and molecular biology?

 

No good, say ID supporters, because you can’t show that the evidence was produced by unguided changes.  They might have been guided.

 

I have three responses:

 

a. In making this complaint, IDers are undermining their own demand for a direct demonstration of unguided macroevolution.  Suppose that such a demonstration could be arranged.  How would we know that it was unguided?  After all, it’s possible that the Designer has his fingers in our demonstrations.  (This, by the way, is what critics mean when they say that ID is unfalsifiable).

 

b. If evolution is guided, why are there no saltations?  Why does the designer always happen to choose the small changes that we would expect to see if natural selection were operating — the same small changes that allow us to deduce the nested hierarchy?

 

c. Apart from their YEC brethren, IDers tend to accept the evidence for geologic processes operating over vast timescales, and they don’t dispute it when geologists contend that these processes were unguided.  Why don’t they demand proof that these processes were unguided?  Could it have anything to do with the fact that their religious beliefs conflict with unguided macroevolution, but not with unguided geology?

 

3. Mathematical or computer modeling of Darwinian processes could demonstrate the plausibility of unguided macroevolution, but as the reaction to Avida indicates, IDers can always insist that a particular model is unrealistic in some crucial way that invalidates the results.

 

IDers demand empirical evidence of unguided macroevolution, but it’s not clear to me what sort of evidence they would actually accept, short of an authentic handwritten note from God.

 

I ask them: In your view, what would count as sufficient empirical evidence for unguided macroevolution?

 

 

ID PROPONENTS’ REBUTTAL:

 

gpuccio writes:

 

ribczynski:

 

When you make specific points, I am always ready to answer.

 

1) is not really a point.  I agree that the supposed unguided macroevoution operates at large time scales:  nobody is asking that it should be “directly” observed.  But we do ask that it may be “indirectly” inferred form observed facts according to a credible model, which is what we can and must ask of all scientific theories.

 

2)

 

a) Wrong. If you can arrange a demonstration, be it direct or indirect, where macroevolution happens in an understandable way, according to a credible model, without any apparent intervention of a designer, that would be falsification of ID.  The objection you suggest, that a designer could still be acting “behind the scenes” is imply unacceptable.  I would never make it, and the same is true for any serious IDist.  Maybe some theistic evolutionists…

 

b) First of all there are saltations. Have you ever heard of “punctuated equilibrium”? That’s not an ID theory.

 

Anyway, I don’t see why a designer should not act gradually.  That’s the usual way of working of designers. Obviously the time scale depends on the nature of the designer.

 

And by the way, we do not observe “the small changes that we would expect to see if natural selection were operating.”  If that were the case, we should see an almost infinite number of “small changes,” not only at the fossil level, but also at the molecular level.  And a credible and detailed model for macroevolution could be inferred.  And that has never happened.  Rather, what we do observe are “the small changes that we would expect to see if intelligent variation and selection were operating.”  I refer you again to the example of intelligent protein engineering.

 

c) About geological processes: personally, I am not completely sure that they are absolutely unguided:  I just don’t know.  The fact is that, as far as we know, geological processes, and other similar processes (evolution of the universe, and so on) do not explicitly exhibit CSI (the fine tuning argument is about the whole universe, and not specific internal processes of it).  So, the ID theory is not at present applicable to them.  They can apparently be explained by laws of necessity, usually with only a few random components.  The model is credible, and we can well accept it.  Religious beliefs have nothing to do with that.

 

3) Existing computer models have in no way demonstrated either the “plausibility of unguided macroevolution” or the emergence of any CSI from unguided processes.  Avida and similar are intellectual frauds.  In case you have not noticed, all the recent work by Dembski and Marks is dedicated to that problem.

 

But it is possible, in principle, to give a demonstration that would falsify ID (and that again shows that ID is falsifiable).  We are eagerly waiting to be falsified!  But Avida?  Please, be serious.

 

Show me a computer model where unplanned and unexpected CSI emerges from random noise on the basis of “spontaneous” self-selection, without the system having been planned in any way to select anything specifically, and we can discuss. After all, that’s what the Darwinist affirm has happened.

 

Jerry then writes:

 

[quoting Rib] “The question for jerry is this: Is he prepared to provide a real-time demonstration of guided macroevolution? If not, why the double standard?”

 

What a silly question.  You are saying that we do not have a video tape of the designer in his/her lab preparing the new species that we have a double standard?  ribczynski, you need to get a reality check.  ID says that the formation of new species with novel complex functions is a mystery.  We are not saying that there is proof that there is a designer but only that it is a very likely explanation for what happened.  Come on; the double standard comment means you are really flailing.

 

Is such a thing as a designer possible.  Certainly, no one doubts that within 50-100 years, engineering genomes to do completely novel things may be possible in labs such as those that exist at MIT.  That my friend will be an example of intelligent design in action.  If such a thing is possible in today’s world what is to say it was not possible in the past.

 

[quoting Rib] “If evolution is guided, why are there no saltations? Why does the designer always happen to choose the small changes that we would expect to see if natural selection were operating — the same small changes that allow us to deduce the nested hierarchy?”

 

Gould said the whole history of the fossil record was one of apparent saltations. That was why he developed his absurd fix for Darwinian processes called punctuated equilibrium.  I suggest you read Gould and as suggested by other, his ideas on punctuated equilibrium.  Everybody immediately just lapped up his ideas and it is now part of the evolutionary canon.

 

[quoting Rib] “If a direct demonstration of macroevolution is not possible, then what about the indirect evidence of the fossil record, comparative anatomy and molecular biology?”

 

The indirect evidence refutes a gradualistic approach which is why Gould proposed his theory.  Comparative anatomy and molecular biology could have been the result of micro evolution once a population gene pool arose.  ID believes and supports micro evolution.  See my comment #88.  The question is where did the original gene pool come from.

 

[quoting Rib] “Apart from their YEC brethren, IDers tend to accept the evidence for geologic processes operating over vast timescales, and they don’t dispute it when geologists contend that these processes were unguided. Why don’t they demand proof that these processes were unguided? Could it have anything to do with the fact that their religious beliefs conflict with unguided macroevolution, but not with unguided geology?”

 

You should study geology. There is evidence of both gradual and catastrophic forces having occurred in the past and operating today in the world.  We can witness massive earth quakes, volcanos, tsunamis and rock slides, sedimentation and erosion before our eyes as well as plate tectonic movements, plate formation at the mid ocean ridges.  All the pieces fit together and I am sure there will be adjustments in it over time.  So all holds together but one thing geology has never done is form any complex specified information.

 

Now biology has nothing similar except for micro biology which we all accept and yet life has complex specified information forming over time and no known process that can do it.  Nothing in the current world shows this tendency to form complex specified information.  Geology produces complexity but it is not specified.  That is why we can accept geology and not biology.  One process leaves a host of forensic evidence on how the non specified complexity has formed, the other leaves no information on how the complex specified information has formed.  In fact the geological evidence is extremely persuasive for ID.  There are gradual processes working over time that can be observed in the current world for geology but none in biology except for micro evolution which does not produce complex specified information.  There is no forensic evidence that micro evolution leads anywhere but to devolution which is the opposite of macro evolution.

 

[quoting Rib] “I ask them: In your view, what would count as sufficient empirical evidence for unguided macroevolution?”

 

How about some examples either in the fossil record or in the current world.  None exist.  Macro evolution has no empirical evidence behind it.  It is not science, but an ideology.  Why don’t you start presenting empirical evidence for macro evolution.  If you could, you would be a Nobel prize winner.

 

Please, provide some evidence, not just the tired old clichés we see all the time.

 

Comments
Khan: Very interesting discussion, thank you! "would you consider a eukaryotic cell with organelles to be more complex than a eukaryotic cell without organelles?" Yes: it has gained the complexitu of the organelles. But id the organelles pre-existed, then there is no real gain in information. I can agree, anyway, that some information is necessary to effectively realize the symbiosis, but as I told in my previous post, I assume that such information comes from active adaptive processes, and that it depends on previous abilities inherent in the two cells. I have no reason to believe that an effective symbiosis process may happen randomly. "that organelle got there by symbiosis. so symbiosis can lead to increased complexity." Again, if you consider the union of set A and set B, it is obviously greater than A and B. That's almost trivial. Regarding any possible new function deriving from the interaction of the two cells, see previous point. Anyway, cooperation in nature is a general rule, beginning with the cooperating behaviour of bacteria (see Shapiro) up to the organized patterns of flight in migrating birds. Cooperation does not even require symbiosis. And it is generally a very organized, active and intelligent (and highly mysterious) process. "and the mitochondria is radically different then its progenitor cell, so it’s not simply a combination of two existing life forms- a lot changed in both the guest and host cell after they combined- the “information” is v different." That's why I am not sure we really understand the origin of mytochondria. A simple loss of no more necessary genes is still in some way explainable, but what about all the other differences? "you could even say it evolved." You could even say it was designed. Again, natural history is not a causal explanation. "and your assertions on mutation not being able to generate a single functional protein are incorrect" I really thank you for bringing the debate on technical knowledge about proteins. That's exactly the kind of discussion which can let us understand more about the real problems, even if experimental data are still not abundant. I have always affirmed that data from protein engineering will let us know more precisely what is reasonable and what is not in our respective models. But I must say that I don't share your enthusiasm that the papers you cite falsify in any way my affirmation. Let us see: 1) I could not access the full text of the Keefe and Szostak paper, which is probably the most interesting of the three. So, I had to use a comment by Rachel Brem on Genome Biology, which I found on the Internet. I paste here part of it: "Keefe and Szostak began with a library of 1012 80-mers. Following eight rounds of selection and amplification, 6.2% of the library bound the ATP column. After mutagenesis and further selection, 34% of the library bound the ATP column. From the final generation, eight clones were purified in milligram quantities and characterized as free proteins. All shared about 80% sequence identity among themselves but are not related to any other known sequence." Well that looks very much as protein engineering here. There is vast use of intelligent selection. And the final function is just ATP binding, which in itself seems scarcely selectable in a natural context. Here is one final note from the above commenter (who is in no way an IDists): "As a protein design study, this paper hits the mark expertly. As a study of sequence evolution rates, there are some gray areas. For example, proteins from Keefe and Szostak's first eight rounds of selection appear to use their tethered mRNA in binding ATP; thus, strictly speaking, 10^11 80-mers alone may not yield one functional protein." 2) I could reqad, instead, the full text of the paper by Davidson and Sauer, and I must say that I am not very impressed by it. The study is about very artificial random proteins, made of 3 aminoacids only, and the authors could only demonstrate some secondary alpha helix structure, and indirectly argue for some unknown tertiary structure and oligomeric organization. Obviously, no function at all. The question of how many proteins can fold is obviously a fundamental question, but its true form is: how many truly random proteins (made of all 20 aminoacids) can fold stably enough in one of the known folding patterns which are associated with function in biology? That's the right question, and I don't believe that this study helps much to answer it. And, as you know, folding is not function, but only a prerequisite for it. 3) I will not comment in detail about that, because Behe has already done that in TEOE. Behe concludes that this example is in the range of what unguided evolution can do. But I will cite here the last words in the abstract of the paper, which are indeed revealing: "The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly." Interesting, isn't it? I would add "the first 'and only' clear example". And Behe shows the reasons why it is not a real example of emergenge of complexity (in the sense of CSI). The first example: how does that ring for a theory which, in the minds of most, is considered "a fact"? Anyway, again I must say that I appreciate your line of discussion. Science is done by reasoning openmindedly on known facts, and not by sticking to dogmatism.gpuccio
December 12, 2008
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Khan,
Margulis’ ideas were not readily accepted bc they seemed to be opposed to the classic Darwinian paradigm. But she and her coworkers eventually compiled enough evidence to make a convincing case (not “prove” it bc no one ever “proves” anything in science), and the endosymbiosis theory is now widely accepted.
Really? Last time I read up on this subject I was under the impression her ideas were still fairly controversial. I guess it depends on what circles you travel in... *shrugs* Personally I considered the evidence "potentially convincing" and I don't hold a preference. Whether widely accepted or not I already made my opinion on this issue in the first paragraph of #47. And gpuccio makes a good point that we should probably not consider symbiosis to be a subset of Darwinian mechanisms. But if you insist that we define it as such I have no problem with conceding that under your definitions that a subset of Darwinian mechanisms is "apparently" capable of producing macro-evolution. But it's not like you can define ID away...Patrick
December 12, 2008
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gpuccio, would you consider a eukaryotic cell with organelles to be more complex than a eukaryotic cell without organelles? that organelle got there by symbiosis. so symbiosis can lead to increased complexity. and the mitochondria is radically different then its progenitor cell, so it's not simply a combination of two existing life forms- a lot changed in both the guest and host cell after they combined- the "information" is v different. you could even say it evolved. and your assertions on mutation not being able to generate a single functional protein are incorrect: Keefe and Szostak, 2001: functional proteins from a random-sequence library. Nature 410, 715-18 Davidson and Sauer 1994. Folded proteins occur frequently in libraries of random amino acid sequences PNAS 91, 2146-50 CHen et al. 1997. evolution of antifreeze glycoproteins in Antarctic notothenoid fish PNAS 94, 3811-16Khan
December 12, 2008
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Khan: I may agree on some of your points, but some clarifications are due: It's OK for me to consider exchanhe of information and symbiosis as important elements in the modeling of living beings. They are, from bacteria to humans. But that changes nothing in the fundamental problem of the genesis of information. Biological information must exist before it can be exchanged or remixed. All biological information, at its fundamental level, cannot just be the product of "exchange". Proteins with their functions, the DNA code, regulation networks, complex molecular machines, body plans, transcriptome regulations, and so on, all must exist and work, and then they can sometimes be exchanged and/or shared between different living beings. So, arguments such as symbiosis and similar mechanisms are of no help to explain the origin of information. You say: "mutation and recombination may build simpler systems and then symbiosis combines them to form more complex systems" No, that's exactly the wrong way to look at it. Mutation and recomlbination cannot even build a single functional protein. Moreover, symbiosis does not combine simpler systems to form more complex systems; symbiosis is rather an adaptive phenomenon where two complex systems share existing functions, probably according to modalities partially or totally inherent in their complexity. There is no evidence that symbiosis may happen randomly. In other words, sharing complexity is a complex issue. It happens, but we don't know well how, or why. In the end, RV and NS are the only "non design" mechanisms for the generation of biological information for which some model, although unsatisfying, exists. In that sense, I don't agree that "we’ve progressed a lot since Darwin". That's not true. It's still RV + NS, and practically nothing else, whatever McNeill and others may think in their "lists" of engines which are not engines, of causes which are not causes. At present, the only structured alternative to RV and NS is design.gpuccio
December 12, 2008
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Obviously, Darwin didn't explicitly propose mutation/recombo.. just variation.Khan
December 11, 2008
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gpuccio, "Both exemples seem to interestingly show that there is very active interaction between host and symbiont, and different forms of adaptation. Frankly, nothing of that seems to have the characteristics of random variation." You're right, but why does it have to be random mutation/recombination? THat's what Darwin proposed, but we've progressed a lot since Darwin. In fact, as you probably know, Margulis' ideas were not readily accepted bc they seemed to be opposed to the classic Darwinian paradigm. But she and her coworkers eventually compiled enough evidence to make a convincing case (not "prove" it bc no one ever "proves" anything in science), and the endosymbiosis theory is now widely accepted. As you note, symbiosis is a powerful force in evolution and can clearly contribute to the evolution of complex systems. mutation and recombination may build simpler systems and then symbiosis combines them to form more complex systems. the human body has tons of symbioses- we have more bacterial cells than eukaryotic cells in our bodies! so ID folks should not overlook symbiosis when they think about how complex systems could evolve. there's more to evolution than RV and NS- This is one of the reason most evolutionary biologists don't call themselves "Darwinists" anymore.Khan
December 11, 2008
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Khan: I have read both references you give. They are interesting papers, but they are about naturally occurring processes of symbiosis, the first between two eukaryotes, the second between an eukaryote and a prokaryote. Both exemples seem to interestingly show that there is very active interaction between host and symbiont, and different forms of adaptation. Frankly, nothing of that seems to have the characteristics of random variation. And, after all, I am still unconvinced that those kinds of observation prove anything about the origin of mithochondria, even if thet may rightly be the basis for a model. But, as I have told before, I would not call those things "macroevolution", or, if we want to call them that way, they are examples of a kind of "macroevolution" which is very different from the classical form, based on RV and NS. Here we onserve active adaptation between existing species, and the biologic information for the expressed functions is already there, it is rather actively mixed, shared, and in some way readjusted. The process, although more complex, seems similar to lateral gene transfer bewteen bacteria. Shall I remember that LGT is a common procedure, and that it is in some way part of the natural functions of bacteria? Symbiosis too is a common event in nature. It is a form of cooperation, not of generation of new functions from random events. And again, the details of how the various kinds of symbiosis are realized are usually missing. The fact that we see it happen does not mean that we understand how it happens.gpuccio
December 11, 2008
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gpuccio, if you'd read the sources I've cited above, you'd see that we have observed the same processes occurring in the lab. there is a vast body of literature on the mitochondria endosymbiosis. please read up on it and tell me if you remain unconvinced.Khan
December 11, 2008
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Khan: By the way, if you want to call lateral gene transfer, even in massive form, or symbiosis, "macroevolution", I have no problem with that. I usually don't fight about words, I just try to define them in a context, to avoid ambiguities. And I think there is no doubt that we do observe lateral gene transfer (although usually not massive) and symbiosis in nature. You have still to prove that those processes were the real and sufficient cause of the emergence of mitochondria in eukaryotes.gpuccio
December 10, 2008
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Khan: ID has no problems with horizontal gene transfer, in any form. It's obviously "exchange" of information, and not "creation" of information, whatever language you are using. And if you want to debate ID, anyway, you have to understand its language. Moreover, you must admit that in the theory about mitochondria a lot remains to be explained: even if it were true that mitochondria originated that way, still you have to explain how that really happened: in other ways, either make it happen again in the lab, or give a detailed enough, and credible, molecular model of how it happened. And I do believe that such a model would still have huge gaps from a deterministic point of view, and would need to be explained in terms of design, or at least of active, intelligent, programmed adaptation. As far as I can see, that kind of model is still at the level of "natural history hypothesis", and nowhere near to a true "causal theory". In other words, darwinists, in all parts of their "theory", still have to make the shift (and probably never will) from "it happened that way" to "it happened that way because these causal factors can and did accomplish it". In other words, from myth to scientific explanatory models.gpuccio
December 10, 2008
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ribczynski: "Within a certain small margin of error, you get the same phylogenetic tree regardless of which characteristic you look at, whether it is phenotypic or genetic." You must be kidding. "One" phylogenetic tree? What kind of scientific literature do you read? Unless, when you say "within a certain margin of error", you are thinking of that "margin" as very, very large!gpuccio
December 10, 2008
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What I meant is I don't care to argue over definitions, not whether it is or should be defined. As in, I'm ignoring the recent argument in my discussion.Patrick
December 10, 2008
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Patrick "What you’re missing is that evidence for potential/speculative generalized macro-evolutionary events–which many ID proponents might agree with–is very, very different from evidence that Darwinian mechanisms are capable of producing said macro-evolution in a uniform manner." we have good evidence both that endosymbiotic events occured and that they proceeded through standard processes of evolution by natural selection- I don't know if you'd define it as "uniform" but whatever. some of the nicest evidence is that we have observed cases of similar processes occurring in real time: Okamoto, N. & Inouye, I. (2005), "A Secondary Symbiosis in Progress?", Science, 310, p. 287 Jeon, K. W. 2004. Genetic and physiological interactions in the amoeba-bacteria symbiosis. J Eukaryot Microbiol 51:502-8 p.s. and if you won't define macroevolution and don't care how it's defined then why do you keep using it? It is very confusing. words need to have specific meanings or we can never have meaningful dialogues.Khan
December 10, 2008
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Khan, What you're missing is that evidence for potential/speculative generalized macro-evolutionary events--which many ID proponents might agree with--is very, very different from evidence that Darwinian mechanisms are capable of producing said macro-evolution in a uniform manner. I don't care how macro-evolution is defined but personally I believe that given the prior existence of CSI (OOL) in an intelligently designed system that Darwinian mechanisms "should" be capable of producing a limited set of macro-evolutionary events. I haven't seen evidence for this yet but I will not be surprised if we do.
and when you think about novelty, think about both morphological and genetic novelty. Part of Valentine’s argument is that the novelty of body forms in the Cambrian came about through relatively simple changes in patterns of gene expression. this is because of the modular nature of their body plans.
Heh. Sounds like you're describing a common ID-compatible hypothesis. Whence came the modularity? And foresighted mechanisms? Why should ID proponents reject the capabilities of LGT if the system is designed to take advantage of it? (Although I will add that so far evidence for the extent of the capabilities of LGT is fairly limited yet it is assumed to be very active regardless.) #45, Nice assertions. Bushes in the Tree of Life “recent analyses of some key clades in life’s history have produced bushes and not resolved trees.” “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.” “Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom” “The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.” ID proponents typically interpret homology as compatible with universal common descent, common descent from multiple LUCAs, or Designer Information Reuse (which is itself compatible with multiple scenarios). Instead of resolving a tree we’re getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Continuing the theme of “islands of functional information”, these bushes could also be called “archipelagos of functional information” which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent. EDIT: I'd also like to add that there probably should be made a distinction between Undirected/Non-Foresighted LGT and Active/Foresighted LGT. Now it's possible that a Designer could build a system in expectation of undirected processes, but at least one ID-compatible hypothesis would expect A-LGT. For example, viruses as a whole could have once contained the functionality of networking all organisms and triggering macro-evolutionary events. The problem with such functionality is that it would be expected to be highly susceptible to deleterious mutations since it's not necessary for survival and thus this particular biosphere system for evolving would degrade with time. Eventually we'd be left with simple replicators totally focused on self-survival as we see today. BUT since they're such fast replicators we might hope that some remnant of this functionality might survive.Patrick
December 10, 2008
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gpuccio I won't use the language of ID bc it is unclear to me (return the favor with bio terminology, please?), but I will say that the genome and metabolic abilities of the guest cell degraded as it became the mitochondria. However, massive lateral gene transfer from the guest to the host occurred and the host acquired some completely novel abilities and structures. so there is both loss and gain from genetic, metabolic and morphological perspectives. neat stuff, huh?Khan
December 10, 2008
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My comments are still being held up in the moderation queue, but I'll take a chance on responding here. gpuccio wrote:
Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings... The same could be said of computer operating systems. And of course, the number and nature of the designers would strongly condition those aspects.
I hear this from ID supporters all the time, but it's not true. Sure, you can form a nested hierarchy of cars based on, say, engines. But the hierarchy you derive by examining engines won't match hierarchies based on radios or air conditioners or hub caps. Each characteristic yields a different nested hierarchy -- unless the designer goes out of his way to make them match. There is no single "true" nested hierarchy for designed objects. For a group of living species, by contrast, there is just one true nested hierarchy (otherwise known as the phylogenetic tree). Within a certain small margin of error, you get the same phylogenetic tree regardless of which characteristic you look at, whether it is phenotypic or genetic. This is enormously powerful evidence for common descent with gradual change.ribczynski
December 9, 2008
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Khan: I don't want to join your discussion with Jerry about macroevolution, because I too have problems with a clear definition. But, as the important point for me (and, I think, for ID) is the generation of CSI, would you agree that the model about origin of mitochondria (if it is acceptable, which I am not debating here) is not necessarily an example of generation of new CSI? After all, if I understand the essence of the model (and may be I don't), it is essentially one of adaptation by loss of information.gpuccio
December 9, 2008
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Jerry, Re: Ediacara. THere are two components to this fauna. 1) preserved impressions of soft-bodied organisms. these are plentiful, but their phylogeny is debated. they are prob not direct ancestors of the Cambrian fauna bc they are not bilaterally symmetrical. 2) trace fossils of bilateral worms. These worms increase in complexity through time and are prob the direct ancestors of the Cambrian fauna. Valentine suggests that most of the major diversification in metazoans occured before the explosion, and that the explosion just represented further branching within already existing diversity. the bilateral symmetry, modularity and presence of the same developmental gene clusters common to almost all living things suggests that this branching could have occurred through relatively simple changes in gene expression. but that is an ongoing (and very hot) area of research right now and no one claims to have it all figured out. the point of the mitochondria is a simple one. you have claimed in numerous posts that there is no evidence for macroevolution. You have still not defined what you mean by macroevolution, but from piecing things together it seems to be something like "not a process but something else, involves large changes in phenotypes leading to changes in taxonomic classification sometimes at the genus and family level but not always and not in single-celled organisms except when talking about the flagellum." i don't know how to respond to this definition, except to say that it seems somewhat, um, personal and arbitrary. closer to art than science. my definition, while admittedly also vague is at least consistent and would definitely include the origin of the flagellum. I am even willing to say that we don't know how the flagellum evolved. we do, however, have a very good idea of how the mitochondria evolved and it is a very complex structure and is one of the defining characters of an entire Kingdom. If that is not macroevolution I don't know what is. so, with that in mind, I bring us back to my original point: there is evidence for macroevolution. maybe it's not exactly what you had in mind, but by anyone's definition except your own it is true. so please, you can say that there is no evidence for the gradual evolution of the flagellum or the eye or whatever but you can not say there is no evidence for macroevolution in general. It is simply false. I would never say that the mitochondria falsifies ID, and likewise you should not say that our ignorance about flagella falsifies evolution. Agreed? p.s. Margulis also hypothesized that the flagellum arose through endosymbiosis- you should check it out sometime! unfortunately, the evidence isn't v good :(Khan
December 9, 2008
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Khan, I said "You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils" I believe that is true. There were some others but I believe they were small and hard to determine what they were but maybe there was one small one that may possibly be a predecessor to one of the many phyla. I haven't time to go an look this up now but I believe that is what the state was. I quickly went to wikipedia and here is what they say "The Ediacara, formerly Vendian) biota are ancient lifeforms of the Ediacaran Period, which represent the earliest known complex multicellular organisms. They appeared soon after the Earth thawed from the Cryogenian period's extensive glaciers, and largely disappeared soon before the rapid appearance of biodiversity known as the Cambrian explosion, which saw the first appearance in the fossil record of the basic patterns and body-plans that would go on to form the basis of modern animals. Little of the diversity of the Ediacara biota would be incorporated in this new scheme, with a distinct Cambrian biota arising and usurping the organisms that dominated the Ediacaran fossil record. The organisms of the Ediacaran Period first appeared around 580 million years ago and flourished until the cusp of the Cambrian 542 million years ago, when the characteristic communities of fossils vanished. While rare fossils that may represent survivors have been found as late as the Middle Cambrian (510 to 500 million years ago), the earlier fossil communities disappear from the record at the end of the Ediacaran, leaving only controversial fragments of once-thriving ecosystems, if anything.[1] Multiple hypotheses exist to explain this disappearance, including preservation bias, a changing environment, the advent of predators, and competition from other lifeforms. Some Ediacaran organisms might have been closely related to groups that would rise to prominence later; for instance, Kimberella shows some similarity to molluscs, and other organisms have been thought to show bilateral symmetry, though this is controversial. Most microscopic fossils are morphologically distinct from later lifeforms: they resemble discs, mud-filled bags, or quilted mattresses. Classification is difficult, and the assignment of some species even at the level of kingdom — animal, fungus, protist or something else — is uncertain: one paleontologist has even gained support for a separate kingdom Vendozoa (now renamed Vendobionta).[2] Their strange form and apparent disconnectedness from later organisms have led some to consider them a "failed experiment" in multicellular life, with later multicellular life independently re-evolving from unrelated single-celled organisms" If all the body plans were the result of relatively simple changes in patterns of gene expression then why is that not true today and can one change a jelly fish into a vertebrate through gene expression. Well we will have to see on that one. I am not sure I would go to the wall on this. Also let me explain the debate for you. If you do not like to accept my definition of macro evolution, that is fine but then you cannot use your definition to say that because there is macro evolution under your definition, there is a partial refutation of ID. That is a complete non sequitur. On the case of the endosymbiotic origin of mitochondria, it is a non issue. Suppose it did happen. So what. It has nothing to do with the debate. If it did happen, it represents an interesting occurrence and nothing more and ID would not be upset about it because it does not invalidate the ID hypothesis. So it is not something ID is going to care a lot about. Maybe you should explain why ID should care. ID is very interested in things like the flagellum because of its complexity and function and its efficiency. But I am not sure I would classify mitchochondria the same way. Maybe they would. I have not seen a discussion on it. Why should ID care about it? Some ID people believe all the necessary information for all of life was front loaded into some original cells so a process that happened 2 billion years after life began is a yawner to them. For those who don't think all was front loaded, it remains an interesting phenomenon but whether it is true or not is to be seen. In general ID is not as interested in single celled changes as they are in multi-celled changes. The flagellum is a particular example of interest and there may be others. What ID is interested in is how novel information can arise that governs systems of new capabilities. Now your other examples may fit this category but I haven't the time to examine them. Since you are interested, I suggest you bring these examples forth with the relevant data about what new and complex and functional developed in each. That shouldn't be too hard if you have an interest in them.jerry
December 9, 2008
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p.s. Jerry, if you're saying that all Precambrian fauna are known from trace fossils, you're wrong. look up Ediacara fauna again. and when you think about novelty, think about both morphological and genetic novelty. Part of Valentine's argument is that the novelty of body forms in the Cambrian came about through relatively simple changes in patterns of gene expression. this is because of the modular nature of their body plans. that's how i interpet it, but I could be wrong.Khan
December 9, 2008
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Jerry, "I am sorry bit I am bewildered by this. Just that all the phyla with their unique body plans appeared out of no where with no predecessor and you are saying that “very little truly novel appeared.” Actually, I didn't say this. I said Valentine said this in the paper. and he did: Just look under "tempo and mode of body plans" on page 6755. I also didn't say that nothing in the quotation contradicts what he says in the paper. I said that he says something similar but then goes on in the rest of the paper to discuss evidence that the statement may not be completely accurate. "You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils, that is no organism but disturbances in the sediment that indicate something live caused them." I never said we had complete fossils of precambrian worms. I used the exact same word you did- trace fossils. "There is no known predecessor to the Cambrian fauna and all Valentine is doing by hypothesizing what it must be and after assuming there is one, he then uses molecular clocks to estimate its content and appearance." Yes, he made a hypothesis and tested it. In any case, this is all a distraction from the main point. I will ask again: do you think that the evolution of mitochondria by endosymbiosis in primitive cells and the evolution of bacteriocytes for symbiotic bacteria in aphids are examples of macroevolution? I have provided several papers and links. Have you looked at them?Khan
December 9, 2008
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Khan, you said "But then he goes on to point out data suggesting that very little truly novel appeared in the Cambrian." I am sorry bit I am bewildered by this. Just that all the phyla with their unique body plans appeared out of no where with no predecessor and you are saying that "very little truly novel appeared." I am sort of stunned by such a comment. I would tend not to take anything else by someone who made such a comment with any seriousness. You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils, that is no organism but disturbances in the sediment that indicate something live caused them. Thus, using the methods of intelligent design Valentine and others have concluded that they were due to non law, non chance origins and probably due to some living fauna. You know what we agree with Valentine's use of ID methods in this case. There is no known predecessor to the Cambrian fauna and all Valentine is doing by hypothesizing what it must be and after assuming there is one, he then uses molecular clocks to estimate its content and appearance. He is again using intelligent design principles, which uses science to estimate what must have happened but he begs three questions, first that such an organism must exist, second that changes in this organism must follow a certain time pattern and third there must be a naturalistic process to explain it. He has to show each is more than just a reasonable assumption, not just beg them. All these speculations get into a peer reviewed paper. I wouldn't mind that they do as long as them admit the questions they are begging. My quote from Valentine post dates this paper and still stands. So deal with the content of Valentine's statement and as you said nothing in this paper is contradictory to Valentine's video statement from a latter time. At least we agree on something.jerry
December 9, 2008
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Jerry, Re: Valentine. Again, he says the same thing in the paper I linked to. But then he goes on to point out data suggesting that very little truly novel appeared in the Cambrian. do you agree that peer-reviewed papers in top-tier journals are a better source for scientific information than quotations from videos? The significance of the Ediacara fauna to the Cambrian explosion is that they are most likely the ancestors to the Cambrian fauna. While the systematics of many of the soft-bodied fauna is unclear (jellyfish-like? sea pen-like? completely unique?), clearly Bilaterian worms (from trace fossil evidence) from this period are most likely the ancestors of the Cambrian fauna. Again, it's all in the paper I linked to. OK, macroevolution examples. Mitochondria: Do I really have to explain how an entirely new organelle capable of performing aerobic respiration is a novel, complex and highly useful feature for the host cell? The guest cell gets so many goodies from the host cell that its genome has degraded and it is no longer capable of living outside of the host. But it still replicates independently and in some cases behaves in a selfish manner. Similar story for the aphids- the aphids get essential amino acids from the bacteria and have evolved specialized cells (bacteriocytes) to house them in- kind of like bacteria farms. These bacteriocytes are complex, novel structures as you would see if you read the other paper I linked to (open access, so it's yours for the taking). Again, the Buchnera bacteria get so much other stuff from the host that their genome has degraded and they can not live outside the host. I argue that these two well-understood examples represent strong evidence of macroevolution however you define it. If you disagree, please explain why. And you can talk about how information is lost in one species and gained in another or whatever, but the basic point that new complex structures can arise through natural processes is unchanged.Khan
December 8, 2008
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Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings, so much so that many times darwinists have taken that as example of how their model of evolution works, momentarily forgetting that automobiles are designed. Very good point, GP.tribune7
December 8, 2008
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ribczynski (#15): "If so, read my later comments in the 60 minutes thread. " And you, read my other answers to your posts in the same thread: #122, answering in detail your posts @115 and # 117; and #125, answering in detail your post #123. Hadn't you eve realized that I had already promptly answered all your posts in that thread? "Not unless you stipulate that the designer will not interfere with the demonstration. But if you allow that the designer might be God, how can you know this?" Why repeat that? I have already answered. You can find my answer in my point a) above, but I will copy it here for your convenience: "The objection you suggest, that a designer could still be acting “behind the scenes” is simply unacceptable. I would never make it, and the same is true for any serious IDist. Maybe some theistic evolutionists…" In other words, to be more clear I have never, and never will, gone out of the scientific approach. I I should appeal to a God who might act without any possible inference form the observable, I would be doing philosophy or religion, not science. I have never done that. So you may be reassured, if you give me scientific confutation of ID, I will promptly accept it. And, like me, all serious IDists. ID is science, not religion. And it is scientifically falsifiable. It's darwinists who, being unable to falsify it, hide behind false religious arguments. "Sure, but those aren’t the kind of saltations I’m talking about. I’m talking about changes, instigated by a designer, that happen much faster than they possibly could if natural selection were responsible." Who tells you that those changes are not instigated by a designer? That's exactly our hypothesis. And they happen fast enough to make classical darwinian theory completely uncomfortable, so much so that Gould had to create a whole new (and vastly unbelievable) approach to try to save what could be saved. And why are you so sure to know how fast a designer would act? What's your model? Bill Gates? "Why does the designer always choose to behave in a way that happens to conform to what natural selection would do?" He certainly doesn't do that. Indeed, nothing in natural history happened according to what "natural selection would do". If that were the case, we would still have a planet without life (but, of course, we would not be here to know that). "Designers will make incremental changes to a design for a while, then abandon it and start fresh when further tweaking becomes unwieldy." Have you ever heard of "object oriented programming"? That's the most effective modality of software design, and it is based on reutilizaton of software parts (objects) even when you change radically the general structure of the program. "They definitely do not derive all of their designs from a common predecessor, forming a single continuous nested hierarchy that can be deduced from a careful analysis." Why not? Because you say that? Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings, so much so that many times darwinists have taken that as example of how their model of evolution works, momentarily forgetting that automobiles are designed. The same could be said of computer operating systems. And of course, the number and nature of the designers would strongly condition those aspects. "The geological community has no such qualms. Nor do most ID supporters." I have nothing to add. I just don't know, but I'm fine with the current scientific explanations. "As I said, I suspect that this is because unguided geological processes pose no particular challenge to their religious beliefs." Your accusing IDists for what they "accept" of current science is just a new culmination of the objective and fair approach of darwinists. "Avida showed how so-called “irreducible complexity” could be produced by a Darwinian process. " That's really news for me. I thought Avida was a software carefully written to show that programmers can obtain what they want, if it is simple enough (and even if they are not that good). Dembski and Marks, and many others, have commented on Avida. See also next point. "“Spontaneous self-selection”?? What are you talking about? That’s not a Darwinian concept." It's simple. Natural selection, even if it's something which is usually conceived as some force coming from the environment, is in reality linked to intrinsic properties of the replicator, and to how those properties can cope with the environment. That's what I mean with "Spontaneous self-selection". In a GA we should have selection for the spontaneously emerging properties of the replicators. The environment must not be programmed to select a specific result we have in mind: that's again design. This is an important point, so I will elaborate more on it. The environment must exert the selection in a completely unprogrammed way, because of its inherent rules. A computer environment has some properties, like any natural environment. Those properties must nor be in any way "designed" to select something: they must select in an unguided way, according to the natural constraints inherent in the system. the replicators, on their part, must be able to replicate, and must be subjected to random variation. The programmer can try any kind and level of random variation, and any kind of replicator. But then the new information must arise form that random noise, and create some new function, not programmed or anticipated by the programmer, and selected only according to the new properties emerged by random variation and how they interact with the inherent laws of the system. That would be a computer simulation of the darwinian theory. In darwinian theory, nobody has ever instructed the system about what has to take place. And nobody instructs the replicators about how they can or cannot change. Most important of all, nobody instructs the system about what should be selected or not: what is selected is totally unexpected by the system, and is selected only because its inherent emerging properties give the replicator true and objective advantages, which work in the system for their own merit, and not because the system "recognizes" them because we have instructed it to recognize them and because that was the purpose we had in mind. That's why no simulation of darwinian theory exists: they are all bad simulations of design.gpuccio
December 8, 2008
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The point is that reproduction itself was viewed as occurring naturally even by Aristotle. It's important to note that Aristotle didn't see a contradiction between natural and rational explanations or the supposed logic of "natural and therefore not designed, specified or set in motion by intelligence." I'm not sure what he would think of the logic of: "intelligent, therefore just a gap in scientific knowledge which will inevitably be filled with unintelligent mechanisms." After all, he viewed the ultimate unmoved Mover or unchanged Changer (or unevolved Evolver) as the ground of all scientia/knowledge and the beginning of science because although he thought the Cosmos eternal causal patterns still trace back to something at present. Instead of asking, as many modern naturalists do, what past events “cause” the Cosmos as we see it now it is just as relevant to ask what causal patterns are the foundation of everything at present. And after all, if we are always seeking past events to explain the world around us we may begin to imagine things about the past based on naturalism while losing a more rational focus rooted in studying things which can be observed empirically and understood by the intellect at the moment.mynym
December 8, 2008
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Here’s my observation: Every time we get a full science explanation, it’s a naturalistic one. Not at all, not if naturalistic stands as opposed to theistic or designed as most proponents of "Enlightement" and the mythological view of Progress typical to it insist. The theory of gravity is an example, note how proponents of a mythological view of Progress said one thing while Newton himself said another:
One of the first actions of those who proclaimed the ‘Enlightenment’ was the ‘deification of Newton.’ Voltaire set the example by calling him the greatest man who ever lived. Thus began an unexcelled outpouring of worshipful prose and extravagant poetry. David Hume wrote that Newton was ‘the greatest and rarest genius that ever rose for the ornament and instruction of the species.’ As Gay noted, ‘the adjectives ‘divine’ and ‘immortal’ became practically compulsory.’ [...] In 1802 the French philosophe Claude-Henri de Sain-Simon (1760-1825) founded a Godless religion to be led by scientist-priests and called it the Religion of Newton (his pupil Auguste Comte renamed it ’sociology’). However, as the ‘Enlightenment’ became more outspokenly atheistic and more determined to establish the incompatibility of science and religion, a pressing matter arose: what was to be done about Newton’s religion? Trouble was that Newton’s religious views were not a matter of hearsay or repute. He had, after all, in 1713 added a concluding section to the second editions of his monumental Principia, the ‘General Scholium’ (or proposition), which was devoted entirely to his ideas about God. In it, Newton undertook to demonstrate the existence of God, concluding that: ‘…the true God is a living, intelligent, powerful Being….’ ‘…he governs all things, and knows all things that are done or can be done.’ ‘….He endures forever, and is everywhere present.’ ‘…As a blind man has no ideas of colors, so have we no idea of the manner by which the all-wise God perceives and understands all things.’ Worse yet, Newton had written four letters during 1692-1693 explaining his theology to Richard Bentley. In the ‘Bentley Letters’ Newton ridiculed the idea that the world could be explained in impersonal, mechanical terms. Above all, having discovered the elegant lawfulness of things, Newton believed that he had, once and for all, demonstrated the certainty that behind all existence there is an intelligent, aware, omnipotent God. Any other assumption is ‘inconsistent with my system.’ (For the Glory of God: How Monotheism Led to Reformations, Science, Witch Hunts and the End of Slavery by Rodney Stark :167-168)
Natural explanations rooted in the rational structure of the universe are possible based on theism. I’m wondering: has there been a time in the history of science (outside of ID’s hope for the demise of Darwinism) when a naturalistic causal explanation has been replaced by an explanation based on intelligence? You are proposing a contradiction based on the mythology of "Enlightenment" which was rooted in a denial of historical facts. Science seems to explain by moving in the other directiion. If science is moving away from rational explanations and toward "natural" explanations then it will become increasingly irrational and pseudo-scientific. If we use an ignorant view of Progress to shift towards explanations which seem "natural" while maintaining a blindness to rational explanations is to undermine our knowledge as rational beings. If science is constantly moving away from intelligent agency then it is moving towards the view that your own language has more to do with natural selection operating on the mating habits of ancient worm-like creatures than intelligence. Or it could be some other utterly irrational "explanation" devoid of a rational view of intelligence but given the mythology of Progress it will inevitably be a fundamentally unintelligible view. I've always wondered why proponents of ID don't somehow work a mythology of Progress into everything they say. E.g. "Well, there isn't much evidence now but an explanation of this type will be verified in the future. Our view defines the nature of science itself. It's inevitable." It's not as if they could not because the part of the nature of scientia/knowledge may be that it is intelligible and then there you have it, all Progress will inevitably be associated with or tend towards verifying ID and falsifying "chance"/ignorance based viewpoints. ;-)mynym
December 8, 2008
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Roy [31], In terms of his Four causes, the male was the efficient cause, not the soul. To say otherwise is taking him out of context: "because it is not within the work of art or the embryo that the tools or the maker must exist." Who contributed the soul is not the point. The point is that reproduction itself was viewed as occurring naturally even by Aristotle. If you want to argue the existence of the soul, that is another discussion alltogether, and another in which materialist dogma is being advanced at the expense of reality.Lord Timothy
December 8, 2008
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Khan, Here is the question to Valentine on the video - “Does the fossil record confirm or contradict the bottom to top pattern?” Here is Valentine’s answer “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas. Although once we get into the fossil record where we got a complete fossil record we can see the gradual changes within lineages as Darwin predicted.” Now Valentine is a believer in a naturalistic approach to evolution so I would assume that the above quote is not biased and thus supports the comments I made about the Cambrian Explosion from the world’s pre-eminent invertebrate paleontologist. I have other quotes which express the same sentiment but for the time being this will do. From what I understand his book also is consistent with a non Darwinian explanation for the Cambrian Explosion. For example, one of the chapter sub-headings is “In Sum, the Cambrian Fossils Imply an Explosion of Bodyplans, but the Underlying Causes Remain Uncertain” You brought up the Ediacara fauna so I suggest that you outline their significance. I was under the impression that they are insignificant to the Cambrian explosion from what Valentine and others have said. For your examples, please outline how the changes you referred to represent the origin of novel complex capabilities that represent new systems in both the host and the single celled organism. This is what is under debate and will have to do since we cannot agree on a definition of macro evolution. Maybe we can call it "meaningful macro evolution" where the adjective meaningful refers to the evolution debate and not to whether the changes had any consequence in general.jerry
December 8, 2008
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Lord Timothy [30], just one example: human reproduction. In Aristotle, the material contribution of reproduction comes from the female, while the male seems to contribute an immaterial soul or intellect. From On the Generation of Animals:
Now the reason why it is not all males that have a generative secretion, while all females do, is that the animal is a body with Soul or life; the female always provides the material, the male that which fashions it, for this is the power that we say they each possess, and this is what is meant by calling them male and female. Thus while it is necessary for the female to provide a body and a material mass, it is not necessary for the male, because it is not within the work of art or the embryo that the tools or the maker must exist.
Aristotle, like most ancients, thought the male contributed the soul and the female contributed the body. In terms of his theory of causes, the male was the "efficient cause" and the female was the "material cause" of the offspring. In any event, the male contributes something that is not material -- soul. Science, however, has moved on to explain human reproduction in terms that are entirely material.RoyK
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