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Author
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Topic: Parsimony and Intelligent Design
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Drosera
Member
Member # 139
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posted 30. March 2002 02:58
Hmmm. I was writing a reply to Mike Gene in the recently closed thread on relative & absolute complexity, but it was closed before I posted.
Anyhow, one subtopic that I saw diverging from that thread was parsimony. Mike argued a number of interesting contentions about inferring intelligent design based on the lack of evidence for mutation and natural selection in the case of the bacterial flagellum.
It seems to me, however, that for ID to get off the ground as a nascent science, it is going to have to employ the principles of parsimony and self-consistency rigorously. For example, if one compares the study of proposed design in biology to the study of human designs, one had best carefully determine the disanalogies in the comparison as well as the analogies.
Regarding parsimony, it seems to me that if you have significant warrant for a simple explanation but can construct a more complicated explanation but without additional warrant, then the former should be preferred.
For example, in the previous thread Mike writes,
quote:
Charlie,
I can appreciate that you perceived my discussion of mechanisms as a cop-out, but I think of it as insight that stems from thinking through the implications of design (especially, intelligent intervention). From where I sit, the two objections that you raise don't directly tackle any of the points I made. ID is a mechanism - a free and rational mind imposes boundary conditions on nature to serve a conceptualized end.
Here, the issue is the comparison between known (human) design as an explanatory mechanism, and "rarefied", completely-unknown-designer design as an explanatory mechanism. Mike mentions that design has a "conceptualized end"... but crucially, Mike has not told us what the conceptualized end was for designing the flagellum. "Making a swimming bacterium" isn't really an end, just like "making a tool" isn't an end. A real design explanation would give us some idea of *why* the designer would want to make something, e.g. a tool or a swimming bacterium. Regarding the flagellum, the question seems totally obscure to me, I can't fathom why an intelligent designer would bother with helping out some microscopic pond scum.
(the question gets even tougher when you start looking at the pattern of 'IC' "design" -- e.g., immune systems vs. disease infection systems, multiple 'IC' swimming systems, e.g. the archaeal flagellum, gliding and crawling systems, etc.)
If the Intelligent Desinger were doing it to communicate his existence into the future, there are far easier ways to do this, e.g. put a spaceship on the moon for us to find or something. This is just one of many ways to design something that doesn't have to survive natural selection for a few billion years (so, your argument that ID would design things that would be naturally selected is also weird...)
With ancient stone tools, for example, we at least know that there were reasonably intelligent hominids at the right time and place, and that they had needs like skinning and cutting up animals, thus positing design for primitive hand axes is a reasonable basic explanation.
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This is what engineers do. And engineering is a mechanism. I'm not suggesting that any design theorist stop at "it was engineered."
But in practice, that's all I've ever seen ID proponents do.
Note that in archaeology, on the other hand, scientists have spent a great deal of time learning exactly how stone tools were made, e.g. which rocks to bang together, what angles/forces to use to get the right chipping patterns, etc. And crucially, archaeologists spend a lot of time working out *what these tools were designed for*, "getting into the heads of" the designers in question, primitive humans. We have none of this for ID.
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But the notion that we need to have the actual design protocols or blueprints (plus an understanding of the technology that implemented them) before we can seriously explore from a teleological perspective makes no sense to me. Is it a cop-out to admit I don't have psychic powers and admit I have no time machine in my basement?
The idea that one must come up with a replacement mechanism before we can dismiss RM&NS behind the origin of something doesn't make much sense either. When Louis Pasteur debunked the mechanism of spontaneous generation, he did so without having to replace it with an explanation for where bacteria came from on the first place.
Actually, he did have an explanation for where the organisms that appeared in rotting meat etc. (the actual question he was addressing) came from: bacteria come from pre-existing bacteria, etc.
Whether or not Pasteur had any sense of the non-organic origin of the earth/universe (only once this is established is an explanation for the origin of life required -- otherwise one can just say life began with the Creation), I have no idea.
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As for science and teleological mechanisms, I suppose it all turns on how you define teleological. I happen to use the common dictionary definition: the use of design or purpose as an explanation of natural phenomena. From where I sit, a teleological cause ultimately traces it way back to mind. In what sense are you defining adaptive mutagenesis as 'teleological?'
You also contributed some other stuff to this thread worth commenting on.
Actually, Paul, I think there are 2 issues here that tend to become confused, but shouldn’t. The first one is: is RM/NS a sufficiently powerful explanatory mechanism for the generation of biological novelty?
The problem here is what we mean by "biological novelty" and whether all novelties are equivalent. Take erythromycin-resistance in bacteria. When this evolves and spreads, we can refer to this as a biological novelty spawned by RM/NS. But would you now argue that we have demonstrated RM/NS is sufficient cause for the origin of the bacterial flagellum? If so, please spell it out.
This is where parsimony comes up.
Why the bacterial flagellum all of the time? This is one of the most ancient systems around, so whatever happened, it happened a very long time ago and evidence is going to be difficult to come by. A large number of gene-origin events like those mentioned in the previous thread, with a number of intermediate systems with different functions, would be the path that natural processes can follow to these complex systems.
Why not look at systems that are equally, or more, complex, but that originated much more recently? This would be the place to test your contentions. Two of Behe's other examples were the immune system and blood-clotting. When we look here, we see a large mass of scientific literature on the origin and evolution of these systems (which of course didn't happen until multicellular animals existed). E.g.:
Blood-clotting:
- Doolittle, R. F. and Feng, D. F. (1987). Reconstructing the Evolution of Vertebrate Blood Coagulation from a Consideration of the Amino Acid Sequences of Clotting Proteins. Cold Spring Harbor Symposia on Quantitative Biology: The Evolution of Catalytic Function, LII: 869-874.
- Patthy, L. (1990). Evolution of blood coagulation and fibrinolysis. Blood Coagulation and Fibrinolysis, 1(2): 153-166.
Kenneth Miller,
"The Evolution of Vertebrate Blood Clotting",
[this one is both blood clotting & immune system]
- Krem MM, Cera ED. Evolution of enzyme cascades from embryonic development to blood coagulation. Trends Biochem Sci 2002 Feb;27(2):67-74
Immune system:
[a whole book! -- checked it out, tried reading it, but it is a very seriously technical work]
- Pasquier, L. D. and G. W. Litman (2000). Origin and Evolution of the Vertebrate Immune System (Series: Current Topics in Microbiology and Immunology). Berlin, Springer, pp 1-324.
- Nonaka M, Miyazawa S. Genome Biol 2002;3(1):REVIEWS1001 Evolution of the initiating enzymes of the complement system.
Online articles:
Is the Complement System Irreducibly Complex? by Mike Coon
Don Lindsay, "How Could The Immune System Evolve?"
There are also other systems that could be mentioned, e.g. Krebs cycle:
Online introduction here
Melendez-Hevia, E., Waddell, T. G. and Cascante, M. (1996). The Puzzle of the Krebs Citric Acid Cycle - Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution. Journal of Molecular Evolution, V43(N3): 293-303.
quote:
The attempt to smear biotic reality into some homogenous, blurry mass in order to make it all accessible to RM/NS doesn't make much sense to me. For example, we could go through all the biotic examples listed in this thread to see if they give us any reason to be confident that RM/NS generated the bacterial flagellum and I'd think we (or at least I) would find no such reason for confidence.
...but if the evolution of more complex systems, ones that are also 'IC' on Behe's authority, have significant literature indicating that scientists are making progress in understand their evolution, then why should one particular example from a much less accessible time period indicate ID?
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You also write:
quote:
-------------------------------------------------- Incidentally, this approach is used all the time in science: we built ourselves a good model of how stars work based on the laws of physics (as we currently know them), and on a limited number of careful astronomical measurements and observations, and as far as I know nobody seems to insist that we have to check equally carefully every star to avoid “just so” stories about how things work in the Crab Nebula.
--------------------------------------------------
Okay, then by all means, lay out in detail why changing color in moth wings in response to industrial pollution is convincing evidence for the non-teleological origin of life and the non-teleological origin of the bacterial flagellum.
All of the individual examples mentioned on the previous thread are just parts of a cumulative body of evidence. Molecular geneticists started with understanding how mere beneficial mutations originate and spread, then building on that to how new genes originate and spread, from there to gene families and multiple gene systems...and right now they're working on how various very complex systems like blood-clotting and the immune system originated. These efforts are proving successful, so why should we be impressed by the bacterial flagellum, which is of about equivalent complexity (maybe), just a lot older so the evidence is tougher to come by?
quote:
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So the question is: are these plausible, evidence-based evolutionary scenarios sufficient to nick ID’s IC/CSI armor, or do detailed evolutionary pathways need to be spelled out?
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You don't need detailed evolutionary pathways (from my perspective). It's as simple as this - If you believe something like the bacterial flagellum did indeed arise by RM/NS, provide the evidence that the bacterial flagellum did indeed arise by RM/NS. What are the data about the flagellum that tells us this? In a world where both bioengineering and RM/NS can co-exist, it does no good to point to the mere existence of RM/NS over there and over here.
The existence of bioengineering before the existence of humans is completely unevidenced. However, RM/NS will exist as a logical necessity wherever imperfectly replicating systems exist and resources are limited.
Earth/rock-moving machinery and erosion both exist, so why assume that ancient, weird rock formations in deserts were formed by erosion? Maybe someone formed them with machinery millions of years ago. The mere existence of erosion over here or over there does no good, on Mike's logic.
We can even extend the analogy to Mike's argument even further. Let's say on the basis of microscopic examination there is evidence that wind-blown sand grains are currently doing the scratching away of the rock. This would appear to be a piece of evidence for the natural, rather than ID, explanation. But no, according to Mike any extrapolation is ruled out. Never mind that eroding rocks will, by nature, only show evidence of the most recent erosion.
Looking for more evidence, we turn to looking at broader patterns. E.g., perhaps based on knowledge of wind erosion, we can predict that structures of only type X, not type Y, will be found in this desert. This is closely analogous to natural selection predicting that only gene-reproduction-enhancing designs will be found in biology. But no, argues Mike, on his hypothesis the designer acted to be consistent with this natural process, long ago. Never mind why a designer would feel limited to this natural pattern, or why he wouldn't use one of the many possible methods of circumventing this natural process, or why he wouldn't have acted in the recent enough past so that the natural process would have had insufficient time to act...never mind all that, ID is still the preferred explanation.
It seems to me that parsimony rules out saying "IC indicates design here (flagellum), but not over here (blood clotting) or here (immune system)."
Drosera
[ 30 March 2002, 03:02: Message edited by: Drosera ]
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James A. Barham
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Member # 50
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posted 30. March 2002 08:48
Drosera:
You raise a very important topic with parsimony, and of course the technical details are very important, but I would like, if I might, to step back on reflect on the parsimony question itself.
First of all, one of the things that makes this whole debate so difficult is its reflexive character. We are ourselves intelligent systems attempting to investigate the origin and nature of intelligent systems. We are therefore in constant danger of moving back and forth unconsciously between epistemical and ontological levels. This is one reason why I never use the word "design" at all, but rather the term "immanent teleology," to indicate the manifest goal-directedness of all biological processes.
I think your comment about why the Creator would bother with "pond scum" is a good illustration of the dangers here. Surely, this discussion is not about "design" in this transcendent sense---the sense in which human beings have purposes in regard to their tools that are transcendent with respect to the tools themselves. (Even assuming there was a Creator, how on earth could we ever hope to have access to his designs in this sense?)
Rather, this dialogue is about the nature of the teleology that we observe empirically in living things---including "pond scum"---or so it seems to me.
One last point. I think parsimony is absolutely essential, not only as a method, but as an object of study. In fact, it points directly to our central topic---the intelligence manifest in life. Intelligence, or rational agency as I like to say, is about the appropriate adjustment of means to ends. Parsimony is simply an aspect of rationality in this sense. All goal-directed action is aimed at fulfilling a goal---anything above and beyond that is extraneous to the purpose at hand. So all goal-directed action does the best it can given the constraints it must work under. Again---this rationality is local and immament, not global and tanscendent---it is intelligence, not clairvoyance---all discussions of what the Creator "ought" to have done under some assumption of transcendence and omnipotence, are irrelevant, or so it seems to me.
One way to look at our problem is this. Inorganic processes seem to obey a minimum action principle---i.e., they minimize energy under a set of constraints. This idea was first articulated by Maupertuis. Living things of course obey Maupertuis's principle as well, since they are real physical systems. However, in addition to Maupertuis, living things also obey Ockham's Razor, which goes beyond merely minimizing energy, and involves using energy to move matter about into particular configurations so as to achieve predetermined goals. So, you might say that our problem is how to bridge the conceptual gap between Maupertuis and Ockham.
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charlie d.
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Member # 159
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posted 30. March 2002 09:56
I agree with what Drosera says, by and large, but I would like to add a small clarification about the concept of "biological novelty", since it was brought up here, and since I think it may touch on the concept of parsimony, as related to design.
It seems to me that when we talk about "biological novelty" we are really not talking about new genes, or new structures, Shannon information, CSI and stuff: we are talking essentially of new functions, that is, new phenotypes that allow an organism to adapt to new ecological conditions, or to better perform old "tasks" necessary for - ultimately - its reproduction (engineered or not, that's what life is all about, after all).
Thus, I think it is irrelevant how complex a structure is, what the "information" content of a gene/protein is, and so on. In fact, I would argue that, from an engineering/design perspective, the simpler the solution to a problem, the better. So, as much as the flagellum seems sophisticated, if a flap on the bacterial wall requiring just 2 new proteins waving back and forth could achieve the same result in term of bacterial locomotion, then the flagellum is simply over-engineered, and I suspect, like many haphazardly "designed" biological features, it would be most likely a reflection of the classic RM/NS "bricolage" pattern (e.g. by using pre-existing secretory and cytoskeletal components).
Further, even if we reason in teleologic terms, it still is the adaptation goal that has to be kept in mind. To me, allowing a fish to swim happily in sub-0C seas seems as much an engineering challenge as making a bacterium swim at all. That it was solved by making ice-binding large expanded tri-peptide proteins from existing enzymes and such is just a marvelous solution. That it appears to have been solved in manner consistent with RM/NS is a testament to the inherent engineering "ability" of darwinian mechanisms.
[ 30 March 2002, 10:01: Message edited by: charlie d. ]
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Micah Sparacio
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Member # 6
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posted 30. March 2002 12:58
quote:
A real design explanation would give us some idea of *why* the designer would want to make something, e.g. a tool or a swimming bacterium. Regarding the flagellum, the question seems totally obscure to me, I can't fathom why an intelligent designer would bother with helping out some microscopic pond scum.
....
If the Intelligent Desinger were doing it to communicate his existence into the future, there are far easier ways to do this, e.g. put a spaceship on the moon for us to find or something. This is just one of many ways to design something that doesn't have to survive natural selection for a few billion years (so, your argument that ID would design things that would be naturally selected is also weird...)
Drosera,
I think that this portion of your post reveals something about the way in which you are approaching design. Your comment about the worth of "pond scum" has absolutely no place in science. It reveals a bias of yours in reference to the size and role of an organism. In addition what do you make of the fact that humans are actively pursuing the design of nano-technology? Is the size indicative of the worth?
Also, who has ever indicated that the designer designs to communicate its existence into the future? Speaking of parsimony, it is exceptionally rare for human designers to design something with the primary intent to "communicate their existence into the future."
And finally, it makes perfect sense to me when Mike talks of design with natural selection in mind. Especially when one of the most sought after holy grails in the engineering world is to develop "adaptive designs." Primitive examples that are still in the "raw stage" are self-powered lawn mowers and vacuum cleaners that "learn" your lawn and interior layout respectively.
One of the most fascinating realities about life is the remarkable ability to respond and adapt to a wide variety of environments. It is a design feature that researchers in AI, robotics, nano-technologists, etc. would love to happen upon.
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Jesse
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Member # 112
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posted 30. March 2002 13:09
Micah Sparacio:
And finally, it makes perfect sense to me when Mike talks of design with natural selection in mind. Especially when one of the most sought after holy grails in the engineering world is to develop "adaptive designs." Primitive examples that are still in the "raw stage" are self-powered lawn mowers and vacuum cleaners that "learn" your lawn and interior layout respectively.
But here the issue of "parsimony" becomes important again. If one argues that, for example, all the design was in the original cells and all subsequent evolution was due to random mutation and natural selection, this position is self-undermining, because surely if Darwinian evolution is powerful enough to turn a single-celled organism into a fish or an elephant then it's more parsimonious to treat it as the default explanation for other complex adaptations like the flagellum. Only those who feel Darwinian evolution is much more limited in its ability to produce new structures will want to seriously consider the possibility of design.
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Drosera
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Member # 139
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posted 30. March 2002 14:34
quote:
Drosera,
I think that this portion of your post reveals something about the way in which you are approaching design. Your comment about the worth of "pond scum" has absolutely no place in science. It reveals a bias of yours in reference to the size and role of an organism. In addition what do you make of the fact that humans are actively pursuing the design of nano-technology? Is the size indicative of the worth?
Hi Micah,
The "pond scum" line was put in to make things a little more interesting and thought-provoking, that's all. I would assert that even those of us (present company here on ISCID) on the planet who have the greatest respect for "pond scum" and know that it is wonderous stuff (whether we're ID types or not), still in our everyday lives don't give it a second thought.
Consider this: if "pond scum" didn't have flagella, would any of us care, and can we think of any likely reason why we would design one for them?
At least with things like photosynthesis, one could perhaps argue that a designer was terraforming the planet or something. I just don't see this applying in the case of the flagellum -- it might be minorly useful for, for example, keeping bacteria up in the water column in the ocean, but if I recall correctly large groups of photosynthetic bacteria do this just fine without flagella, for example in cyanobacteria via gas vesicles.
quote:
Also, who has ever indicated that the designer designs to communicate its existence into the future? Speaking of parsimony, it is exceptionally rare for human designers to design something with the primary intent to "communicate their existence into the future."
I would agree, but this is the only way I was able to make heads or tails of Mike Gene's suggestion that an IDer would only make designs that would be preserved by natural selection. E.g., if a designer wanted to leave a design in life that would persist, he would make it selectable. That's the thinking anyway. It seems to me that any desire to leave a long-persisting identifiable design could be equally satisfied, and much more clearly, by leaving something on the moon, as I suggested.
It is probably also possible to design a life-form in such a way that natural selection could not, in fact, "trim" out the "message". Some cases, e.g. the inverted retina of vertebrate eyes, indicate that at least some prior constraints natural selection cannot get around.
And anyhow, I can't see any very good reason for why a hypothetical designer, who had the power & knowledge to get to this planet and to do all of this biochemistry, would only act in the long-distant pass. The easiest to make a design persist to present times would be to do the designing in, well, something close to present times.
We can of course dream up reasons (a "dying civilization" or whatever), but we've already killed parsimony, why dance on his grave?
quote:
And finally, it makes perfect sense to me when Mike talks of design with natural selection in mind. Especially when one of the most sought after holy grails in the engineering world is to develop "adaptive designs." Primitive examples that are still in the "raw stage" are self-powered lawn mowers and vacuum cleaners that "learn" your lawn and interior layout respectively.
Right, but here again we have an ultimate purpose that serves the designer of the lawnmower, not the lawnmower itself. Get a similar motive for a designer that explains the putative design cases (e.g. 'IC' systems), and then you've got the beginnings of a potentially parsimonious explanation.
(self guided lawnmowers? Anyone remember "Lawnmower Man?" [insert Jaws music])
quote:
One of the most fascinating realities about life is the remarkable ability to respond and adapt to a wide variety of environments. It is a design feature that researchers in AI, robotics, nano-technologists, etc. would love to happen upon.
Wait, I thought "natural selection can't design anything", to quote Dembski. To me it seems that anything but the most minor adaptations would involve way more than "500 bits of CSI", commonly described as ~120 "meaningful" amino acid substitutions (whether or not this is really the correct interpretation of Dembski's arguments).
Anyway, I don't see anything parsimonious about saying "life was designed to adapt" when adaptation is a direct logical consequence of (1) imperfect replication and (2) limited carrying capacity.
Drosera
[ 30 March 2002, 14:39: Message edited by: Drosera ]
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Mike Gene
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Member # 149
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posted 31. March 2002 01:02
Drosera,
I'm not comfortable replying to your thread. According to the forum rules, "The start of a thread needs to present some positive insight into complex systems rather than some purely negative criticism." And I have a hard time finding your positive insight into complex systems. On the contrary, your post comes across as one lengthy criticism, employing a scatter-shot argument intended to naysay what I have stated. This is okay with me personally, as my 1800-or-so postings on ARN show that I am more than happy to defend my views. But I'm afraid this type of thread will quickly wander off into all kinds of directions and quickly give rise to posturing. And that type of thing, in my opinion, will pollute this rather unique forum. Nevertheless, I will provide one reply since your post is clearly targeting my expressed views (although the lion's share of this thread has already been hashed out on ARN) and I suspect you would like a reply. But I am not going to add anything more and will instead allow you the last word.
In the case of the flagellum, my inference to ID is built on more that a lack of evidence for RM/NS. But certainly that lack of evidence is quite relevant.
As for comparing biological structures with human designs, I have in fact considered 'disanalogies.' In cases where they differ, I think biological-specific features make more sense in terms of "superior design" rather than "no design."
As far as the "conceptualized end" for the bacterial flagellum, without lab notes or psychic powers, one can only come up with a working hypothesis. In this case, I hypothesize that flagella were designed to disperse the originally seeded bacteria so that they, in turn, could carry out another designed end to be discussed later. The objective at this point is to seed, take root, and spread and flagella would help. One might complain that this end is not "final" enough for a teleological approach. But consider engineering. What is the conceptualized end of the spark plugs in an engine? One can answer that question teleologically without having to address the ultimate purpose of the car.
Drosera is perplexed by the notion of an intelligent designer bothering to help out pond scum. But the issue here may be an intelligent designer crafting a set of cells to seed and transform a sterile planet. Flagella would be one component built into the cells to facilitate this objective.
As for "the question" getting tougher when we begin to look at the pattern of IC, the response to tough questions is not resignation, but to roll up one's sleeves and get to work. Yes, one trick is looking for the pattern amidst the IC systems. And it would seem to me that the examples Drosera brings up already suggest a pattern. For example, the "immune system vs. disease infection systems" may be nothing more than the emergent dynamic that stems from the designer designing the original cells such that they would establish symbiotic relations rather than exist as autonomous islands. As cells dispersed on the planet, an impetus for symbiotic relationships would be extremely helpful in designing emergent complexity. And in fact, many traditional evolutionists argue that symbiosis is often behind the major advances in evolutionary complexity (i.e., the origin of mitochondria, the Cambrian explosion, etc.).
As for the intelligent designer communicating his existence to the future, there is no reason to think this was the intention behind the original designs. Thus, the point about putting a spaceship on the moon is irrelevant. There is nothing weird at all about the notion that a designer of biological entities would factor random mutations and natural selection into the equation. Would Drosera have the designer's design such that they are ignorant of biology?
As for archaeologists, they have the luxury of a vast independent base of knowledge about the designers. When it comes to the putative designers of the first cells, we don't have this luxury. In fact, the truth of the design of the first cells does not logically entail that we would have this type of knowledge. Thus, we have a choice. We can throw in the towel and declare any attempt to explore biotic reality with the concept of design is doomed without the independent knowledge of the designers (basically the position of mainstream science) or we can recognize the truth that design does not entail we'd have access to the designers and attempt to adapt our research to this reality (the approach of IDers).
As for Pasteur, it's rather clear that he understood the topic of spontaneous generation in its larger metaphysical context. Here are some excerpts from an address he gave on April 7, 1864
quote:
A number of imposing problems now have our best minds in thrall. These include questions regarding the unity or plurality of the races of Man, whether his creation ought to be dated thousands of years or thousands of centuries past, whether species are fixed, or rather undergo a slow, progressive transformation into new species, how supposedly eternal matter relates to the nothingness outside of it, and whether the idea of God is useless. These are just a few of the issues now subject to learned debate.
You need, however, have no fear that my address tonight has any pretensions toward resolving any one of these earnest questions. But in the neighborhood of such mysteries lies another question, more or less closely related, to which I may, perhaps, venture to direct your attention; for its complexities, which I have made the object of concerted and conscientious study, are accessible to experiment.
This is the question of what we call "spontaneous generations."
Mightn't matter, perhaps, organize itself? Or posed differently, mightn't creatures enter the world without parents, without forebears? This is the question I seek to resolve.
It must be acknowledged that the belief in spontaneous generation has been with us throughout the ages; universally accepted in antiquity, it has become more disputed in modern times, and especially in our own lives. It is this belief I have come to challenge.
[snip]
Heated controversies, such as those which arise today among our scientists, are all the more lively, all the more impassioned, for having their counterpart in popular opinion, which, as you know, is always divided between two schools of thought, as old as the hills; these days we call them "materialism" and "spiritualism." What a victory would be won by materialism, gentlemen, if it could cite in its support the demonstrable fact that matter organizes itself, brings itself to life--matter, in which all the known forces of nature may already be said to reside! Do you recall how it appeared in the first of these lectures, in that exhibition of nature's most beautiful phenomena? Do you recall how powerful it is,and how weak, how obedient to the scientist's will? Ah! If we also granted matter this other force we call life, life in all its many manifestations, varying as it does according to the conditions under which it is encountered, what would remain but to deify it? What could then be gained from recourse to the notion of an original creation, to whose mystery we must defer? What use the idea of a divine Creator? But listen, instead, to an adherent of the doctrine of spontaneous generation. This eminent author invites us,
Let us assist in divine works. In a drop of sea-water, we see earliest creation recapitulated. God does not work in one way today and another tomorrow. I do not doubt that my little droplet of water will, by its transformations, tell me the history of the universe. Let us wait and observe. Who can foresee the droplet's history? Animal-plant, or plant-animal: which will be the first to emerge from it? Mightn't this droplet be the infusorium, the primordial monad who, by its own vibrations, soon becomes a vibrion, who, ascending rung by rung, becomes a polyp, a coral, a pearl, and perhaps in ten-thousand years attains the stature of an insect?
Will this droplet, or that which will become of it, be a vegetable fiber, a light, silky bit of down one would hardly even take for a living creature, but still, no less than the first hair of a newborn goddess, a sensitive, loving hair: the hair of Venus? This is no fable, this is natural history. This hair with two natures (vegetable and animal), the descendent of our droplet, is the ancestor of life itself. . .
These confervae, as they are called, are universally found in fresh water, and in salt water when it is calm. They begin the twin series of plants, marine plants and those which became terrestrial when the oceans formed. Above the water the family of the innumerable mushrooms arises, below the water that of confervae, algae, and similar plants.
And so, gentlemen, we see that once the doctrine of spontaneous generation is admitted, the history of creation and the origins of the organic world follow without further ado. We simply take a drop of sea-water, and (as M. Michelet's tells us in beautiful prose) out of this water, which contains a bit of inanimate nitritic matter, sea-mucus, or, as he calls it, fertile jelly, the first creatures emerge by spontaneous generation. Transforming themselves bit by bit, they climb the ranks of creation, reaching, after, say, ten thousand years, the level of insects, and doubtless, after a hundred thousand years, the level of apes, and of Man himself.
Now, perhaps, you see the connection between the issue of spontaneous generation and the grander problems I enumerated at the beginning of my lecture.
One can also see my essay on the inherent metaphysical ties to spontaneous generation (and its offspring, abiogenesis) here
I wrote: The problem here is what we mean by "biological novelty" and whether all novelties are equivalent. Take erythromycin-resistance in bacteria. When this evolves and spreads, we can refer to this as a biological novelty spawned by RM/NS. But would you now argue that we have demonstrated RM/NS is sufficient cause for the origin of the bacterial flagellum? If so, please spell it out.
Rather than spell it out, Drosera invokes philosophy. For "this is where parsimony comes up." The problem is that parsimony is only as good as our frame of reference, our background knowledge. For example, at one time, parsimony dictated that proteins were the genetic material.
Since our knowledge about basic biology and evolution itself is still largely incomplete, I don't think it a good idea to invoke parsimony as some final judge. Instead, parsimony only has a vote in the debate. When we are finished exploring biotic reality and have all the facts on the table, then parsimony can speak with some authority.
But even here, I'm afraid the appeal to parsimony won't help because Drosera and I don't share the same frame of reference. Specifically, I think the cause behind the original cells on this planet was intelligent design (and I do so because of various data patterns). Drosera, I assume, thinks the original cause is found in geochemistry (this is the mainstream view). And this changes the meaning of what is considered most parsimonious. (As I have argued in other forums, the origin of life is the central question of biology. Everything else revolves around this question. To discuss the origin of the bacterial flagellum by ignoring the context set up by the origin of the first cells does not make sense to me.)
Let me put it this way. The are several aspects of the biotic world that, in my opinion, speak more strongly to a teleological origin of life than a non-teleological origin of life. Thus, from where I sit, the situation is not simply extrapolating from the non-teleological origin of antibiotic resistance to the non-teleological origin of the bacterial flagellum. Instead, it is an attempt to extrapolate from the non-teleological origin of antibiotic resistance to the non-teleological origin of the bacterial flagellum in a reality where the first cells were likely designed. Your parsimony test no longer works for me because I already admit ID as the most likely cause behind the first cells. Why does parsimony dictate that I ignore the implications of life's original design?
The only way to make your parsimony argument stick is to demonstrate that the Earth spawned life through non-teleological mechanisms. And I'm not talking about speculative models that imagine how things might have happened and then look for some supporting circumstantial evidence. I'm talking about looking at the world and explaining why the data from the world clearly indicate the Earth spawned life, that non-teleological abiogenesis did indeed happen. I'm talking about the evidence that should compel us all into thinking non-teleological abiogenesis did indeed happen on this planet.
A quick review. My views are not built around the notion X can't evolve. Instead, I argue whether it makes more sense to attribute the origin of X to teleological or non-teleological means. The foundation for this approach lies in the design inference behind the origin of life on this planet. For once this hypothesis is accepted, the game rules change when it comes to evolution. Yes, we have evidence that things like crystallins and AFGPs evolved. But from my position, there is also evidence that life exists because of ID. Thus, the question now is how to approach from both directions to better reconstruct this originally designed state and then to better answer which of the following causes are behind the origin of new functions and traits subsequent to this original state:
a. Further intelligent interventions.
b. An unfolding of the potential contained with the original state (which can be further extended with examples of (a).
c. Traditional non-teleological mechanisms (which may also be constrained by the initial conditions, given that evolution tends to borrow from what exists).
Since many are conditioned to interpret reality through a non-teleological filter, it is to be expected such people will exclusively employ c (without too much concern for the initial states). This is fine with me. The ID proponent can accept these interpretations (as a teleological approach can easily tolerate and incorporate non-teleological causes). But the ID proponent feels no obligation to adhere to this type of explanation if the evidence is lacking. In fact, even if some evidence does exist, like all evidence, it is open to reinterpretation. For example, similarities are typically attributed to common descent. But such attributions are not made using a teleological null hypothesis. There are made using chance as the null hypothesis (and chance is clearly not a teleological expression).
What this all means is that the job is most difficult and demands a case-by-case consideration to determine which explanation works best and then to determine if some form of pattern emerges. From where I sit, generic questions about "novelties" or such are not very useful, as each origin event is contingent and vulnerable to ID. For me, evidence that X evolved is not evidence that everything evolved. For it's not a question of what can happen, it's a question of what did happen (after all, things that can happen often don't happen, not to mention that ID is something that can happen).
Anyway, if the extrapolation/parsimony argument is to be embraced by all, then why bother with science any more? Why not simply take antibiotic resistance in bacteria and then use philosophy to settle these disputes once and for all? We don't need any new evidence. We don't need any new discovery. The evidence is in, the case is settled, and we can all go home. But that Drosera, and others, busy themselves trying to find new examples highlights that they are not quite as confident about the extrapolation argument as they advertise. If they themselves tacitly recognize its shaky foundation through not being satisfied with what has already been found, why are their skeptics supposed to be more believing?
Drosera then asserts that the flagellum is too old to expect evidence for RM/NS and argues I should instead focus on more recent events. However, this claim quickly falls apart upon closer inspection. First, we can note that included in Drosera's list of examples is the Kreb's Cycle. According to traditional evolutionary theory, the Kreb's cycle is much older than the flagellum. Thus, the complaint that the flagellum is too old is clearly special pleading. If Drosera can find evidence for the evolution of the Kreb's cycle, it's time to abandon the "it's too old" excuse. Secondly, if this excuse is to have teeth, Drosera needs to tell us how old is too old. That is, at what point can we all (teleologists and non-teleologists) abandon any attempt to uncover evidence of a non-teleological origin? This cut-off point needs to be determined independently of the flagella question and we then need to reach an agreement that we'll all stop looking (since it would be futile, right?). Then we can see where the flagella fall out. Without accomplishing this feat, the excuse comes off, using the description of someone else here, as "an intellectual cop-out." Third, Drosera doesn't seem to understand my position on this. It is not about looking for design "somewhere" or "anywhere." It is about fleshing out the hypothesis that the original cells were bioengineered and used to seed the planet. Logically speaking, one should stay near this event unless the research that comes from studying this event leads to further reason to expand outwards in time.
Drosera asks "why the bacterial flagellum all of the time." The answer seems rather clear to me. Several scientific experts who study the flagellum have commented on how much it looks like something a human would design. What better place to start? Thus, it would seem most logical to begin with such a structure. This is especially true when coupled with the fact that the flagellum can reasonably be said to have come into existence with bacteria (which can reasonably be interpreted as among the original cells) and that the flagellum (along with bacteria) are among the best understood biological phenomena. Why the flagellum? Because it is as focus that stems from a sound research approach. In its place, I'm supposed to look willy-nilly into some vague "recent" time?? Why would I even think intelligent intervention would be out that far? Of course, it is not my intention to focus solely on the bacterial flagellum. I do indeed plan to move on to other systems, however, lack of time is the only current constraint.
Drosera then turns to other " equally, or more, complex" IC systems. Apart from the fact that he has not shown these systems to be "equally, or more, complex," I have made it clear on both the ARN forum and my web page why I do not consider these systems good analogs for something like the bacterial flagellum. Drosera is extrapolating apples to oranges. An easy way to show this would be for Drosera to take every bit of information he has learned from these systems and actually apply it as a guide to finding evidence for the non-teleological origin of the bacterial flagellum. He'd quickly find how useless this information base would be. One would think that if we are too extrapolate, doors would open everywhere with all this new information and insight.
Consider the blood clotting example Drosera brings up. First, Miller writes:
quote:
Does the human clotting system lend itself to the same kind of analysis? At its core, the actual mechanism of clotting is remarkably simple. A fibrous, soluble protein called fibrinogen ("clot-maker") comprises about 3% of the protein in blood plasma. Fibrinogen has a sticky portion near the center of the molecule, but the sticky region is covered by little amino acid chains with negative charges. Because like charges repel, these chains keep fibrinogen molecules apart. When a clot forms, a protease (protein-cutting) enzyme clips off the charged chains. This exposes the sticky parts of the molecule, and suddenly, fibrinogens (which are now called fibrins) start to stick together, beginning the formation of a clot.
Now compare to the views of Macnab, when we learned how FliD acts as a rotating, processive chaperone used to construct the flagellar filament:
quote:
The latest technical discoveries in flagella fascinate biologists such as Robert Macnab, a professor of molecular biophysics and biochemistry at Yale University who also studies flagella. He marvels at how organisms as simple as bacteria have evolved such complex methods to develop propelling features, especially since motility in bacteria is not directly necessary for survival, like DNA replication or protein synthesis. "We think it would not be possible for the system to work with any significantly lower complexity."
Like I said, apples and oranges. (BTW, this renders Charlie's "two-part flap" quite unscientific, especially given that Macnab is a leading expert on the flagellum).
What's more, neither Drosera (nor his links) have shown that RM/NS alone are behind the evolution of these systems. Consider two excerpts from the blood clotting papers he links to:
quote:
Molecular evolution of these enzymes therefore suggests that they are descendants of an ancestral protease responsible for degradation of extracellular proteins. It is shown that the regulatory extensions of the proteases of the blood coagulation, fibrinolytic and complement cascades were assembled from domains borrowed from other proteins. Most non-protease components of these systems were also constructed by this evolutionary mechanism.
and
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Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades.
It looks to me like front-loaded evolution may be stamped all over this. I suppose it is may have been mere coincidence that an ancestral protease responsible for degrading extracellular proteins was no nicely poised to expand into a key component of the protostome and deuterostome developmental, clotting and complement cascades. On the other hand, things may have been rigged (initial states carefully selected) to increase the likelihood of such evolution, meaning that RM/NS did not function alone, but instead, was simply employed.
Drosera: but if the evolution of more complex systems, ones that are also 'IC' on Behe's authority, have significant literature indicating that scientists are making progress in understand their evolution, then why should one particular example from a much less accessible time period indicate ID?
It's not a question of the amount of complexity, but the type of complexity that finds itself in a particular context. And as I noted above, when you cite the Krebs cycle (as you did), you have completely undercut the "it's too old" excuse.
Drosera: All of the individual examples mentioned on the previous thread are just parts of a cumulative body of evidence. Molecular geneticists started with understanding how mere beneficial mutations originate and spread, then building on that to how new genes originate and spread, from there to gene families and multiple gene systems...and right now they're working on how various very complex systems like blood-clotting and the immune system originated. These efforts are proving successful, so why should we be impressed by the bacterial flagellum, which is of about equivalent complexity (maybe), just a lot older so the evidence is tougher to come by?
First of all, I am not asking you to be impressed by the bacterial flagellum. Remember that you are a naysayer posting on a forum that seeks to explore ID. I'm just pointing out why I am not impressed by the excuses as to why you have no evidence for your belief that the flagellum arose by RM/NS. As for the "cumulative body" of circumstantial evidence, I am quite sympathetic to this approach. If one has no evidence that the flagellum arose by RM/NS, one must invoke this indirect route back to the flagellum. But the point is that you can't simply plop down a laundry list of findings without demonstrating relevance to the system in question. You need to make the connections. Otherwise, you may very well have a mountain of irrelevant material. So which part of this cumulative case is relevant to the origin of the flagellum? Be specific and demonstrate the relevance.
Drosera: The existence of bioengineering before the existence of humans is completely unevidenced. However, RM/NS will exist as a logical necessity wherever imperfectly replicating systems exist and resources are limited.
The truth of the design of life does not entail that we'd have evidence of the bioengineering apart from the bioengineered things we call cells. Thus, the "unevidenced" observation is meaningless. After all, I am sure you would not find it meaningful that also we have no fossils of the hypothetical Last Universal Common Ancestor. As for the point about RM/NS, three points stand out:
1. You have no clear and unambiguous evidence that "imperfectly replicating systems" or anything else much simpler than bacteria existed prior to the origin of flagella. It is true that non-teleological metaphysics mandate belief in such things (thanks to Pasteur), but the clear evidence is not there. Yes, one can appeal to the various speculations about a universal common ancestor, but none of this amounts to clear evidence, as most of it is data interpreted through a non-teleological filter (i.e., similarities are uncritically assigned to common descent).
2. There still remains the question about the capability of RM/NS. One may assume or assert that RM/NS here and there means RM/NS behind the origin of the flagellum, but no one has really made the real connection by explaining flagellar data in this light. Why in the world, for example, do you think the origin of the blood clotting system by RM/NS translates as the origin of the bacterial flagellum by RM/NS? Be specific.
3. Your interpretations assume a non-teleological origin of life. If one accepts a teleological origin of life, then the mere existence of RM/NS, regardless of its abilities, is not enough. If you cannot outline the fingerprints of RM/NS behind the origin of the flagellum, then simply admit your explanation is not powerful enough to overcome my skeptical position. This won't prove I am right, of course. But perhaps we can agree that there is no reason that I need to think as you do.
It also seems to me that the whole analogy about Earth-moving is a faulty analogy that also begs the question. It is a faulty analogy in the sense that biology is fundamentally different from geology in many ways. For example, no one is interested in the origin of this rock formation vs. that rock formation. But even you are interested in the origin of the Krebs cycle, blood clotting, etc. Clearly, even you are not satisfied with antibiotic resistance as the basic story behind the origin of the immune system. And is the difference between this rock and that rock really equivalent to the difference between antibiotic resistance through a point mutation in a ribosome gene and the origin of the bacterial flagellum? No one has ever made that argument.
More significantly is that your analogy works only if we know that life originated through non-teleological means. Then, we can attempt to blur all biotic reality into one non-teleological mass. But as I explain above, since I already infer ID behind the first cells (that the basis for my inference may not convince you is not relevant), the analogy does not apply. Now, if we lived in a reality where there was evidence that the very first rock formations on this planet were designed, and we knew that all subsequent rock formations stemmed from those rocks to this day, then yes, I'd consider rock formations on a case-by-case basis.
Finally, Drosera writes: But no, argues Mike, on his hypothesis the designer acted to be consistent with this natural process, long ago. Never mind why a designer would feel limited to this natural pattern, or why he wouldn't use one of the many possible methods of circumventing this natural process,
And what process are you talking about? How does a functional biological feature escape the effects of mutation and the culling act of selection? Why wouldn't a designer employ RM/NS into his/her service? We often hear about the wonders of GAs. If they are so truly remarkable, don't you think life's designer would know about them and employ them?
or why he wouldn't have acted in the recent enough past so that the natural process would have had insufficient time to act..never mind all that, ID is still the preferred explanation.
Why would a designer act in the recent enough past so that natural processes would have had insufficient time to act? My thesis is that life was designed. You, on the other hand, seem to be looking/asking for the designer. There is a fundamental gap between our respective frame of reference.
[ 31 March 2002, 01:09: Message edited by: Mike Gene ]
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charlie d.
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posted 31. March 2002 09:22
Hi Mike:
I know you won't respond, but I just wanted to make myself more clear regard this:
quote:
The latest technical discoveries in flagella fascinate biologists such as Robert Macnab, a professor of molecular biophysics and biochemistry at Yale University who also studies flagella. He marvels at how organisms as simple as bacteria have evolved such complex methods to develop propelling features, especially since motility in bacteria is not directly necessary for survival, like DNA replication or protein synthesis. "We think it would not be possible for the system to work with any significantly lower complexity."
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Like I said, apples and oranges. (BTW, this renders Charlie's "two-part flap" quite unscientific, especially given that Macnab is a leading expert on the flagellum).
My point was NOT that the flagellum can work as a 2-protein flap (it can't). My point was that bacterial locomotion as efficient to that achieved by a flagellum could be - plausibly - generated by simpler systems, in which case the flagellum would seem over-engineered. Bacteria obviously use several different strategies for locomotion: is the flagellum undoubtly superior, and on what parameters (speed, energy-efficiency, maneuverability)? Has anyone analyzed this seriously? Maybe bacterial "squirming" is a much better solution.
The general issue then is that it's not always true that the more complex the machine, the more sophisticated the engineering; in fact, once the machine task is set, it is often the opposite (parsimony in design, as opposed to parsimony and Design, if you will). The adaptive value (or the "engineering goal") of any phenotype/system must be first kept in mind for any such analysis to make sense. For any problem, the simpler the solution, the better. The process of RM/NS cannot always use this "logic", because it has to work with gradual, progressively adaptive modification of existing structures, while conscious engineering can and does. However, RM/NS has been able in some instances to provide incredibly elegant solutions to complex biological problems, and we have evidence for it.
So, to claim that the flagellum is a paradigm of engineering that natural selection a priori(for complexity or "probabilistic" reasons) cannot achieve could be entirely misleading, especially if we just focus on the machine's complexity and lose sight of the organism it is working for.
[ 31 March 2002, 11:34: Message edited by: charlie d. ]
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Drosera
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posted 31. March 2002 18:48
Hi Mike,
Thanks for your...extensive...reply. You've obviously thought about these things quite a bit.
I think the main thrust of my post was this, which I think is a positive suggestion within the bounds of ISCID topics:
quote:
It seems to me, however, that for ID to get off the ground as a nascent science, it is going to have to employ the principles of parsimony and self-consistency rigorously
...perhaps things came off as somewhat critical in the details as the original post was partially written as a reply to a previous post of yours in the previous thread. Apologies. My main point though was to make the above positive suggestion.
You have said a number of interesting things about the parsimony topic, so I will think about those things and reply here. "Front-loading" seems to me to be a new creature, and as far as I can tell, significantly different than Behe's version in Darwin's Black Box, so that might not get discussed much in this thread, perhaps you could start a thread on that specifically some time and lay out more what you mean, what criteria you use for distinguishing front-loading from natural evolution, etc.. My initial take is that parsimony might be an even more severe difficulty for front-loading than for direct intervention, but that is probably best discussed in a front-loading thread or a later date.
Drosera
[ 31 March 2002, 18:50: Message edited by: Drosera ]
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Drosera
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posted 31. March 2002 21:52
Hi Mike,
I won't be able to address everything, but some salient points:
quote:
As far as the "conceptualized end" for the bacterial flagellum, without lab notes or psychic powers, one can only come up with a working hypothesis. In this case, I hypothesize that flagella were designed to disperse the originally seeded bacteria so that they, in turn, could carry out another designed end to be discussed later.
You will understand if I retain my point about conceptualized ends until I have some idea what you think the further "designed end" is. That you recognize that designers do things not just willy-nilly, but for specific ends, and that understanding these ends is really the key to perceiving "design" is, I think a key point of agreement between us...and I'm not sure this point is broadly recognized across the ID movement as a whole.
quote:
The objective at this point is to seed, take root, and spread and flagella would help. One might complain that this end is not "final" enough for a teleological approach. But consider engineering. What is the conceptualized end of the spark plugs in an engine? One can answer that question teleologically without having to address the ultimate purpose of the car.
A better analogy, I think, would be to take a set of solar power panels, and then add a whole locomotion system to them. Why the locomotion system? Sure, a locomotion system helps move the solar panels, but why do that? Why not just put them where you want them?
Even on its own terms, however, the "disperse the bacteria" explanation for flagella seems highly debatable. Brownian motion plus currents/winds will disperse things almost as well in the primitive earth -- I suspect that on the planetary scale, currents are still the dominant method of long-distance dispersal for bacteria in the ocean. I doubt that the time difference for "getting the bacteria spread all over the planet" would be significantly different with or without flagella.
And anyway, it seems that intelligent designers could seed bacteria in a whole bunch of different places around the planet if they were in a hurry, and by the way being in a hurry seems rather unlikely given the long time periods required to travel between stars.
quote:
Drosera is perplexed by the notion of an intelligent designer bothering to help out pond scum. But the issue here may be an intelligent designer crafting a set of cells to seed and transform a sterile planet. Flagella would be one component built into the cells to facilitate this objective.
Ah, I see. My "pond scum" comment only applies if one's idea is that the the designer gave bacteria just to be nice, or for the pure heck of it, or whatever. Having a larger goal, like designers usually do, makes things potentially more understandable (although see my comments above for still being skeptical of flagella specifically).
quote:
As for "the question" getting tougher when we begin to look at the pattern of IC, the response to tough questions is not resignation, but to roll up one's sleeves and get to work. Yes, one trick is looking for the pattern amidst the IC systems. And it would seem to me that the examples Drosera brings up already suggest a pattern. For example, the "immune system vs. disease infection systems" may be nothing more than the emergent dynamic that stems from the designer designing the original cells such that they would establish symbiotic relations rather than exist as autonomous islands.
Symbiosis? We're talking about diseases, which attack multicellular creatures via extremely complex mechanisms, and immune systems, which defend against these attacks via their own extremely complex mechanisms.
quote:
As cells dispersed on the planet, an impetus for symbiotic relationships would be extremely helpful in designing emergent complexity. And in fact, many traditional evolutionists argue that symbiosis is often behind the major advances in evolutionary complexity (i.e., the origin of mitochondria, the Cambrian explosion, etc.).
Symbiosis for mitochondria is well known, I've never heard of it applied to the Cambrian explosion, which is about the diversification of bilateral animals...
quote:
As for the intelligent designer communicating his existence to the future, there is no reason to think this was the intention behind the original designs. Thus, the point about putting a spaceship on the moon is irrelevant.
This was just a guess to try and figure out why you thought a designer would mimic natural selection. The original context was the strong pattern in biology that all apparent "designs" appear to have the mere "purpose" of helping to reproduce the genes of the organism. Given what we know about designers (namely us), who do not follow such a pattern in the designs they make (which instead serve the purposes of the designer), this is a very strange pattern.
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There is nothing weird at all about the notion that a designer of biological entities would factor random mutations and natural selection into the equation. Would Drosera have the designer's design such that they are ignorant of biology?
No, but to think that this pattern would be apparently universally followed makes the ID hypothesis less than parsimonious. I.e., we've got one theory, based on natural selection, that makes the strong prediction that selection-favored designs are all that should be seen. ID makes no such prediction, rather one has to have an auxilliary hypothesis to explain this observation.
Find a monument on the moon, though, and things change completely.
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As for archaeologists, they have the luxury of a vast independent base of knowledge about the designers. When it comes to the putative designers of the first cells, we don't have this luxury. In fact, the truth of the design of the first cells does not logically entail that we would have this type of knowledge.
But, to use a double-negative, it doesn't imply that we wouldn't, either.
quote:
Thus, we have a choice. We can throw in the towel and declare any attempt to explore biotic reality with the concept of design is doomed without the independent knowledge of the designers (basically the position of mainstream science) or we can recognize the truth that design does not entail we'd have access to the designers and attempt to adapt our research to this reality (the approach of IDers).
I think the proper postition would be to simply acknowledge that the whole prospect of ID in biology is extremely doubtful until someone finds something that really is better explained by an non-vague ID hypothesis rather than by modern evolutionary theory. Independent evidence of designers would qualify (e.g., a monument on the moon), as would finding a pattern that we would not expect in biology based on mutation and selection, e.g. designs with a purpose other than self (genes) reproduction.
Thanks for the Pasteur quote, although what he thoughts the implications were seems rather complicated to me...can you post the source?
quote:
One can also see my essay on the inherent metaphysical ties to spontaneous generation (and its offspring, abiogenesis) here
I wrote: The problem here is what we mean by "biological novelty" and whether all novelties are equivalent. Take erythromycin-resistance in bacteria. When this evolves and spreads, we can refer to this as a biological novelty spawned by RM/NS. But would you now argue that we have demonstrated RM/NS is sufficient cause for the origin of the bacterial flagellum? If so, please spell it out.
Rather than spell it out, Drosera invokes philosophy. For "this is where parsimony comes up." The problem is that parsimony is only as good as our frame of reference, our background knowledge. For example, at one time, parsimony dictated that proteins were the genetic material.
Whoa whoa whoa. I'll try and re-state this very clearly. Things like erythromycin-resistance, moth adaptation, etc., which you repeatedly are inappropriately using in isolation, are part of a large body of evidence for what natural mechanisms can accomplish. The origin of genes with new functions, you appear to concede, is suitably explained by mutation & selection processes. So this establishes one level of competance of natural mechanisms.
The relevance of this to things like the evolution of highly complex systems like Behe's examples of blood-clotting, the immune system, and the flagellum, is that the low-level processes that result in the capacity to build new genes, are in turn also being used to explain even higher levels of complexity. This is explicitly being done, in the peer-reviewed scientific literature, by experts, for the blood-clotting and immune systems. I have no doubt that sooner or later scientists will get around to doing it for the flagellum as well
Indeed there are hints that this is already occurring, I typed "flagellum homology" into a search engine, and pretty quickly came up with this page:
quote:
ExbB-ExbD are homologous to (but distantly related to) the MotA-MotB proteins of the Mot family (TC# 1.A.45). The latter proteins serve as the motor of the bacterial flagellum. While the MotA-B proteins have been shown to provide a transmembrane proton translocation pathway, the same has not yet been demonstrated for the ExbB-D proteins. It is expected, however, that they will serve this function and thereby energize outer membrane transport. It is likely that all of these proteins can be considered both as proton channel proteins and as pmf-dependent energizers, and that they belong in a single family.
...in other words, the same kinds of explanations that work for blood-clotting and the immune system, that of co-opting parts from different, simpler functions, appears to have the prospect of working in the case of the flagellum, as well (although it has not yet been applied in the case of the flagellum). That is the connection between citing numerous other cases where co-option has occurred, and the flagellum.
quote:
But even here, I'm afraid the appeal to parsimony won't help because Drosera and I don't share the same frame of reference. Specifically, I think the cause behind the original cells on this planet was intelligent design (and I do so because of various data patterns).
???
quote:
Drosera, I assume, thinks the original cause is found in geochemistry (this is the mainstream view). And this changes the meaning of what is considered most parsimonious. (As I have argued in other forums, the origin of life is the central question of biology. Everything else revolves around this question. To discuss the origin of the bacterial flagellum by ignoring the context set up by the origin of the first cells does not make sense to me.)
Let me put it this way. The are several aspects of the biotic world that, in my opinion, speak more strongly to a teleological origin of life than a non-teleological origin of life. Thus, from where I sit, the situation is not simply extrapolating from the non-teleological origin of antibiotic resistance to the non-teleological origin of the bacterial flagellum. Instead, it is an attempt to extrapolate from the non-teleological origin of antibiotic resistance to the non-teleological origin of the bacterial flagellum in a reality where the first cells were likely designed. Your parsimony test no longer works for me because I already admit ID as the most likely cause behind the first cells. Why does parsimony dictate that I ignore the implications of life's original design?
So you've already concluded that the origin of life was intelligently designed, and then based on that you try to use that to strengthen design inferences which would otherwise be weak? Isn't that doing things completely backwards? Behe's argument had the advantage of looking at a variety of systems with different ages, and attempted to argue that there was a pattern at all of those times. You, on the other hand, appear to be starting from the point of the least evidence in science, and then taking whatever shaky conclusion you can get from that and then "bootstrapping" that into further, even more shaky inferences.
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The only way to make your parsimony argument stick is to demonstrate that the Earth spawned life through non-teleological mechanisms. And I'm not talking about speculative models that imagine how things might have happened and then look for some supporting circumstantial evidence. I'm talking about looking at the world and explaining why the data from the world clearly indicate the Earth spawned life, that non-teleological abiogenesis did indeed happen. I'm talking about the evidence that should compel us all into thinking non-teleological abiogenesis did indeed happen on this planet.
Well, if the whole argument is about the origin of life, why don't we just drop discussion of anything else and talk about that exclusively. It seems to me that you think your design inference for the flagellum is strong *because* you already have concluded that life was designed. So again, what's the point of the flagellum? It seems extraneous to your case, yet you talk about it more than anything else.
I am of the opinion that we could simply put a '?' on the origin of life, and then work from what we know to what we don't. This is the general habit of science I think.
quote:
A quick review. My views are not built around the notion X can't evolve. Instead, I argue whether it makes more sense to attribute the origin of X to teleological or non-teleological means. The foundation for this approach lies in the design inference behind the origin of life on this planet.
As I said above, it seems to me that the believability of your argument then hangs on this, and all else is extraneous, e.g. most of the ID movement's arguments about blood clotting and flagella and whatnot.
An additional point, however, is this: how can your view be distinguished from one where life was accidentally seeded from somewhere else? E.g.:
Hypothesis #1, from Mike Gene: life was intelligently seeded
Hypothesis #2, from someone else: life was accidentally seeded by a visiting contaminated spacecraft
#1 would support all of your further implications, but #2 wouldn't, but at least on your criteria ("we wouldn't expect to find any evidence of designers") they are observationally indistinguishable.
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For once this hypothesis is accepted, the game rules change when it comes to evolution. Yes, we have evidence that things like crystallins and AFGPs evolved.
Just as an aside: doesn't this mean that Dembski's arguments are basically disproved, then?
<snipping a bunch of further stuff that appears to hang on the ID-origin of life inference>
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The ID proponent can accept these interpretations (as a teleological approach can easily tolerate and incorporate non-teleological causes). But the ID proponent feels no obligation to adhere to this type of explanation if the evidence is lacking.
...sounds pretty squishy, doesn't it?
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In fact, even if some evidence does exist, like all evidence, it is open to reinterpretation. For example, similarities are typically attributed to common descent. But such attributions are not made using a teleological null hypothesis. There are made using chance as the null hypothesis (and chance is clearly not a teleological expression).
What, exactly, would the teleological null hypothesis predict for, for example, sequence comparisons?? The same pattern as common descent? Again, all of this seems to be an elaborate attempt to promote a complicated hypothesis that, by construction, explains something that a simpler hypothesis naturally explains. This is exactly what the parsimony principle is meant to rule out.
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What this all means is that the job is most difficult and demands a case-by-case consideration to determine which explanation works best and then to determine if some form of pattern emerges. From where I sit, generic questions about "novelties" or such are not very useful, as each origin event is contingent and vulnerable to ID. For me, evidence that X evolved is not evidence that everything evolved. For it's not a question of what can happen, it's a question of what did happen (after all, things that can happen often don't happen, not to mention that ID is something that can happen).
Anyway, if the extrapolation/parsimony argument is to be embraced by all, then why bother with science any more? Why not simply take antibiotic resistance in bacteria and then use philosophy to settle these disputes once and for all? We don't need any new evidence. We don't need any new discovery. The evidence is in, the case is settled, and we can all go home.
Again, it's not just antibiotic resistance, it's a large body of features that build up to explaining complex things. Oversimplifying of the evolutionary case to mere antibiotic resistance is really overreaching.
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But that Drosera, and others, busy themselves trying to find new examples highlights that they are not quite as confident about the extrapolation argument as they advertise. If they themselves tacitly recognize its shaky foundation through not being satisfied with what has already been found, why are their skeptics supposed to be more believing?
If all evolution had was antibiotic resistance, you would have a point. But my point is that there is far, far more than that just in the extant peer-reviewed literature. That this is not widley-enough realized among ID advocates is the primary reason for bringing it up repeatedly.
We now come to specific cases of highly complex systems:
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Drosera then asserts that the flagellum is too old to expect evidence for RM/NS and argues I should instead focus on more recent events.
All I would argue is that the evidence will be somewhat slower in coming, on average, for older systems than for younger ones. See the above bit on motor protein homologies for some evidence that the evidence is beginning to come in.
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However, this claim quickly falls apart upon closer inspection. First, we can note that included in Drosera's list of examples is the Kreb's Cycle. According to traditional evolutionary theory, the Kreb's cycle is much older than the flagellum.
This depends on how old each of these are, and what "traditional evolutionary theory" you're referring to. Considering that the ordering of branches in bacteria is still in a state of flux I'm not sure that any conclusion at all has been reached on these matters.
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Thus, the complaint that the flagellum is too old is clearly special pleading. If Drosera can find evidence for the evolution of the Kreb's cycle, it's time to abandon the "it's too old" excuse.
C'mon, let's be fair here. Having enough evidence for a decent evolutionary explanation will be more or less likely depending on several factors:
#1) ...is the age of the system
#2) ...is the state of the understanding of the system
#3) ...is the state of the understanding of the system across a wide range of organisms
#4) ...is the state of the understanding of systems that are related either by homology or analogy.
...and there are probably other factors including a significant chance component.
The Krebs cycle and the flagellum may be of approximately the same age -- all we can really say at the moment is that they are both widely distributed among eubacteria, which are at least usually thought to be the most basal lifeforms.
But, in contrast to the flagellum, the Krebs cycle was figured out, basically completely, decades ago, whereas the flagellum is only approaching such a state at the moment -- and then only in a few model organisms. The archaeal flagellum, which I gather is an important nonhomologous structure that is functionally equivalent, is very poorly understood and serious molecular study has only begun in the mid-1990s. (By the way, was this flagellum designed as well? Archaea might be only 2.5 billion years old, did the designer come back so that they could disperse slightly more easily just like their eubacterial relatives?)
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Secondly, if this excuse is to have teeth, Drosera needs to tell us how old is too old. That is, at what point can we all (teleologists and non-teleologists) abandon any attempt to uncover evidence of a non-teleological origin? This cut-off point needs to be determined independently of the flagella question and we then need to reach an agreement that we'll all stop looking (since it would be futile, right?). Then we can see where the flagella fall out. Without accomplishing this feat, the excuse comes off, using the description of someone else here, as "an intellectual cop-out."
Again, we're talking about a continuum here. See above. Expecting rigid lines to be drawn is silly. All I'm saying is that "no evidence for evolution" (even if true, which is doubtful even for the flagellum), is a stronger argument for ID for more recent systems, and much weaker the further back in time you go. As age increases, there is an increasing chance for evidence to be lost just because of extinctions, losses of traits, etc.
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Third, Drosera doesn't seem to understand my position on this. It is not about looking for design "somewhere" or "anywhere." It is about fleshing out the hypothesis that the original cells were bioengineered and used to seed the planet.
We've been over this, see above. But again, (a) *why* seed the planet, and (b) even if you have a reason, like setting up a resort or something *why* seed the planet in this oh-so-slow manner?? I mean, the clock is ticking, the designers spent a good 35-40% of the sun's lifespan letting the planet schlep around with not much more than "pond scum" on it -- it just seems like a big waste. Why why why??
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Drosera asks "why the bacterial flagellum all of the time." The answer seems rather clear to me. Several scientific experts who study the flagellum have commented on how much it looks like something a human would design. What better place to start? Thus, it would seem most logical to begin with such a structure.
Similar comments have been made about the immune system and blood-clotting, I don't see why the flagellum should be singled out and considered in isolation from other complex systems.
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This is especially true when coupled with the fact that the flagellum can reasonably be said to have come into existence with bacteria (which can reasonably be interpreted as among the original cells) and that the flagellum (along with bacteria) are among the best understood biological phenomena. Why the flagellum? Because it is as focus that stems from a sound research approach.
Wait, what is that? Extrapolation from the uncertain premise that life was designed? Again, if that is your contention, that is the central part of your case that you need to make. All further extrapolations are moot until this central case is made.
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In its place, I'm supposed to look willy-nilly into some vague "recent" time?? Why would I even think intelligent intervention would be out that far?
I don't know about you, but blood-clotting and the immune system have been repeatedly cited as instances of "irreducible complexity" and therefore intelligent design. You use "irreducible complexity" repeatedly also, therefore scientific literature on the evolution of some such systems undermines the irreducible complexity argument in other situations.
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Of course, it is not my intention to focus solely on the bacterial flagellum. I do indeed plan to move on to other systems, however, lack of time is the only current constraint.
Drosera then turns to other " equally, or more, complex" IC systems. Apart from the fact that he has not shown these systems to be "equally, or more, complex,"
I would merely cite Behe. He spent significantly more time on these systems, talked an awful lot about their complexity -- he spent only 2 or 3 pages on the flagellum. Plus, there are whole books on just how the immune system works, but it seems that the basic functioning of the flagellum can be summed up in a good thorough review article.
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I have made it clear on both the ARN forum and my web page why I do not consider these systems good analogs for something like the bacterial flagellum.
...as far as I can tell, you've only made this argument for things like antibiotic resistance. But I haven't read all 1800 of your posts, so perhaps you could point me to such. I've tried to explain the connection several times in this thread, and to bring it back to parsimony: Behe has written things like "if the evolution of the flagellum *or any equivalently complex system* were shown", then he would give up his arguments (that quote was a paraphrase, just to be clear). It seems that, while Behe and I would therefore be following the principle of parsimony in ID that I am advocating in this thread, Mike Gene would not.
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Drosera is extrapolating apples to oranges.
This is a rather dangerous analogy in biology, now isn't it? ![[Smile]](smile.gif) I suspect that apples and oranges are rather closely related in the grand scheme of things. I am proud to be comparing apples and oranges, that is just the kind of comparison that I am advocating (along with equal treatment by the principle of parsimony).
Just to bring in a little humor here...
From the Annals of Improbable Research (AIR) (here)
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We have all been told that you can't compare apples and oranges, but this cliche is just not true. This volume includes an article entitled "Apples and Oranges: A Comparison", by Scott A. Sandford, which contains the transmission IR spectra of a desiccated apple and orange. In the 4000-400 cm-1 region the two spectra are remarkably similar. I think I will follow the author's suggestion and keep a copy of the figure in my wallet for use in discussions.
I'm not sure if someone has done a DNA comparison, but considering that they're both angiosperms I have a rather solid prediction based on evolutionary theory. I bet one could even get their own article in the Journal of Improbable Research...
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An easy way to show this would be for Drosera to take every bit of information he has learned from these systems and actually apply it as a guide to finding evidence for the non-teleological origin of the bacterial flagellum.
Based on those other examples, as I've stated, we should:
1) Look for analogous systems
2) Look for homologous systems with different functions
3) Look for related proteins with different functions
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He'd quickly find how useless this information base would be. One would think that if we are too extrapolate, doors would open everywhere with all this new information and insight.
...recent research seems to be indicating that scientists are using and finding all three suggested avenues, above.
<snip>
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What's more, neither Drosera (nor his links) have shown that RM/NS alone are behind the evolution of these systems. Consider two excerpts from the blood clotting papers he links to:
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Molecular evolution of these enzymes therefore suggests that they are descendants of an ancestral protease responsible for degradation of extracellular proteins. It is shown that the regulatory extensions of the proteases of the blood coagulation, fibrinolytic and complement cascades were assembled from domains borrowed from other proteins. Most non-protease components of these systems were also constructed by this evolutionary mechanism.
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and
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Here, it is proposed that a single ancestral developmental/immunity cascade gave rise to the protostome and deuterostome developmental, clotting and complement cascades.
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But this is exactly what I've been talking about, namely that the very processes that you brush off as accounting for things like the origin of antifreeze genes, appear to be working just fine in explaining the origin of these highly complex systems!!
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It looks to me like front-loaded evolution may be stamped all over this. I suppose it is may have been mere coincidence that an ancestral protease responsible for degrading extracellular proteins was no nicely poised to expand into a key component of the protostome and deuterostome developmental, clotting and complement cascades. On the other hand, things may have been rigged (initial states carefully selected) to increase the likelihood of such evolution, meaning that RM/NS did not function alone, but instead, was simply employed.
Mike's "front-loading" is another entire topic methinks. How can one protein be front-loaded for so many different things?? Isn't it just that a proteases can be proteases on many different things? And anyhow, isn't this even less accessible to empirical testing that than everything we've b | | |
