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Author
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Topic: The Other Flagellum
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Nel
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Member # 614
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posted 23. August 2003 16:27
C-S wrote:
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."
Sigh. They can bend because of dynein. A dynein ATPase has been demontrated in axostyles that can bend. So this example doesn't contradict anything that Behe wrote. I don't even think this thing is that simple. It is composed of a stack of sheets of microtubules which are interlinked by intra/inter row bridges. Completely different plane eh?
[ 23. August 2003, 16:29: Message edited by: Nelson-Alonso ]
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yersinia
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posted 23. August 2003 17:03
?? What's the problem? My impression is that there are immotile axostyles, and motile ones, and that they are found in fairly derived organisms, so the origin-at-the-beginning-of-eukaryotes idea doesn't wash. Are you saying that an IDer intervened, *again*, in order to basically re-do the cilium?
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Nel
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posted 23. August 2003 18:30
Nic writes:
quote:
?? What's the problem?
C-S stated that MTs can bend without dynein. That was the point of this statement:
quote:
, evolved from bundles of microtubules by acquiring the capacity to bend, which he implies is impossible
But they can bend because of dynein. Behe stated you can't have bending without dynein.
Nic writes:
quote:
My impression is that there are immotile axostyles, and motile ones, and that they are found in fairly derived organisms, so the origin-at-the-beginning-of-eukaryotes idea doesn't wash. Are you saying that an IDer intervened, *again*, in order to basically re-do the cilium?
No, origin-at-the-beginning-of-eukaryotes washes just fine. Derived forms, like Spiroplasma, can occur and probably depends on the existence of more complex system, like cilia. So it doesn't contradict the origin-at-the-beginning-of-eukaryotes at all. However that wasn't C-S's point at all.
[ 23. August 2003, 18:33: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 07:40
So Nelson, did axostyles evolve, or were they a late creation of the IDer, millions of years after the origin of eukaryotes? We know that they are relatively late additions to eukaryotes.
Please explain your opinion.
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Nel
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posted 24. August 2003 11:38
If they are truly derived then I would say it is something similar to the bacterial flagella ---> Type III secretory system (the latter evolved from the former and not the other way around). Like axopodia, it is interesting that axostyles never evolved a flagellum.
[ 24. August 2003, 11:46: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 14:21
But I don't care if they evolved a flagellum/cilium specifically, what's important is that some axostyles developed active motility, as proved by the abstract on the previous page. I've never heard anyone suggest that axostyles are modified cilia.
Are you saying (a) active motility evolved in motile axostyles, or (b) are you saying it was designed? Either way it happened long after the origin of eukaryotes. It's a simple question.
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Nel
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posted 24. August 2003 16:16
Yersinia writes:
quote:
But I don't care if they evolved a flagellum/cilium specifically, what's important is that some axostyles developed active motility, as proved by the abstract on the previous page. I've never heard anyone suggest that axostyles are modified cilia.
I do. First, it suggests that axostyles may have developed active motility because of cilia. Secondly, this is another example of what Mike Gene refers to how the co-option story is misleading. Dynein is there, MTs are there, and yet it doesn't evolve into the far more robust and complex cilia-like structure.
Nic writes:
quote:
Are you saying (a) active motility evolved in motile axostyles, or (b) are you saying it was designed? Either way it happened long after the origin of eukaryotes. It's a simple question.
I already answered this. I am saying a) possibly because of cilia which arrived at the origin of eukaryotes. How does your axostyle example contradict the latter? Why do you keep asking me the same question?
[ 24. August 2003, 16:58: Message edited by: Nelson-Alonso ]
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Mike Gene
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posted 24. August 2003 19:54
Although I normally restrict myself from posting in a thread once is has 50 postings, I also originally noted, “it is my intention to hold to the spirit of these rules, rather than the letter of the rules, as sometimes a very good discussion may be cause for me to bend them.”
Since Yersinia raised the existence of axostyles in his last reply to me, I really want to respond. So I’ll bend my own rules. However, time will be really limited for a while, so follow-ups to relevant arguments will likely be delayed.
I had hoped that Yersinia would address the three specific questions I raised. He did address one. Kind of. Yersinia states the evolution of motility is relatively easy. But I was asking whether the evolution of the flagellum was easy, which is quite a different question. That question remains in play.
As for the axostyles, I’m not quite sure why yersinia think they represent the “the re-evolution of cilia.” Here’s a picture of the axostyle from the organism described in the paper he cited:
Axostyle(A), cytostome (C), endosymbiotic bacteria (E), nucleus (N), symbiotic spirochetes (S), flagella(U), wood particle (W).
As can be seen, the axostyle isn’t even a “protrusion.” As I have been arguing, if we focus on the cilia as simply microtubules, dyneins, and linkers, the issue remains ambiguous. This is why I noted, “If the assembly of flagella require multiple, independent parts shuttling material in and out of the flagellum, then the serious IC challenge posed by the flagellum may not so much reside in the structure described by Behe, but in the manner this structure is assembled.” In other words, the highly conserved and essential assembly mechanism behind the flagellum may be one area that helps resolve the ambiguity. As I also noted, “As we begin to better understand flagellar formation, a distinct IC theme is appearing. Eukaryotic flagella form at the tip, posing a logistical assembly problem. Basically, how do you get about 250 different proteins into the flagellum such that they assemble in a very specific fashion?” Since the axostyle is not a protrusion and probably does not face this logistical problem, its relevance is highly questionable.
Yersinia also writes: but you'll probably never get exactly the same thing (e.g. cilia) twice
I would agree, if we are talking about forming the same structure from the same components. But the flagellum is composed of over 200 proteins. Is there really only one way to make an oscillating protrusion from 200 parts? Why wouldn’t there be millions of different types of functioning flagella? For example, what’s wrong with making a flagellum using actin and myosin? Actin-based protrusions are not uncommon in protozoa, so why didn’t an actin-based ‘cilia’ evolve?
Finally, I get the sense that yersinia is arguing that if we accept the evolution of something like the axostyle, we are obligated to accept the evolution of the flagellum. Am I correct?
[ 24. August 2003, 19:55: Message edited by: Mike Gene ]
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yersinia
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posted 24. August 2003 21:24
Mike writes,
quote:
Since Yersinia raised the existence of axostyles in his last reply to me, I really want to respond. So I’ll bend my own rules. However, time will be really limited for a while, so follow-ups to relevant arguments will likely be delayed.
I had hoped that Yersinia would address the three specific questions I raised. He did address one. Kind of. Yersinia states the evolution of motility is relatively easy. But I was asking whether the evolution of the flagellum was easy, which is quite a different question. That question remains in play.
As for the axostyles, I’m not quite sure why yersinia think they represent the “the re-evolution of cilia.” Here’s a picture of the axostyle from the organism described in the paper he cited:
[snip]
As can be seen, the axostyle isn’t even a “protrusion.”
A matter of quibbling. They have a pointier end that is mostly axostyle. All cilia are enveloped in the cell membrane, just like everything else in the cell. Some cilia are substantially internal also, yet they don't get disqualified.
Motile axostyles are MT-based structures that wiggle with patterns similar to cilia in many respects as noted in the abstract I previously posted. In the article they go on and on about similarities to cilia in terms of beat pattern, mechanism, etc.
If I might quote their conclusion:
quote:
In conclusion, the axostyle is shown to have many features in common with cilia and flagella but to be simpler in structure and organization and therefore be a good model of microtubule-associated movement. Since the axostyle in Pyrsonympha exhibits both cilia- and flagella-like behavior, this dualism further emphasizes the similarities between these two bending processes. The axostyle has a semicrystalline arrangement of microtubules, and therefore it may be suitable for analysis by x-ray diffraction. Studies which will expand our knowledge of each of the different cross-bridges with the axostyle will significantly help understand the mechanism which localizes and coordinates bending in the axostyle. A radial spoke-central sheath complex is not required for bend formation, since these structures are not present in the axostyle.
This further emphasizes one of Miller's points of showing nonstandard cilia: even free-form arrangements of doublet MTs can make a functioning motility organelle (Miller 1999, p. 142)
quote:
Since the axostyle is not a protrusion and probably does not face this logistical problem, its relevance is highly questionable.
Oh, I'm sure it faces similar "problems". I bet a structure that big has all kinds of regulatory and assembly-specific proteins. The basic point of all this is that you can develop an MT-based structure "internally", e.g. for mitosis or the structural role of some axostyles, and then all you really have to do is make it longer and add a mutant dynein complex, probably in either order.
quote:
Yersinia also writes: but you'll probably never get exactly the same thing (e.g. cilia) twice
I would agree, if we are talking about forming the same structure from the same components. But the flagellum is composed of over 200 proteins. Is there really only one way to make an oscillating protrusion from 200 parts? Why wouldn’t there be millions of different types of functioning flagella?
No, there is the axostyle, the freeform cilia of the sperm of some arthropods (see Miller), axopodia, etc. So there are several ways to do it. There may be millions of potential ways, but then in general evolution doesn't replace something that already works.
quote:
For example, what’s wrong with making a flagellum using actin and myosin? Actin-based protrusions are not uncommon in protozoa, so why didn’t an actin-based ‘cilia’ evolve?
There's plenty of actin-based motility around. You take the very peculiar position that implementation is less important than function. But function is what natural selection acts on. Why should we expect the independent evolution of millions of kinds of cilia, based on evolution? Mike Gene wanting to have a straw-man to knock down is not a good enough answer...
I'd have to know something about the structure of actin filopodia to say something about them. However in general, tubulin is the load-bearing cytoskeletal protein, and actin is the tension-bearing protein. It's easy to see how these two kinds of proteins would be more likely to coopted for motility involving (1) stiff structure-based or (2) contractile-based motility, respectively.
quote:
Finally, I get the sense that yersinia is arguing that if we accept the evolution of something like the axostyle, we are obligated to accept the evolution of the flagellum. Am I correct?
Pretty much, yeah. If you care about self-consistency and self-coherancy, that is...
[ 24. August 2003, 21:26: Message edited by: yersinia ]
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yersinia
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posted 24. August 2003 21:57
And anyway, sometimes axostyles do protrude:
quote:
Arising from the blepharoplast is a prominant tubular structure, the axostyle, which curves in a shell like manner around the nucleus and passes through the centre of the cell often emerging from the posterior end as a spike.
Trichomonas tutorial
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Nel
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posted 24. August 2003 22:06
Nic writes:
quote:
And anyway, sometimes axostyles do protrude
Thats talking about another type of axostyle thats not even contractile. There are two types of axostyles one occurs in parabasalids protists such as Trichomonas, it is composed of a sheet of interlinked microtubules and is not contractile. The second occurs in oxymonads protists, it is composed by a stack of sheets of microtubules.
I don't really see the point of bringing up axostyles. Axostyles are less complex than the cilia/flagella both by their structure and composition. Doesn't really address the complexities of cilia and how it is assembled. And it probably exists by virtue of pre-existing cilia.
Which cilia are mostly internal?
[ 26. August 2003, 17:42: Message edited by: Nelson-Alonso ]
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yersinia
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posted 24. August 2003 23:08
Nelson writes,
quote:
Thats talking about another type of axostyle thats not even contractile.
So, you admit that talking about nonmotile MT appendages is not "fuzz" dreamt up by my lively evolutionist imagination...
quote:
There are two types of axostyles one occurs in parabasalids protists such as Trichomonas, it is composed of a sheet/ribbon/row of interlinked microtubules and is not contractile. The second occurs in oxymonads protists Oxymonas, Saccinobacculus, it is composed by a stack of sheets/ribbons/rows of microtubules.
And another is apparently Pyrsonympha, with its "cilialike" bending abilities. The whole suite of them is screaming that transitions between MT bundles and MT-based motility is not that difficult.
quote:
I don't really see the point of bringing up axostyles. Axostyles are less complex than the cilia/flagella both by their structure and composition. Doesn't really address the complexities of cilia and how it is assembled.
All MT structures are, I'm quite sure, assembled by similar mechanisms by largely homologous transport systems (there's an answer to one of MG's questions, although it should have already been obvious).
quote:
And it probably exists by virtue of pre-existing cilia.
"By virture of" isn't explanation, you've been extraordinarily vague on this assertion.
quote:
I don't really see the point of bringing up axostyles. Axostyles are less complex than the cilia/flagella both by their structure and composition.
...and yet, they can produce similar motor motions anyway!! Wonder of wonders! My, what a shock from the IC perspective.
Regarding internal-ish cilia, I was thinking of things like this, although I vaguely recall reading about additional examples somewhere:
quote:
The genus Tetratrichomonas is different from Trichomonas not only with respect to minor morphological characteristics (parabasal body typically disc-shaped; trunk of axostyle more often slender, relatively stout in some species) but also in the structure of the well-developed undulating membrane, the outer margin of which continues into a free posterior flagellum.
some webpage
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Nel
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posted 25. August 2003 19:05
Nic writes:
quote:
So, you admit that talking about nonmotile MT appendages is not "fuzz" dreamt up by my lively evolutionist imagination...
No, what I am pointing out is that the protusion issue is still a real problem that needs to be addressed.
Nic writes:
quote:
And another is apparently Pyrsonympha, with its "cilialike" bending abilities.
I already mentioned that they are found in oxymonads. The bending abilities aren't "cilia-like", they resemble cilia but there are differences, such as the fact that the "waves" resemble "sawtooth waves", as the reference discusses.
Nic writes:
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The whole suite of them is screaming that transitions between MT bundles and MT-based motility is not that difficult.
Exactly, but thats not Mike's question. Mike's question isn't if evolution of motility given MTs, and even dynein is simple, rather Mike's question is that
quote:
the flagellum is composed of over 200 proteins. Is there really only one way to make an oscillating protrusion from 200 parts?
Axopodia,axostyles that can bend, etc aren't oscillating protrusions that contain 200 parts. They are derived simple versions that point to how misleading the co-option story really is. The question then is, why havn't these structures evolved the more complex, robust cilia-like structures. The basic point here is that building the cilia requirse dynein, in that there is a building balance between construction (driven by kinesin) and destruction (driven by dynein) in the IFT system.
Nic writes:
quote:
All MT structures are, I'm quite sure, assembled by similar mechanisms by largely homologous transport systems (there's an answer to one of MG's questions, although it should have already been obvious).
Again this doesn't address the complexity (or rather, the irreducible complexity) of assembly of the eukaryotic flagellum. None of the examples you show encounters the logistical problems that needs to be overcome when building a system composed of 200 parts. So I don't know why you think this answeres one of MGs questions.
Nic writes:
quote:
"By virture of" isn't explanation, you've been extraordinarily vague on this assertion.
Not at all. I gave two examples. The bacterial flagellum ---> type III secretory system and Spiroplasma. In other words, where did dynein, MTs, nexin, etc come from in the first place, in order for these derived forms to evolve their simple systems? Probably eukaryotic cells that already had the more complex cilia. In other words, they didn't evolve from simple co-option events from simple precursors, into what they are now, they probably evolved from more complex precursor, the ancient 200 part cilia. What supports this is the fact that these lineages, none of them, despite having all the ingredients of the co-option story, have not evolved anything like the 200 part cilia.
In other words, the experiment Behe proposed for bacterial flagella has basically been done with axopodia, axostyles, etc for the eukaryotic flagellum. Put in some ingredients, throw in deep time, mutation, selection, and lets see if it evolves something like the 200 part flagellum. It did not.
Nic writes:
quote:
...and yet, they can produce similar motor motions anyway!! Wonder of wonders! My, what a shock from the IC perspective.
Again, there is a resemblance between the waves (and there are differences) and there huge differences between the structure and composition, and it is much less complex, and it is a late addition. So I have no idea what relevance that has from an IC perspective.
Nic writes:
quote:
Regarding internal-ish cilia, I was thinking of things like this, although I vaguely recall reading about additional examples somewhere:
Nic the "free posterior flagellum" looks to be exterior and not "mostly interior" from the figures. Epithelial cells sometimes grow cilia internally, but this is not too common. This is thought to be a misregulation of normal ciliary development and probably involves problems in positioning of the basal body.
Some other comments. I hope Mike doesn't mind.
When Mike asked:
quote:
For example, what’s wrong with making a flagellum using actin and myosin? Actin-based protrusions are not uncommon in protozoa, so why didn’t an actin-based ‘cilia’ evolve?
You wrote:
quote:
There's plenty of actin-based motility around.
But these are not actin-based cilia. Actin based motility is extremely different from cilia, sort of like propulsion via growth of actin.
[ 25. August 2003, 20:15: Message edited by: Nelson-Alonso ]
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yersinia
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posted 25. August 2003 21:38
Well, on most points I'd just be repeating myself so I will let things stand. However, these points should be mentioned:
(1) AFAIK the 200+ proteins required estimates are derived from experiments where you shear off the cilia, break them up, and run them on gels, and count the bands. Needless to say this could include cytoplasmic proteins and/or proteins associated with the cilium that are just generally associated with tubulins/dyneins/etc. everywhere in the cell. It's not a "required parts list".
I suspect that gene knockouts have discovered a fair number of required genes, but then we will still have the problem of how many of those are really cilia specific, how many just muck up general cell function, how many are actually not required in various organisms, etc.
(2) Even the above experiments haven't been done, AFAIK, on a diversity of cilia. I'd bet that many get by with way less than 200 parts. The 3+0 cilia certianly have dispensed with one major kind of dynein and its associated proteins, many of the linkers, etc.
(3) Nor has it been done on axostyles. I'm sure they use more proteins than just tubulin and dynein. What would be worth comparing is a complex axostyle and a simple cilium. I predict that the required-parts-counts would be close or overlapping. Nelson can't establish a radical difference by mere assertion.
(4) It's not at all clear that axostyle tubulin/dynein are derived from cilia-specific versions of these proteins, as Nelson asserts, or from cytoplasmic versions.
Which brings me back to my original point, which is that we lack much of the data that we'd need to have to answer these questions.
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Nel
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posted 26. August 2003 13:41
Nic writes:
quote:
(1) AFAIK the 200+ proteins required estimates are derived from experiments where you shear off the cilia, break them up, and run them on gels, and count the bands. Needless to say this could include cytoplasmic proteins and/or proteins associated with the cilium that are just generally associated with tubulins/dyneins/etc. everywhere in the cell. It's not a "required parts list".
Wrong. The 200+ number is derived from experiments from Chlamydomonas flagella, which is the system they usually use to study the eukaryotic flagellum (sort of like e.coli for eukaryotes). Chlamydomonas can remove their flagella when there is low pH, so there is no need for shearing.
Nic writes:
quote:
I suspect that gene knockouts have discovered a fair number of required genes, but then we will still have the problem of how many of those are really cilia specific, how many just muck up general cell function, how many are actually not required in various organisms, etc.
I've just read some studies where the researchers can do western blots to detect MT binding proteins from the cytoplasm but detect no signal from them. They say that the contamination level (confusing cytoplasmic proteins with cilia specific ones) is less than one picogram of cytoplasmic protein per mg of cilia-specific protein, and the gel detection limits are lower than this, so cytoplasmic proteins would not be counted in the 200+ count.
Nic writes:
quote:
(2) Even the above experiments haven't been done, AFAIK, on a diversity of cilia. I'd bet that many get by with way less than 200 parts. The 3+0 cilia certianly have dispensed with one major kind of dynein and its associated proteins, many of the linkers, etc.
The 3 + 0 pattern seems to be derived as well. So it would only prove my point.
Nic writes:
quote:
(3) Nor has it been done on axostyles. I'm sure they use more proteins than just tubulin and dynein. What would be worth comparing is a complex axostyle and a simple cilium. I predict that the required-parts-counts would be close or overlapping. Nelson can't establish a radical difference by mere assertion.
Not assertion, observation of the structure and composition of axostyles.
Remember that in addition to the 200+ number many of them have thousands of copies, so it is likely the 200+ count may be an underestimation, not the other way around.
[ 27. August 2003, 15:11: Message edited by: Nelson-Alonso ]
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