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Author
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Topic: The Other Flagellum
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Mike Gene
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Member # 149
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posted 21. August 2003 15:44
I’m getting close to my self-imposed 50-rule, so I am not going to introduce new data/arguments in my replies. Instead, I’ll save that type of thing for a new thread related to this topic. Let me now reply to Yersinia.
Behe doesn’t describe the IC components of the flagellum “in fine print.” It is explicitly and clearly spelled out. For example, I was never under the impression that Behe was contending the 9+2 structure is the only way to make a working cilium or flagellum. Maybe one needs a dull axe to see that.
As for the variations away from the 9+2 structure, they appear both rare and derived. If we consider Miller’s list, this is clearly the case with the flagella in eel sperm and mosquito. Diplauxis hatti and Lecudina tuzetae are protozoa, but both are parasitic apicomplexans. Like many parasites, we’re probably looking at stream-lined structures. This is supported by fact that apicomplexans are typically nonmotile and the 3+0 and 6+0 flagella appear only in the specialized male gamete cells. In constrast, the 9+2 structure is widely distributed among protozoa, including trypanosomes, euglena, algae, tetrahymena, dinoflagellates, giardia, paramecium, etc. It would be fun to explore the significance of all this in more detail.
As for front-loading and fuzzy word pictures, I have always been upfront that my fuzzy views about front-loading are speculations and I am exploring the plausibility of the concept. Essentially, they amount to fleshing out an alternative perspective such that traditional non-teleological interpretations are not mandated. Anyway, I’ll eventually bring the front-loading perspective on-line regarding this discussion, as it was, after all, behind my efforts to take a second look at the flagellum.
Now, you would think those who actually believe the eukaryotic flagellum was spawned by Darwinian evolution should likewise admit their notion is mostly speculation and remains stuck in the realm of establishing plausibility. Yet for some reason, such admissions are rare to come by in these contexts.
You note that “cargo transport up and down microtubules with kinesin and dynein-based motors is a common function not restricted to cilia.” Yep. Yet this doesn’t really mean much. For example, as explained in the OP, if you knock out cDhc1b, no functioning flagella are assembled. Yet the cells with this knock out still have cargo transport up and down microtubules with kinesin and dynein-based motors. Clearly, a cell having cargo transport up and down microtubules with kinesin and dynein-based motors is not sufficient for assembling a flagellum.
As for your prediction about cilia construction proteins with homologs, this is not a prediction that stems from Darwinian philosophy. Why not simply argue that several junk sequences were translated and just happened to generate primitive proto-cilia transport proteins and were thus selectively advantageous? Is there something non-Darwinian about that?
The prediction stems from the observation that that evolution borrows. But what is the meaning of this prediction? If, for example, it turns out that many of the components of the assembly machinery don’t have homologs in intracellular transport, will you concede that the flagellum didn’t evolve?
You seem to think I am criticizing evolutionary theory for lacking details. Yet all I am pointing out is that the Darwinian speculation concerning the origin of the flagellum is unconvincing due to lack of evidence and coherency. And as we have begun to figure out the process of assembly, the emerging data paint a picture of a decent IC challenge that only makes the situation worse for the Darwinian perspective.
You then cite the Sdic example to illustrate how cilia-specific proteins could originate from intracellular ones and as an example of how it can happen. Yet I am not arguing that it could not happen or cannot happen (I’ve made this clear for a long time now), thus the example is essentially inconsequential if that’s all you are doing. It is interesting, however, and probably would be worth talking about in another context (note my comments on modularity and dynein in the OP), as it also demonstrates how front-loading could work. Anyway, remember that the thesis of a designed flagellum does not entail that the flagellum could not be tweaked by evolution.
More to the point is whether or not you think the flagellum would be easy or difficult to evolve. Where do you stand on this?
You then make a rather odd observation:
quote:
Y'see, in your head, you are trying to imagine the cilium assembling out of the blue in the cytoplasm.
I would think it was obvious from my OP (and follow-ups) that I am not doing this. For just one example, I just noted: “The burden of the gradualist is to reduce this IC list into smaller chunks, using hypothetical alternative functions along the way; to put flagellar origins in the reach of coincidental cooption.” That the flagella/cilia are elaborate extensions of the cytoskeleton really tells us nothing about their origin. Cavalier-Smith had the chance to respond to Behe’s claim about cilia. Rather than provide us the evidence for their Darwinian evolution, he too focused on the 9+2 straw man.
You then write something interesting:
quote:
You don't just have to address axopodia, you have to make the case that nonmotile appendages would be unselectable. Otherwise, it is obvious that a cilium-like motility system doesn't have to come about all at once, which is the IC argument.
I’m simply using IC as a guide at this point, as it leads me to another pattern that suggests ID (more on that later). I don’t agree that I have to make the case for unselectable nonmotile appendages. That’s really dead end approach given you and PvM are free to imagine selectable states and there doesn’t seem to be a way to test your claims. My discussion on axopodia helps put the spotlight on this type of philosophy. As I noted, the vague and brief selection story you cite would have us predict that axopodia should have evolved into flagella-like things. But they haven’t. Note Mesk’s reply. He doesn’t buy the prediction, in part because “we know nothing about whether or not there are any selective pressures which would favour the generation of such a structure.” Well, the same holds for the flagellum. Imagining untestable, vague selection pressures simply to fit the needs of a story is really no different from the technique of the evolutionary psychologists. Look, don’t take this the wrong way. I am not saying that the Darwinian hypothesis is wrong. In fact, I am not even arguing it is unreasonable. As I said, I simply find it unconvincing. Thus, the real question is whether you think this skepticism/denial of the Darwinian hypothesis regarding the flagellum is unreasonable. Am I being unreasonable for not accepting the Darwinian explanation for the origin of the flagella?
Finally, I do agree that we nee a lot more research on protozoa (and lots of genomes). This is one reason I have long focused on the bacterial flagellum. While people like you have tried to spin my focus as some type of ploy to get away from the realm where evidence exists, the fact is that we have a much larger set of data with the bacteria. Nevertheless, my life span won’t allow me to wait for the protozoan work to catch up, so I do as all people do – make the best with what we have and ensure any conclusion is blatantly tentative. But the data that are beginning to emerge are intriguing – for example, the conceptual similarities between the eukaryotic flagellum and F-ATP synthases, along with the realization that the functioning of the flagellum is far more sophisticated than we originally thought.
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yersinia
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Member # 324
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posted 21. August 2003 16:58
Well, gee Mike, I'm not sure what more you want, given current evidence and my inability to (a) sequence genomes or (b) survey 100 years of protozoan studies in several languages. Your skepticism is based on lack of details in the evolutionary scenario, and the necessary basic knowledge to reach your demanding level of detail (a standard which you've never applied to your or anyone else's ID theories) simply doesn't exist. I've shown that the parts are available in nonflagellar contexts, the molecular transitions to retarget parts (such as with Sdic) are easy to accomplish, and pre-motility intermediate stages are selectable. None of this would be expected if Behe's IC argument -- that systems have to exist all-put-together or not-at-all were correct.
You'll get some more details on how it happened by reading Cavalier-Smith's articles, which (after some development in his ideas over the years) tie cilial evolution into a moderately late stage of his scheme for the evolution of mitosis. You always criticize Cavalier-Smith for not rebutting Behe in detail in his 1-page book review, but what Cavalier-Smith did was reference a bunch of his articles which Behe never addressed. If you and Nelson won't seriously consider the connection to mitosis (Nelson fails to realize that cilial basal bodies are centrioles, which are commonly found in centrosomes, which are in the center of spindles), then you're not even going to be in the ballpark about the big picture of the likely evolutionary scenario. It's like discussing the evolution of the bacterial flagellum with no mention of type III secretion.
Here's *some* of the references that someone would have to deal with to even have a chance of giving a serious challenge to evolution on the topic of the eukaryotic flagellum:
quote:
Co-evolution of cilia and the cytoskeleton
The autogenous origin of cilia
Was the first eukaryote an amoeba or a heliozoan without any cilia or a flagellate with one or more cilia? Since centrosomes are the nucleating sites for centrioles, which in turn nucleate ciliary growth, and since DNA segregation is much more basically essential for cell viability than ciliary motility, they probably, at least slightly, preceded the origin of the vastly more complex cilia (probably needing about 1000 genes). The long drawn-out love affair of Margulis (1970) with the notion that cilia evolved from motile bacterial ectosymbionts (Kozo-Polyansky, 1924) implausibly assumes the reverse, but is unperturbed by this or by the total absence of any chemical, functional or phylogenetic evidence for its basic assumption of a connection between spirochaete and ciliary motility (Cavalier-Smith, 1978a, 1982b, 1992b); its latest reincarnation (Margulis et al., 2000) is as devoid as earlier ones of any recognition of the scientific necessity to be explicit about the structural and functional changes postulated in evolutionary transformations or the utility of Occam's razor. I agree with Margulis only on the ancientness of the connection between nuclei and cilia, seen so well in her favourite complex hairy flagellates. I have long argued that indirect attachment of a single cilium to the nucleus via the centrosome was the ancestral state for all eukaryotes with cilia (Cavalier-Smith, 1982b, 1987c, 1991c, d, 1992c). I argued that a single cilium arose in association with the origin of the nucleus prior to the eukaryotic cenancestor and, thus, postulated that there are no extant primitively non-ciliate eukaryotes. I shall not add to those earlier detailed treatments of the autogenous (non-symbiogenetic) origin of cilia, but will concentrate on the phylogenetic implications of ciliary root structure in the light of increased recognition of the fundamental importance of the remarkable phenomenon of ciliary transformation for understanding eukaryote cell evolution (Cavalier-Smith, 2000a; Moestrup, 2000).
(from: Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol. 2002 Mar;52(Pt 2):297-354. )
[...]
Cavalier-Smith, T. (1978). "The evolutionary origin and phylogeny of microtubules, mitotic spindles and eukaryote flagella." Biosystems, 10(1-2): 93-114. [21]
Cavalier-Smith, T. (1982). "The evolutionary origin and phylogeny of eukaryote flagella." Symposia of the Societyfor Experimental Biology, 35(5896): 465-493. [22]
Cavalier-Smith, T. (1987c). "The origin of eukaryotic and archaebacterial cells." Annals of the New York Academyof Sciences: Endocytobiology III, 503(6111): 17-54. [24]
Cavalier-Smith, T. (1991c). "The Evolution of Prokaryotic and Eukaryotic Cells," in Fundamentals of Medical Cell Biology: Evolutionary Biology. E. Edward Bittar. London, JAI Press. 1:217-272.
Cavalier-Smith, T. (1991d). "Archamoebae the Ancestral Eukaryotes?" Biosystems, 25(1-2): 25-38. [27]
Cavalier-Smith, T. (1992c). "Origin of the cytoskeleton," in The Origin and evolution of the cell: Conferenceon the Origin and Evolution of Prokaryotic and Eukaryotic Cells. Shimoda, Japan April 22-25, 1992. H. Matsuno Hartman, K. Singapore, World Scientific Publishing Co.: 79-106. [29]
I think Behe missed all of these except for the 1978 article (IIRC).
(and, the quote handily confirms what I was saying about the connections between spindles, centrosomes, nucleus, cilia, etc.)
If you really want to have a potentially impressive argument, Mike, write up a critique of Cavalier-Smith's and related work, propose a more detailed alternative explanation, publish it somewhere, and then see what Cavalier-Smith comes back with. We keep experts around for a reason...
Until that happens, you'll be in the same boat as Behe on the cilium, and Cavalier-Smith's critique of Behe on the cilium will still apply:
quote:
[W]hen criticizing existing evolutionary explanations, Behe uses intellectually dishonest double standards. He dismisses my first treatment of the origin of cilia [2] [footnote 2: the 1978 paper] as non-quantitative and therefore 'utterly useless', and ignores my later work on the topic [3,4] [these are the 1982 and 1987 papers, respectively]. But it does not worry him that his empty, religious notion of 'intelligent design' is equally non-quantitative; worse still, lacking in even qualitative detail of what did the designing, and how the hypothetical design was executed, it explains nothing. He states that 'if a theory claims to be able to explain some phenomenon but does not even generate an attempt at an explanation is should be banished' and 'without details, discussion is doomed to be unscientific and fruitless'. If he had applied these strictures to his panacea of 'intelligent design' we would have been spared this worthless book.
[ 21. August 2003, 17:01: Message edited by: yersinia ]
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Nel
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posted 21. August 2003 18:12
Nic writes:
quote:
If you and Nelson won't seriously consider the connection to mitosis (Nelson fails to realize that cilial basal bodies are centrioles, which are commonly found in centrosomes, which are in the center of spindles), then you're not even going to be in the ballpark about the big picture of the likely evolutionary scenario.
Actually, I already addressed most of C-S's contention concerning cilia/nucleus. Also, there are differences between centrioles and basal bodies. The spindle centriole does provide the basal body from which the cilium grows, but that has nothing to do with what I said concerning why a cilium protrudes from a cell. I don't see any of the evolutionary scenarios as likely.
C-S:
quote:
But it does not worry him that his empty, religious notion of 'intelligent design' is equally non-quantitative; worse still, lacking in even qualitative detail of what did the designing, and how the hypothetical design was executed, it explains nothing.
ID is not a religious notion although some do see religious implications. He is also wrong to say that it explains nothing. The design notion explains, just one example, the similarity between the rotating mechanism of the ATP synthase and the cilium. Also, Mike has addressed the "we don't know how it was executed" argument countless times for example here
[ 21. August 2003, 18:14: Message edited by: Nelson-Alonso ]
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RBH
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Member # 380
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posted 21. August 2003 22:51
Nelson-Alonso wrote quote:
The design notion explains, just one example, the similarity between the rotating mechanism of the ATP synthase and the cilium.
Okey dokie. What is the explanation that the design notion offers? Please, in a couple of paragraphs or so, provide the design explanation of that similarity. Along the way you might mention which design notion offers that explanation: front-loading (Mike Gene and Michael Behe), intermittent intervention through deep time (Dembski), instantaneous creation (Paul Nelson (?)), or whatever else might be available. I have never yet read an actual design explanation,, and I'd sure like to see one before I die.
RBH
[ 21. August 2003, 23:00: Message edited by: RBH ]
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Nel
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posted 21. August 2003 22:57
RBH writes:
quote:
Okey dokie. What is the explanation that the design notion offers? Please, in a couple of paragraphs or so, provide the design explanation of that similarity.
A designer with one conceptual way of doing things (or designers with a common plan). No need for a couple of paragraphs.
RBH writes:
quote:
Along the way you might mention which design notion offers that explanation: front-loading (Mike Gene and Michael Behe), intermittent intervention through time (Dembski), instantaneous creation (Paul Nelson), or whatever else might be available.
As Mike noted, the find supports either extrinsic factors or intrinsic principles.
RBH writes:
quote:
I have never yet read an actual design explanation,, and I'd sure like to see one before I die.
No. You have ignored actual design explanations. I have yet to see you actually respond to one.
[ 21. August 2003, 23:00: Message edited by: Nelson-Alonso ]
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RBH
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posted 21. August 2003 23:15
Nelson-Alonso wrote quote:
A designer with one conceptual way of doing things (or designers with a common plan). No need for a couple of paragraphs.
That invokes a property attributed to a designer. What grounds are there for that attribution?
Nelson-Alonso further wrote quote:
No. You have ignored actual design explanations. I have yet to see you actually respond to one.
If what Nelson-Alonso means by design "explanation" is represented in his posting, I still have yet to see an explanation. I'd expect an explanation to give us some notion of what was done, how it was done, when it was done, and maybe even what or who did whatever it did in order to produce the phenomenon to be explained. Things like that would constitute a design explanation. Saying (in effect) 'the designer(s) did it the same way twice' is far from an explanation of anything. It merely replaces one unknown (the similarity) with another (the designer did it that way).
RBH
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Nel
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posted 21. August 2003 23:21
RBH wrote:
quote:
That invokes a property attributed to a designer. What grounds are there for that attribution?
The conceptual similarity.
RBH writes
quote:
If what Nelson-Alonso means by design "explanation" is represented in his posting, I still have yet to see an explanation. I'd expect an explanation to give us some notion of what was done, how it was done, when it was done, and maybe even what or who did whatever it did in order to produce the phenomenon to be explained.
This is what I mean when I say you have yet to respond to an explanation. Delineation of design does not entail knowing who what how the design was implemented. Can you respond to the link above instead of repeating this?
RBH wrote:
quote:
Saying (in effect) 'the designer(s) did it the same way twice' is far from an explanation of anything. It merely replaces one unknown (the similarity) with another (the designer did it that way).
No, it explains why we see similar mechanisms in two completely unrelated and very different systems. That is a question that begs for an answer.
[ 21. August 2003, 23:24: Message edited by: Nelson-Alonso ]
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Mike Gene
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posted 22. August 2003 00:17
Nic,
As I mentioned, I’m up against my own posting limit, so this will be my last reply in this thread.
You begin by portraying me as someone demanding a “level of detail” that simply does not exist. You say that I “always criticize” C-S for “not rebutting Behe in detail.” Yet I am not making a fuss about details. In fact, I addressed this issue in my OP. What was it that I said about C-S?
quote:
Cavalier-Smith had the chance to respond to Behe’s claim about cilia. Rather than provide us the evidence for their Darwinian evolution, he too focused on the 9+2 straw man.
Is evidence for the Darwinian evolution of the flagellum now a detail we need not worry about? That is the odd thing about Darwinian science. Even though I don’t need a lot of detail (as I will eventually explain) and am sympathetic to the ambiguities inherent in reconstructing deeply ancient history, the disdain that is expressed when details are demanded is of concern. The proper way to adjust to the lack of details is not to attack the skeptic for his/her sinful incredulity (to the point where a true believer like Dawkins turns skepticism into a logical fallacy), but too adjust one’s conclusions so they match the missing details. Put simply, the Darwinian evolution of the eukaryotic flagellum is only a working hypothesis . It is not an established fact. It is not a well supported theory. It is a squishy, working hypothesis. Given the lack of details, it can not be anything other. There is nothing wrong with admitting this, as it doesn’t in some way invalidate the Darwinian explanation nor mandate ID. Science often puts up with squishy, working hypotheses. However, I can understand that in the political climate surrounding these debates, admitting something as only a working hypothesis can be counterproductive to a group with an agenda at stake.
The problem comes when someone wants to portray the Darwinian evolution of the flagellum as something more than a working hypothesis. When this step is taken, the demand for details is entirely appropriate. It’s a matter of shouldering one’s epistemic burden. Insist that the Darwinian evolution of the flagellum is plausible and I will agree that the level of detail we have today supports this contention. Insist that the flagellum did indeed evolve by Darwinian evolution and I will not agree that the level of detail we have today supports this contention.
Let’s now turn to the things you claim to have shown.
1. “The parts are available in nonflagellar contexts.” Yet the flagellum is composed of over 200 parts. All you have offered is a retread of the same cooption story that talks only of the MTs and motors. For example, which one of the 16-or-so IFT raft proteins also plays a role in nonflagellar contexts? As for the dyneins and kinesins, I agree that the gene duplication story is inherently plausible. Your Sdic example even lends modest support here. But a deeper look (as I began in the OP) renders this plausibility more fuzzy than you seem aware. For example, I noted that in algae, the flagellum uses 16 different versions of dynein heavy chains (alone). What if it turns out that 4 of these are simultaneously required to impart motility? Yes, I know, we can always imagine some ill-defined protrusion with some ill-defined function that just happens to supply a selective route. But that’s just more fuzz.
2. “The molecular transitions to retarget parts (such as with Sdic) are easy to accomplish.” I suppose it’s always relatively easy to retarget parts, but the question is whether such retargeting is biologically meaningful and/or advantageous and how “easy” that is. More to the point would be the minimal number of fortuitous retargeting events needed to spawn the flagellum and thus how easy that would be. The Sdic example would bring something to the table if I were denying that cooption can happen. But I am not.
3. “Pre-motility intermediate stages are selectable.” You cite only one “stage” – some vague protrusion. Whether the protrusions you imagine are truly selectable is not something that has been shown. You’ve merely asserted it. If we can get to the point where there is data that show these are indeed “selectable,” we can then determine how sensitive this selective value is to the environmental context. The axopodia example I mentioned suggests your selectable states are not universally applicable. Finally, it’s then a question of demonstrating that any particular selectable state was relevant to the origin of the flagellum.
Back to details. Earlier you lamented the lack of details on this topic and came up with six reasons for this state. But now you seem to be arguing that C-S has a pretty good grasp on the issue. Which is it? My suggestion is to start a new thread and simply spell out C-S’s argument and supporting evidence. The quote you provide shows that C-S is still bickering with Margulis about whether mitosis or cilia came first. But that’s not a debate that sheds light on the issue I have brought to the table. For example, note C-S’s argument:
quote:
Since centrosomes are the nucleating sites for centrioles, which in turn nucleate ciliary growth, and since DNA segregation is much more basically essential for cell viability than ciliary motility, they probably, at least slightly, preceded the origin of the vastly more complex cilia (probably needing about 1000 genes).
This argument is meaningless in the context of whether or not the flagellum was designed. More significant, however, is this:
quote:
I argued that a single cilium arose in association with the origin of the nucleus prior to the eukaryotic cenancestor and, thus, postulated that there are no extant primitively non-ciliate eukaryotes.
It would seem the origin of the 9+2 flagellum coincides with the origin of eukaryotes. That’s an ID friendly realization. More later.
Anyway, you keep making an issue of “the connections between spindles, centrosomes, nucleus, cilia, etc.” Yeah, they are called microtubules. MTs are fascinating structures at the heart of the eukaryotic existence. That they, and their motors, are exploited to carry out different functions is not an argument for the Darwinian evolution of the cilia.
I appreciate your advice for my struggle to come up with a “potentially impressive argument.” The mere potential for impressiveness seems forever beyond my reach. Such is the fate of the ID theorist, eh? But I think you are correct in that I should look more closely at C-S’s speculations. Since authors often tend to rehash their same arguments in different contexts, could you suggest which article (or two) is the best one at making the case? Time is not something I have too much of.
Anyway, since I’m past my limit, I’ll let you have the last word. But I’d like to have you address three of the questions in my earlier reply that you must have missed:
1. If, for example, it turns out that many of the components of the assembly machinery don’t have homologs in intracellular transport, will you concede that the flagellum didn’t evolve?
2. More to the point is whether or not you think the flagellum would be easy or difficult to evolve. Where do you stand on this?
3. Am I being unreasonable for not accepting the Darwinian explanation for the origin of the flagella?
In a week or so, I’ll start up another thread to explore another IC aspect of the flagellum that has ironically come to my attention because of Miller’s critique. I’ll also try to add some more stuff about IFT(as promised in the OP). And hopefully get to the front-loading angle. And perhaps even the pattern that leads me to suspect ID.
[ 22. August 2003, 00:18: Message edited by: Mike Gene ]
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RBH
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posted 22. August 2003 00:23
Nelson-Alonso wrote quote:
RBH wrote: quote:
That invokes a property attributed to a designer. What grounds are there for that attribution?
The conceptual similarity.
The conceptual similarity of two phenomena is the grounds for attributing a property to the designer(s) that explains the conceptual similarity of the phenomena that is the basis for the attribution. That's as tight a circle as I've seen in some time.
Nelson-Alonso further wrote quote:
This is what I mean when I say you have yet to respond to an explanation. Delineation of design does not entail knowing who what how the design was implemented.
What does it entail, then? The mere assertion of common design? "Delineation of design" is not what was claimed a couple of posts ago; Nelson-Alonso claimed that a design explanation was available: "The design notion explains, just one example, the similarity between the rotating mechanism of the ATP synthase and the cilium" (emphasis added). But once again, the phenomenon is "explained" by attributing a property to the purported designer(s) - consistency of design themes - that is the property of the phenomenon that is to be explained. As I said, it's replacing one unknown with another. Nothing more is offered: it's the way it is because that's the way the designer(s) did it. That's not an explanation in any useful or informative sense. I have still not seen a design "explanation."
Finally, in response to my remark that saying 'the designer did it the same way twice' is far from an explanation, Nelson-Alonso wrote quote:
No, it explains why we see similar mechanisms in two completely unrelated and very different systems. That is a question that begs for an answer.
It may beg for an answer, but "answering" it by attributing the property to be explained to an otherwise unknowable designer(s) does not answer anything; it merely displaces the question. As I said, it replaces one unknown (similar phenomena) with another (unknown designer(s) that design similar phenomena). And that is not an explanation.
RBH
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yersinia
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posted 22. August 2003 06:02
Well durn it, I think I got hit by the blaster worm halfway through my reply. Everyone make sure you've got your firewalls turned on and go to microsoft.com to get the patch etc., or you'll find your machine crashing for no reason.
I lack the energy to retype everything. Basically it is the describing of perfectly reasonable ideas as "fuzz" that gets me going, and then Mike more-or-less asking that I do all of his research for him, e.g. surveying nonmotile appendages across dozens of protozoan phyla, which is what it would take to answer just one doubt from his apparently bottomless pit of doubts.
As for which of those articles to read, I've read them all, and there isn't just one to recommend, because for TCS the cilium is just a small part of a much larger investigation about the origin of eukaryotes. Plus, he is continually updating his thinking based on new information, so if I recommend a recent publication, you'll find he keeps referring to his older publications, but if I recommend an old one, then the reader will be unaware of which parts TCS has changed, and which not.
I guess if Mike conceeds that the evolution of the cilium is plausible, then I'm basically satisfied. All I can really do to try and communicate what I've been trying to convey is recount my own experience reading Cavalier-Smith's stuff. I read Behe originally in 1997 or 1998, and thought he had at least had some good questions that needed answers, and initially took his word for it that those answers weren't out there in the literature. Ah, well, perhaps there is something worrisome for evolution in this, I thought. Then, while doing other research, I stumbled across TCS' review of Behe in TREE completely by accident. Hmm, I thought, here's some big articles referenced I hadn't heard about from Behe. So I looked them up, and some related ones, etc. It gradually became clear to me that people like Cavalier-Smith were operating several orders of magnitude beyond where the actual ID debate was taking place. The sheer amount of background a guy like TCS has is amazing. The guy has written hundreds of articles, most of them very long, on just the topics that ID claims evolutionists have no clue about. At some point it became clear to me that (a) all I was ever going to achieve was a general understanding of TCS' thinking on these issue, because it would take years of study to get to something like his level of background (b) that no IDists were even on the same scholarly plane of existence, let alone ballpark, as this guy, and that (c) until an IDist took him on, on his own terms, with comparable levels of detail, that ID would never represent a serious intellectual challenge to evolutionary theory on eukaryote-origins-type topics. Later reading on things like blood-clotting and the immune system showed that Behe was way off base on these topics as well, and that ID arguments relied much more heavily on pretending that literature didn't exist, rather than taking it on and seriously rebutting it. We can see this trend even in this thread, where Mike keeps asking where TCS's details are (in his 1 page review of Behe), instead of looking at the references that TCS cited in the article. Book reviews don't contain detailed arguments, that's what articles are for.
There's only so much a non-expert like me can do for you folks. The academic literature is not tailor-made for answering the very peculiar objections of IDists. I can't re-type every article I've read, or summarize a dozen 30-page articles on eukaryote evolution, which I only partially understand. I recommend that everyone go to PubMed, type in "Cavalier-Smith" and start reading. You'll get a more references not in PubMed from the Science Citation Index, several important articles are chapters in various edited books. Many of the refs can be found in that 2002 article I referenced above, as well -- the 2001-2002 articles, 200+ pages when put together, were kind of Cavalier-Smith's most recent update of his work.
PS: Oh yeah, last summer I tried to write up kind of a summary of what I learned on this topic. It was originally posted at Wikipedia but that wasn't really a good place for it. I recently reposted it here: Evolution of flagella
PPS: There's more to life than axopodia. Axostyles, for instance:
quote:
http://www.jcb.org/cgi/content/abstract/80/3/521
Motility of the microtubular axostyle in Pyrsonympha
GM Langford and S Inoue
The rhythmic movement of the microtubular axostyle in the termite flagellate, Pyrsonympha vertens, was analyzed with polarization and electron microscopy. The protozoan axostyle is birefringent as a result of the semi-crystalline alignment of approximately 2,000 microtubules. The birefringence of the organelle permits analysis of the beat pattern in vivo. Modifications of the beat pattern were achieved with visible and UV microbeam irradiation. The beating axostyle is helically twisted and has two principal movements, one resembling ciliary and the other flagellar beating. The anterior portion of the beating axostyle has effective and recovery phases with each beat thereby simulating the flexural motion of a beating cilium. Undulations develop from the flexural flipping motion of the anterior segment and travel along the axostyle like flagellar waves. The shape of the waves differs from that of flagellar waves, however, and are described as sawtooth waves. The propagating sawtooth waves contain a sharp bend, approximately 3 micron in length, made up of two opposing flexures followed by a straight helical segment approximately 23 micron long. The average wavelength is approximately 25 micron, and three to four sawtooth waves travel along the axostyle at one time. The bends are nearly planar and can travel in either direction along the axostyle with equal velocity. At temperatures between 5 degrees and 30 degrees C, one sees a proportionate increase or decrease in wave propagation velocity as the temperature is raised or lowered. Beating stops below 5 degrees C but will resume if the preparation is warmed. A microbeam of visible light shone on a small segment of the axostyle causes the typical sawtooth waves to transform into short sine-like waves that accumulate in the area irradiated. Waves entering the affected region appear to stimulate waves already accumulated there to move, and waves that emerge take on the normal sawtooth wave pattern. The effective wavelengths of visible light capable of modifying the wave pattern is in the blue region of the spectrum. The axostyle is severed when irradiated with an intense microbeam of UV light. Short segments of axostyle produced by severing it at two places with a UV microbeam can curl upon themselves into shapes resembling lockwashers. We propose that the sawtooth waves in the axostyle of P. vertens are generated by interrow cross-bridges which are active in the straight regions.
...sounds like the re-evolution of cilia, except of course they're not cilia. So in answer to Mike's question, I think that the evolution of motility is relatively easy; but you'll probably never get exactly the same thing (e.g. cilia) twice, and you'll mostly only get a new mode of motility if the ancestral one (cilia, as it happened, for us) is lost or inadequate for some reason. Otherwise its easier to modified the motile appendage you've got (e.g. the super-cilia of drosophila sperm -- centimeters long).
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Nel
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posted 22. August 2003 11:55
RBH wrote:
quote:
The conceptual similarity of two phenomena is the grounds for attributing a property to the designer(s) that explains the conceptual similarity of the phenomena that is the basis for the attribution. That's as tight a circle as I've seen in some time.
It's only a circle because you keep repeating it in a sentence. So you create the illusion of a circle. I can do the same thing. Darwinian evolution explains the similarity between two gene sequences because of common descent because it explains the similarity between two gene sequences which is the basis for common descent.
However it is clearly not a circle.
The conceptual similarity between both mechanisms is explained by "mind". How this is circular reasoning is beyond me.
RBH wrote:
quote:
What does it entail, then? The mere assertion of common design?
Looking at two complex systems and realizing that they bear the hallmarks of design (machine-like complexity) and the fingerprint of "mind" (conceptual similarity).
RBH writes:
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"Delineation of design" is not what was claimed a couple of posts ago; Nelson-Alonso claimed that a design explanation was available: "The design notion explains, just one example, the similarity between the rotating mechanism of the ATP synthase and the cilium" (emphasis added).
That is precisely the delineation of design. You must first delineate design before you can find the conceptual tie between two designs.
RBH writes:
quote:
But once again, the phenomenon is "explained" by attributing a property to the purported designer(s) - consistency of design themes - that is the property of the phenomenon that is to be explained. As I said, it's replacing one unknown with another.
It's not an unknown. ID is hypothesizing that the cause was an intelligent agent with advanced human-like intelligence. If what you mean by "unknown" is the identity of the designer, I would have to ask what the relevance of that is in this context.
RBH writes:
quote:
Nothing more is offered: it's the way it is because that's the way the designer(s) did it. That's not an explanation in any useful or informative sense."
No, what is offered is an explanation for the conceptual similarity between two systems that are completely different and unrelated. It's a great explanation, one that I use often when I see a conceptual similarity between two systems. For example, many in the computer science field see conceptual similarities between LE and Microsoft's .NET, so some have made the inference that Microsoft was "watching" IBM. I have no idea who wrote those programs, or when, or how. However, I see conceptual ties between the two programs, not otherwise explainable except through common design, the ties are too complex to be mere coincidence.
RBh wrote:
RBH writes:
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It may beg for an answer, but "answering" it by attributing the property to be explained to an otherwise unknowable designer(s) does not answer anything; it merely displaces the question.
Sure it does. Attributing it to intelligent agency explains it (there is of course still a lot of questions, but good research always leaves open ends). I don't know , and may never know, who designed LE and .NET, or TPU and EMACS. What is important is best explained by design, rather then mere coincidence.
[ 22. August 2003, 13:36: Message edited by: Nelson-Alonso ]
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Nel
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posted 22. August 2003 12:12
I am just now realizing that Nic is getting all of this from Cavalier-Smith, even the axostyle business.
quote:
"[Behe] does not mention the evidence that...other motility organelles much simpler than cilia, for example, protozoan axostyles, evolved from bundles of microtubules by acquiring the capacity to bend, which he implies is impossible."
This quote is taken from Cavalier-Smith (from Wikipedia) which contains a lot of the issues we discussed. It would be interesting to actually look into axostyles to see if it is just another black box or if it truly is a "simpler cilia". I'll get back to that.
[ 26. August 2003, 17:41: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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posted 22. August 2003 12:13
Nelson: Pim thats talking about the bacterial flagellum and has nothing to do with Mike's question. That essay is discussing the possible origin of the bacterial flagellum from an ATP synthase.
Was Mike not talking about the flagellum and ATP synthase? What am I missing here Nelson?
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Nel
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posted 22. August 2003 12:16
Pim,
You do realize, that the bacterial flagellum and the eukaryotic flagellum are two completely different systems?
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yersinia
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posted 22. August 2003 16:01
quote:
Nelson: Pim thats talking about the bacterial flagellum and has nothing to do with Mike's question. That essay is discussing the possible origin of the bacterial flagellum from an ATP synthase.
Was Mike not talking about the flagellum and ATP synthase? What am I missing here Nelson?
Here, they were talking about a "similarity" (a very dubious, vague mechanistic similarity AFAICT) between the eukaryotic cilium/flagellum and the ATP synthase (found in all organisms in various versions, the bacterial one is the F0F1-ATP synth(et)ase.
There are *also* similarities between bacterial flagella and the ATP synthetase, including the fact that both have rotary motors powered by ion force, and have a protein with published homology. But this is different than what they're talking about here.
For the drastic differences between eukaryotic cilia/flagella and bacterial flagella, see here:
http://wiki.cotch.net/wiki.phtml?title=Flagellum
PS: Nelson writes,
quote:
I am just now realizing that Nic is getting all of this from Cavalier-Smith, even the axostyle business.
Ah, the light dawns. Like I've always said, it's not little old me you have to deal with, it's the people I cite...
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