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Author
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Topic: The Other Flagellum
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Mike Gene
Member
Member # 149
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posted 19. August 2003 23:13
Nic,
You think that any discussion of the evolution of the cilium must deal with the six points you raise. Let me briefly address them:
(1) It doesn’t make much sense to quibble about the definition of IC given that Behe explicitly spelled out what he considers the IC essence of the flagellum. The quote is provided in the OP. Do you agree that Ken Miller misrepresented Behe when he asserts that Behe contended the 9+2 structure is the only way to make a working cilium or flagellum?
(2) As for simultaneous requirements, let me simply state the biological facts. Thus far, the data indicate that multiple players are required to merely assemble the flagellum – a motor to transport material into the flagellum, a motor to get the material out, and a raft-like structure composed of more than a dozen proteins to carry the cargo. And, of course, there must also be some minimal number of components to carry into the flagellum. 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. Thus far, there is no real data to support the gradualist contention – only Darwinian philosophy. Or as Behe noted, “fuzzy word pictures.” Of course, this doesn’t mean the Darwinian explanation is wrong. Only unconvincing.
(3-4) I fail to see how the connection between the mitotic apparatus and the cilium sheds light one way or another. It certainly does not address the points I raised in the OP.
(5) This was addressed in my OP. See the discussion on axopodia.
(6) This is much too vague to be meaningful. As I mentioned, this is not a test of one’s ability to imagine vague intermediate stages.
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Mike Gene
Member
Member # 149
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posted 19. August 2003 23:23
Me: quote:
This mechanism looks vaguely familiar to me. Although it’s in a completely different, unrelated system. Let’s see. An asymmetric central structure that spins such that a rotating "bump" coordinates the firing of ATP-binding domains that surround it in circular pattern....
Am I the only one who sees this?
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Nel
Member
Member # 614
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posted 19. August 2003 23:43
Mike writes:
quote:
This mechanism looks vaguely familiar to me. Although it’s in a completely different, unrelated system. Let’s see. An asymmetric central structure that spins such that a rotating "bump" coordinates the firing of ATP-binding domains that surround it in circular pattern....
ATP synthase?
ATP synthase:
compare to this:
[ 19. August 2003, 23:54: Message edited by: Nelson-Alonso ]
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Mike Gene
Member
Member # 149
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posted 20. August 2003 00:12
Nelson,
Cool, eh?
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Nel
Member
Member # 614
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posted 20. August 2003 00:18
Very
[ 20. August 2003, 00:19: Message edited by: Nelson-Alonso ]
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yersinia
Member
Member # 324
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posted 20. August 2003 07:34
quote:
Nic,
You think that any discussion of the evolution of the cilium must deal with the six points you raise. Let me briefly address them:
(1) It doesn’t make much sense to quibble about the definition of IC given that Behe explicitly spelled out what he considers the IC essence of the flagellum. The quote is provided in the OP. Do you agree that Ken Miller misrepresented Behe when he asserts that Behe contended the 9+2 structure is the only way to make a working cilium or flagellum?
Sure. Ken Miller had a similar situation with blood clotting, foolishly taking Behe's diagram as the IC system, rather than Behe's qualifications in the fine print of the text. Then again, a great deal of the popular appeal of the IC argument (such as it is) stems from those very complex-looking diagrams and the impression that the systems must be just so or they don't work at all.
But the actual biology is often, "well, really, a fair number of parts are dispensable in various organisms, and there are lots of variations." Thus quibbling about definitions becomes crucial. This in itself undermines the IC argument, because it is a small step from not-required-but-useful to so-useful-its-required. The variations away from 9+2 show that there are alot of ways to build a functional cilium. 3+0, etc., remain important to keep in mind, to show just how much flexibility biology allows.
quote:
(2) As for simultaneous requirements, let me simply state the biological facts. Thus far, the data indicate that multiple players are required to merely assemble the flagellum – a motor to transport material into the flagellum, a motor to get the material out, and a raft-like structure composed of more than a dozen proteins to carry the cargo. And, of course, there must also be some minimal number of components to carry into the flagellum. 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. Thus far, there is no real data to support the gradualist contention – only Darwinian philosophy. Or as Behe noted, “fuzzy word pictures.” Of course, this doesn’t mean the Darwinian explanation is wrong. Only unconvincing.
Speaking of "fuzzy word pictures", where does frontloading fit? "Ridiculously fuzzy word pictures" would be my term for it. Isn't it drastically more unconvincing, lacking any details whatsoever? Anyhow, cargo transport up and down microtubules with kinesin and dynein-based motors is a common function not restricted to cilia. I've already, with "only" my Darwinian philosophy, predicted that the cilial construction proteins will have homologs in intracellular transport. Care to stick your neck out in the opposite direction based on ID?
We'll be able to get more specific just as soon as someone figures out how transportation is organized in various processes -- mitosis, intracellular transport, and cilial construction. You can't criticize evolutionary theory for lacking details when the biochemists haven't even provided the basics about how construction works.
As for how cilia-specific proteins could originate from intracellular ones (the functions don't change much, just the location of action), we already have a great example of how it can happen, with that old favorite of ours, Sdic -- Sperm Dynein Intermediate Chain, which began its life as a cytoplasmic protein but is now a cilial one.
quote:
http://www.oeb.harvard.edu/hartl/lab/research/function.html
Evolution of novel gene functions
Sdic is a new gene that evolved recently in the lineage of Drosophila melanogaster. It was formed from a duplication and fusion of the gene AnnX, which encodes annexin X, and Cdic, which encodes the intermediate polypeptide chain of the cytoplasmic dynein. The fusion joins AnnX exon 4 with Cdic intron 3, which brings together three putative promoter elements for testes-specific expression of Sdic. Translation of Sdic is initiated within the sequence derived from Cdic intron 3, continuing through a 10 base pair insertion that creates a new splice donor site that enables the new coding sequence derived from intron 3 to be joined with the coding sequence of Cdic exon 4. A novel protein is created lacking 100 residues at the amino end that contain sequence motifs essential for the function of cytoplasmic dynein intermediate chains. Instead, the amino end is a hydrophobic region of 16 residues that resembles the amino end of axonemal dynein intermediate chains from other organisms. The downstream portion of Sdic features large deletions eliminating Cdic exons v2 and v3, as well as multiple frameshift deletions or insertions. The new protein becomes incorporated into the tail of the mature sperm and may function as an axonemal dynein intermediate chain. The new Sdic gene is present in about 10 tandem repeats between the wildtype Cdic and AnnX genes located near the base of the X chromosome. This research is focused on understanding the order of events in which the new gene evolved and the functional significance of the mutational changes that were selected.
Ranz, J. M., A. R. Ponce, D. L. Hartl and D. Nurminsky, 2002 Origin and evolution of a new gene expressed in the Drosophila sperm axoneme. Genetica (in press)
Meiklejohn, C. D. and D. L. Hartl, 2002 A single mode of canalization. Trends Ecol. Evol. 17: 468-473.
Nurminsky, D. I., M. V. Nurminskaya, D. De Aguiar, and D. L. Hartl, 1998 Selective sweep of a newly evolved sperm-specific gene in Drosophila. Nature 396: 572-575.
It's trivial, really, just a matter of retargeting followed by optimization. Probably such cooptions back-and-forth have been going on since the origin of the cilium, so what we really need to know is not what proteins critter X uses for transport, but what the universally conserved proteins are.
quote:
(3-4) I fail to see how the connection between the mitotic apparatus and the cilium sheds light one way or another. It certainly does not address the points I raised in the OP.
Ah, you haven't been reading your Cavalier-Smith. Neither did Behe, unfortunately. Y'see, in your head, you are trying to imagine the cilium assembling out of the blue in the cytoplasm. But if you know even a little bit about protozoan mitosis and cilia, then you'll see that the cilium can be fundamentally understood as a specialized version of just another outgrowth of the spindle. The processes of microtubule assembly, disassembly, dynein-tubulin interactions, nucleation, etc. all existed for this purpose first. It's not like there was some point in cilial evolution where the transport systems didn't exist.
The evolution of mitosis is a different question, but there is a good deal more literature on it than there is for the flagellum.
The evolution of the cilium is more like the evolution of organs (like, say, feet from fins) than it is like scenarios for the origin of bacterial flagella. It's mostly about elaborations on a pre-existing system, none of the core components have functions radically different from their functions in other parts of the cell.
quote:
(5) This was addressed in my OP. See the discussion on axopodia.
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. Contra your OP, Behe actually did not address the possibility of a nonmotile appendage intermediate in Darwin's Black Box, he (as usual) assumed that the only selectable function "in the vicinity" was motility or nothing.
quote:
(6) This is much too vague to be meaningful. As I mentioned, this is not a test of one’s ability to imagine vague intermediate stages.
Get back to me when you've got a hypothesis one tenth as detailed for your ID ideas. Until such time I guess we're justified in considering your ideas "not meaningful"?
yersinia
PS: My continual poorly-organized posts on this topic did not make this clear, but in my previous post the points that I thought *really* had to be addressed/overcome in any discussion of cilial evolution wishing to be serious were these:
quote:
...many of the above points are very difficult to research in detail because (1) most of the literature is based on light- and electron- microscopy of the pre-genomic age and is locked up in old obscure paper journals, (2) many of the workers were German, Russian, etc., (3) the names of the critters are constantly changing, (4) the taxonomy is in continual chaos, (5) the whole lot of single-celled eukaryotes is very poorly studied and is almost the definition of obscurity, (6) it's not even clear that we have much more than a beginner's understanding of the details of mitosis, cilial assembly, protozoan diversity, and several other crucial topics.
If one was *really* interested in a really detailed exploration of cilial evolution, basically you need an combination of Lynn Margulis (minus the spirochete obsession) and a first-rate understanding of biochemistry to even have a shot at thoroughly addressing the topic. I want someone to survey the mitosis and cilia of all known protozoan phyla, place the observations in an up-to-date phylogeny, add in the available genomic data, and see what emerges. Cavalier-Smith seems the only likely candidate, but he appears to be working on other things at the moment. This is what would have to be done to even be in the ballpark of a serious discussion (IMHO). Then we'd want to have genomes and biochemical data from all these groups in order to really get into it.
Until these kinds of things happen, we're doomed to generalities, but it's certainly not the fault of evolutionary theory. Go lobby the NIH to divert some funding from cancer research into basic protozoan taxonomy (good luck!).
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nosivad
Member
Member # 767
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posted 20. August 2003 08:28
There is not a shred of evidence that the flagellum, the centriole, the centromere or the basal body of cilia have "evolved" from earlier, less complex precursors. Why keep postulating a process for which no evidence exists? That is bad science. nosivad
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Pim van Meurs
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Member # 541
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posted 20. August 2003 11:27
Nosivad: There is not a shred of evidence that the flagellum, the centriole, the centromere or the basal body of cilia have "evolved" from earlier, less complex precursors. Why keep postulating a process for which no evidence exists? That is bad science. nosivad
You may not understand 1) how science works 2) what the purpose of these boards. And 3) you are 'overselling' your statement when saying that there 'is not a shred of evidence'.
Unless Nosivad wants to add to the claim 'there is no shred of evidence that the flagellum etc (fill in your favorite idea)' :-)
If there was not a shred of evidence how come that Yersinian and Mike are discussing such potential pathways? Is Nosivad convinced that all relevant questions have been answered?
This board is meant to explore such ideas not to stiffle such exploration with meaningless and imho erroneous single paragraphs.
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nosivad
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Member # 767
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posted 20. August 2003 12:18
I have often wondered what the purpose of some of these boards is. I have published my views and I recommend the same for others. nosivad
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nosivad
Member
Member # 767
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posted 20. August 2003 14:59
Nosivad believes that the origin of the flagellum and many other cellular organelles is at the present time unanswerable just as is the origin of life as well as the number of times it has originated. Nosivad also has a very good idea about how science works and how it doesn't work. Chance had nothing to do with phylogeny just as it has nothing to do with ontogeny.
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Nel
Member
Member # 614
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posted 20. August 2003 17:48
Nic writes
quote:
But if you know even a little bit about protozoan mitosis and cilia, then you'll see that the cilium can be fundamentally understood as a specialized version of just another outgrowth of the spindle. The processes of microtubule assembly, disassembly, dynein-tubulin interactions, nucleation, etc. all existed for this purpose first. It's not like there was some point in cilial evolution where the transport systems didn't exist.
Actually if you know even a little about protozoan mitosis and cilia you would see, as my examples and one of your own references show, that you are mixing apples and oranges. How a spindle works and why a cilium protrudes from a cell are completely unrelated. The alignment of the basal bodies under the cell membrane determines the direction of growth, which is probably genetically controlled.
Nic writes:
quote:
The variations away from 9+2 show that there are alot of ways to build a functional cilium. 3+0, etc., remain important to keep in mind, to show just how much flexibility biology allows.
Ok, show me a cilium without MTs.
[ 20. August 2003, 20:16: Message edited by: Nelson-Alonso ]
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Nel
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Member # 614
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posted 20. August 2003 18:10
The more I think about the differences between the ATP synthase and cilium (and the fact that they are unrelated) the more fascinating the similarity of the rotating mechanism becomes. In the ATP synthase, the complex is both the regulator and rotator (and an ATPase), as opposed to the ~ 100,000 different polypeptides that ~ 300 different polypeptides working in a well defined repeat structure gives rise to, that other flagellum.
[ 21. August 2003, 20:35: Message edited by: Nelson-Alonso ]
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Pim van Meurs
Member
Member # 541
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posted 21. August 2003 13:11
Mike Gene asks: Am I the only one who sees this?
Nope, check out Rizzotti's work on this topic.
quote:
Nel 1998 fu proposta un’ipotesi abbastanza dettagliata (Rizzotti, 1998a, 1998b) che faceva derivare il motore del flagello da un’altra struttura batterica per la quale era stato supposto un meccanismo rotante (Boyer e Kohlbrenner, 1981), cioè l’ATP sintetasi.
Even Behe seems to have a 'cameo appearance' ![[Big Grin]](biggrin.gif)
[ 21. August 2003, 13:13: Message edited by: Pim van Meurs ]
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Nel
Member
Member # 614
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posted 21. August 2003 15:01
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.
[ 21. August 2003, 15:02: Message edited by: Nelson-Alonso ]
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Mike Gene
Member
Member # 149
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posted 21. August 2003 15:42
Nelson,
Yes, I also think the similarity is fascinating, as it is largely conceptual. This is not the only example of such a conceptual tie in biology, as I can think of several others now. In fact, it may be a good idea to start cataloging these examples, as this is something non-teleologists have not been interested in (or they don't see it). It’s all very interesting because these unrelated yet similar examples of form challenge the frozen accident perspective and lend support either to intrinsic principles (front-loading friendly) or extrinsic factors (mind).
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